TW201009073A - Generation of human embryonic stem-like cells using intronic RNA - Google Patents
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201009073 六、發明說明: 【發明所屬之技術領域】 本發明關於一種用來培育、生成與篩選人類類胚胎幹細胞 的方法’該項方法藉由一種能轉殖表現的内含子之微核醣核酸 試劑。具體而S,本發明係關於一種用來生成非天然產生之内 含子之方法與化合物。此内含子之化合物能經由反應而於人類 細胞中生成小夾類先驅微核酷核酸(small hairpin-like precursor microRNA(miRNA))。因此將於細胞中誘發某些與分化發育相 關基因之靜默效應,進而使該等細胞轉分化為類胚胎幹細胞似 的分化多能性幹細胞。更具體來說,類夹先驅微核醣核酸 (hairpin-like pre-miRNA)包含 mir-302a、mir-302b、mir-302c、 mii-302d或與上述核醣核酸同源或近似的衍生物或前驅物。 【先前技術】 近來關於人類幹細胞的研究已顯示其可用來移植治療的潛 力。然而’可用來複製人類幹細胞的來源卻受到限制,並且很 難控制其純度與品質。於1998年,James Thomson等人(如 US5,843,780、US6,200,806、US7,029,913 及 US7,220,584 等專 利)從人類胚胎中分離出第一株人類胚胎幹細胞(Thoms〇n α/.,(1998) 282: 1145-1147)。而 HI 與 H9 兩株典型的細 胞株則由上述分離的幹細胞中衍生出來。兩年後,Gearhart等 人(如 US6,090,622、US6,245,566 及 US6,331,406 等專利)也發 展出從人類胚胎之後桑葚體(post-blastocyst)分離出最初的人 201009073 類胚胎幹細胞(hES-like primordial germ cells)。因為這些胚胎幹 細胞的分離方法必須將原來的胚胎破壞,因此許多道德上、人 文宗教上的疑慮逐漸提升,以至於爭論這些胚胎幹細胞用於臨 床治療的正當性。 近年來,人們逐漸重視使用這些胚胎幹細胞的安全性疑 慮。舉例來說,由於長期培養胚胎幹細胞需要一些由哺乳細胞 (feeder)所釋放之未知因子來維持幹細胞的分化多能性 ❹ (pluripotency) ’因此這些胚胎幹細胞需要培養於小鼠或人類的 纖維母細胞的哺乳細胞層中。Reubinoff等人之先前技術 US6,875,607嘗試完成此方法,然而纖維母細胞的哺乳細胞具 有全然不同的抗原特性,而可能汙染胚胎幹細胞並造成病人免 疫上的排斥。此外,雖然已經有開發出一些不需要哺乳細胞的 培養環境條件,但沒有一種條件能維持穩定、未分化的胚胎幹 細胞持續一段時間。這是因為,被分離出來的人類胚胎幹細胞 ® 的純度通常不高。現今並無任何一株胚胎幹細胞在培養環境中 能達到百分之百的高純度。即使是在最佳培養環境條件下,約 有3〜5%或更多的胚胎幹細胞傾向於分化成其他細胞型態並 喪失其幹細胞的特性。畸胎瘤(terat〇ma)是胚胎幹細胞分化後 常見的現象。時胎瘤係一種衍生自人類胚細胞株(germ iine cells)之腫瘤,其常包含多種癌化的細胞型態,這些型態相似 於内胚層、中胚層及外胚層。因此,如何避免哺乳細胞汙染及 增加幹細胞純度是現今幹細胞研究主要的兩項課題。 5 201009073 誘發型分化多能性幹細胞(Induced Pluripotent Stem)(iPS)細 胞係由Takahashi及Yamanaka於2006年所公諸於世(ce" 126: 663-676)。藉由使用轉殖基因傳遞四種轉錄因子(〇必/4,心成 句進入小鼠纖維母細胞中,成功地於體外如vitro)轉 分化體纖維母細胞(somatic fibroblast cells)成胚胎幹細胞。此 外’ Yu等人藉由相似的轉殖基因((9cM、5bjc2、iVimog及LIN28) 方式’自人類纖維母細胞開發更新穎的iPS細胞(YU占虬, (2007) 化—ce 318: 1917-1920)。iPS的應用不只能解決道德與 純度的問題亦可配合體細胞核轉移(somatic cell nudear transfer (SCNT))提供一種對病患量身定做的治療方式 (Meissner ei α/.,(2006) iVifliwre 439: 212-215)。上述基於 jpg 細 胞技術的體細胞核轉移治療技術已經在小鼠模式中證實能治 療鐮刀型貧血症(Hanna ei a/.,(2007) 5Wewce 318: 1920-1923)。然而,ips的應用仍有缺陷。這些缺陷在於啦 細胞生成方式;其一為使用反轉錄病毒的潛在危險;另一為使 用具有致癌基因特性的轉錄因子卜名。而反轉錄病毒轉 染方式是唯一一種可同時轉染四種全長的轉錄基因進入體細 胞的方法’然而反轉錄病毒載體隨機插入細胞基因體的可能性 可能會影響非標的基因並造成不可預期的結果,尤其當其中一 個轉染基因是致癌基因的危險。 要精確地將四個全長轉錄因子傳遞至正確的位置是相當困 難的-件事。絲,ips技術需要精確絲現這四種轉錄因子 201009073 使其互相調控而激發多樣的訊息傳遞路徑而表現出眾多發育 因子(developmental factor)。雖然詳細的機制仍不清楚,但 〇ct4-Sox2-c-Myc-Klf4 氟 Oct4-Sox2-Nanog-LIN28 之基钽緒 合效應可產生阻擋細胞早期分化所需的發育因子訊息。儘管只 有一個胚胎幹細胞標誌OcM,其他用於生成ips細胞的基因 通常與發育路徑相關。這些基因通常表現於不同胚胎細胞時期 或位置而導引細胞走向特定分化路徑。藉由錯置這些基因,因 © 而使細胞分化的正常路徑被打亂,進而使這些細胞轉分化至類 似胚胎幹細胞的狀態。這一套方法能達到目的但並不自然。在 自然的受精印中,母系物質(maternal materials)主要在調控幹 細胞的維持與複製。這也是胚胎幹細胞在128的細胞時期之前 全都是一樣的細胞具有一樣的分化多能性。母系物質產生於卵 生成過程(oogenesis)時期’並存於成熟的卵子中以供早期胚胎 發育。在小鼠的卵子中,核醣核酸占了母系物質很大的比例, © 約占整體基因物質中的 450/〇(Stitzel ei ar/·,(2007) 316: 4〇7_4〇8)。在印子接合過程(maternal-zygotic transition),母系 物質报快速地降解,接合子的轉錄過程則開始進行如同兩細胞 時期而產生胚胎發育的訊息(0,Farrell 义,(2〇〇4) 細 14· R35-45)。能了解到,許多母系物質係結合子基因產物的抑 制物,其在早期㈣_可抑梅魏息並能轉分化多能性 細胞態樣。因此’幹細胞維持及複製的秘密應該再於母系物質 之中’而非在分化多能性細胞時期後顯現的發育訊息。 7 201009073 簡言之,為了生成並維持類人類胚胎幹細胞(human embryonie stem (hES)4ike cells)如同具有母系物質,需要一種 新穎的方式來轉殖傳遞分離的母系物質於人體幹細胞或體細 胞中,而能維持幹細胞特性或轉分化體細胞成hES細胞。因 此’仍然需要一種有效、簡單、安全的轉殖基因方法來傳遞母 系物質’特別是母系核酶核。 【發明内容】 本發明係一種用來培育、生成與篩選人類類胚胎幹細胞的 轉殖基因方法,藉由使用類小夾微核醣核酸(hairpin_like microRNA)之内含子表現方式,表現mir_302a、mir_302b、 mii:-302c、mir-302d及上述核醣核酸相互重組的先驅微核醣核 酸(precursor microRNA)之同源衍生物(homologues)或組成 物。微核醣核酸通常約長18到27的核苷酸,並能直接降解它 們的標的訊息核醣核酸(mRNA)或抑制標的蛋白的轉譯過程。 直接降解或抑制蛋白轉譯則是由微核醣核酸(miRNA)與標的 物的互補程度(complementarity^mij^i^家族(mir_302s)於所有 哺乳動物中序列一致性(conserved)很高,此家族由四個高度同 源的微核醣核酸(>90%同源性),分別是mir-302a、mir-302b、 mir-302c、mir-302d所組成。mir-302家族表現時,係以基因群 組方式存在於一長條核酷核酸轉錄分子(RNAtranscript)中,並 以 mir-302b-mir-302c-mir-302a-mir-302d-mir-367 從 5 端到 3 端 201009073 的形式連接(Suh β α/.,(2004) £)ev.所〇/· 27〇: 488-498)。雖然 mir-367也共同表現於mir-302家族基因群組中,然而mir_367 實際上的表現程度卻小於mir-302家族。而mir-302家族被發 現在小鼠卵細胞及人類胚胎幹細胞中表現量極高(Tang扣乂, (2007) Genes Dev. 21: 644-648; Suh et al., (2004) Dev. Biol. 270: 488-498)。小鼠的卵細胞缺乏岱塞爾(Dicer),岱塞爾係一種高 度一致性的核醣核酸酶可供微核醣核酸生成,卵細胞限制於維 ❹ 持在減數分裂的分裂時期(division phase of meiosis I),這現象 指出微核醣核酸對於卵細胞生成的過程扮演重要的腳色 (Murchison ei α/.,(2007) Gewas Dev· 21: 682_693)。也因此, mir-302家族非常有可能係維持幹細胞功能與重新複製的主要 母系物質。. . 與先前iPS細胞技術藉由提升四種細胞轉錄因子基因的表 現量相異’每一 mir-302家族的成員接可調控超過445種細胞 ® 基因。此外’根據 miRBase::Sequencesrhttp://micr〇ma ggRger.ac.uk/)的資料庫,每一 mir-302家族的成員共同的標的 基因幾乎相同。許多mir_3〇2的標的基因實質上為參與胚胎發 育之細胞分化的發育訊息。因此,mir_3〇2的功能很可能係阻 斷或抑制發育訊息的大量產生而不是干擾特定訊息路徑。例 如’類騰島素生長因子(insulin_like growth factors (IGF))對於 神經元幹細胞及其先驅細胞係潛在發育訊息,此訊息係經由201009073 VI. Description of the Invention: [Technical Field] The present invention relates to a method for cultivating, generating and screening human embryonic stem cells. The method comprises a microRNA reagent capable of transducing introns. . In particular, the invention relates to a method and compound for producing non-naturally occurring introns. The compound of this intron can generate small hairpin-like precursor microRNA (miRNA) in human cells via reaction. Therefore, the silent effects of certain genes involved in differentiation and development are induced in the cells, and the cells are then transdifferentiated into differentiated pluripotent stem cells like embryonic stem cells. More specifically, the hairpin-like pre-miRNA comprises mir-302a, mir-302b, mir-302c, mii-302d or a derivative or precursor homologous or similar to the ribonucleic acid described above. . [Prior Art] Recent studies on human stem cells have shown their potential for transplantation therapy. However, the sources that can be used to replicate human stem cells are limited and it is difficult to control their purity and quality. In 1998, James Thomson et al. (US Patent Nos. 5,843,780, US 6,200,806, US 7,029,913 and US 7,220,584) isolated the first human embryonic stem cell from human embryos (Thoms〇n α/., (1998). ) 282: 1145-1147). Two typical cell lines, HI and H9, are derived from the above isolated stem cells. Two years later, Gearhart et al. (such as US 6,090,622, US 6,245,566 and US 6,331,406) also developed the isolation of the original human 201009073 embryonic stem cells (hES) from post-blastocyst after human embryos. -like primordial germ cells). Because these methods of isolating embryonic stem cells must destroy the original embryos, many moral, humanistic and religious concerns have escalated, arguing about the legitimacy of these embryonic stem cells for clinical treatment. In recent years, people have gradually paid attention to the safety concerns of using these embryonic stem cells. For example, long-term culture of embryonic stem cells requires some unknown factors released by mammalian feeders to maintain stem cell pluripotency. Therefore, these embryonic stem cells need to be cultured in mouse or human fibroblasts. In the layer of mammalian cells. Prior art of Reubinoff et al. US 6,875,607 attempts to accomplish this method, however, mammalian cells of fibroblasts have completely different antigenic properties and may contaminate embryonic stem cells and cause immunological rejection of the patient. In addition, although some culture conditions have been developed that do not require mammalian cells, none of them maintain stable, undifferentiated embryonic stem cells for a period of time. This is because the purity of the isolated human embryonic stem cells ® is usually not high. No embryonic stem cells today can achieve 100% high purity in a culture environment. Even under optimal culture conditions, about 3 to 5% or more of embryonic stem cells tend to differentiate into other cell types and lose their stem cell characteristics. Teratoma is a common phenomenon after embryonic stem cell differentiation. A fetal tumor is a tumor derived from a human germ cell line, which often contains a variety of cancerous cell types similar to endoderm, mesoderm, and ectoderm. Therefore, how to avoid breast cancer cell contamination and increase stem cell purity are two major issues in stem cell research today. 5 201009073 Induced Pluripotent Stem (iPS) cell line was published by Takahashi and Yamanaka in 2006 (ce" 126: 663-676). By using a transgenic gene to transfer four transcription factors (〇必/4, the heart into a mouse fibroblast, successfully in vitro, such as vitro), transgenic somatic fibroblast cells into embryonic stem cells. In addition, 'Y et al. developed a new iPS cell from human fibroblasts by similar transgenic genes ((9cM, 5bjc2, iVimog, and LIN28)) (YU Zhan, (2007) - ce 318: 1917- 1920). The application of iPS can not only solve the problem of morality and purity, but also provide a tailor-made treatment for patients with somatic cell nudear transfer (SCNT) (Meissner ei α/., (2006) iVifliwre 439: 212-215) The so-called jpg cell-based somatic cell nuclear transfer therapy technique has been shown to treat sickle-type anemia in a mouse model (Hanna ei a., (2007) 5 Wewce 318: 1920-1923). However, the application of ips is still flawed. These defects are in the way of cell production; one is the potential danger of using retroviruses; the other is the use of transcription factors with oncogene properties. The retrovirus transfection method is The only way to simultaneously transfect four full-length transcripts into somatic cells. However, the possibility of random insertion of retroviral vectors into cellular genomes may affect non-target genes and cause Expected results, especially when one of the transfected genes is at risk for oncogenes. It is quite difficult to accurately transfer the four full-length transcription factors to the correct position. Wire, ips technology requires precise The transcription factor 201009073 regulates each other and stimulates a variety of message transmission pathways and exhibits many developmental factors. Although the detailed mechanism remains unclear, 〇ct4-Sox2-c-Myc-Klf4 Fluor Oct4-Sox2-Nanog The basic effect of -LIN28 produces a developmental factor message that blocks the early differentiation of cells. Although there is only one embryonic stem cell marker, OcM, other genes used to generate ips cells are usually associated with developmental pathways. These genes are usually expressed in different embryos. The cell stage or location directs the cell to a specific differentiation path. By disposing these genes, the normal pathway of cell differentiation is disrupted by ©, and these cells are transdifferentiated to a state similar to embryonic stem cells. It is not natural to achieve the goal. In natural fertilization, maternal materials are mainly Regulates the maintenance and replication of stem cells. This is also the same differentiation pluripotency of embryonic stem cells before the cell cycle of 128. Maternal substances are produced during the period of oogenesis and coexist in mature eggs for Early embryonic development. In mouse eggs, ribonucleic acid accounts for a large proportion of maternal material, © about 450/〇 in the whole genetic material (Stitzel ei ar/·, (2007) 316: 4〇7_4〇8 ). In the maternal-zygotic transition, the maternal material is rapidly degraded, and the transcription process of the zygote begins to generate embryonic development like the two-cell period (0, Farrell, (2〇〇4) · R35-45). It can be understood that many maternal substances are inhibitors of the binding gene product, which can be transduced into pluripotent cellular states in the early stage (4). Thus the secret of 'stem cell maintenance and replication should be in the maternal material' rather than the developmental message that emerges after the differentiation of pluripotent cells. 7 201009073 In short, in order to generate and maintain human embryonic stem (hES) 4ike cells as if they had a maternal material, a novel way is needed to transfer the isolated maternal material to human stem cells or somatic cells. It can maintain stem cell characteristics or transdifferentiate somatic cells into hES cells. Therefore, there is still a need for an efficient, simple, and safe method of transferring genes to deliver maternal material, especially maternal ribozyme nuclei. SUMMARY OF THE INVENTION The present invention is a method for culturing, generating and screening human embryonic stem cells, which expresses mir_302a, mir_302b, by using intron expression of hairpin-like microRNAs. Mii:-302c, mir-302d and homologues or compositions of precursor microRNAs in which the ribonucleic acids are recombined with each other. Microribonucleic acids are typically about 18 to 27 nucleotides in length and are capable of directly degrading their target message ribonucleic acid (mRNA) or inhibiting the translation of the target protein. Direct degradation or inhibition of protein translation is due to the degree of complementarity of microRNAs (miRNAs) with the target (complementarity^mij^i^ family (mir_302s) is highly conserved in all mammals, this family consists of four A highly homologous microRNA (>90% homology) consisting of mir-302a, mir-302b, mir-302c, and mir-302d. The mir-302 family is represented by a gene group. The method exists in a long RNAtranscript and is mir-302b-mir-302c-mir-302a-mir-302d-mir-367 linked from the 5th to the 3rd end 201009073 (Suh β //.,(2004) £)ev.〇/· 27〇: 488-498). Although mir-367 is also present in the mir-302 family of genes, mir_367 actually performs less than the mir-302 family. The mir-302 family has been found to be extremely high in mouse egg cells and human embryonic stem cells (Tang Kou, (2007) Genes Dev. 21: 644-648; Suh et al., (2004) Dev. Biol. 270 : 488-498). The egg cells of mice lack Dicer, a highly consistent ribonuclease for microRNA production, and egg cells restricted to the division phase of meiosis I. This phenomenon indicates that microRNA plays an important role in the process of egg cell formation (Murchison ei α/., (2007) Gewas Dev. 21: 682_693). Therefore, the mir-302 family is very likely to be the main maternal material that maintains stem cell function and re-replication. Compared with previous iPS cell technology, the expression of four cell transcription factor genes is different. Each member of the mir-302 family can regulate more than 445 cells ® genes. In addition, according to the database of miRBase::Sequencesrhttp://micr〇ma ggRger.ac.uk/), the common target genes of each member of the mir-302 family are almost identical. Many of the target genes of mir_3〇2 are essentially developmental messages involved in the differentiation of cells involved in embryogenesis. Therefore, the function of mir_3〇2 is likely to block or suppress the massive generation of developmental messages rather than interfering with specific message paths. For example, 'insulin-like growth factors (IGF)) are potential developmental messages for neuronal stem cells and their precursor cell lines.
Ras/Ra仏mitogen-activated protein kinase MAPK 路徑或經由 9 201009073 phosphatidylinosital 3-kinase(PI3K)/Akt 訊息路徑。超過 μ 種 IGF受體(IGFR)與Ras/PI3K訊息路徑被發現係mir_3〇2的標的 基因。此現象亦顯示在哺乳卵細胞及胚胎幹細胞中有一嚴密的 調控來阻止神經細胞分化。mir_3〇2家族互補地與標的基因的 轉錄分子之同源序列結合’進而經由核醣核酸干擾效應(RNa interference)抑制他們的蛋白轉譯。相似的mir_3〇2家族抑制效 應在許多不同細胞組織甲被發現。據上述證據,mir_3〇2家族 很可能對於胚胎幹細胞的維持與自我複製扮演很重要的角 色。藉由抑制細胞發育及分化的標的基因,mir-302家族可能 可用來轉分化體細胞成脏胎幹細胞並維持該細胞的分化多能 性與自我複製的胚胎幹細胞能力。Ras/Ra仏mitogen-activated protein kinase MAPK pathway or via 9 201009073 phosphatidylinosital 3-kinase (PI3K)/Akt message pathway. More than μ of the IGF receptor (IGFR) and Ras/PI3K message pathways were found to be the target genes of mir_3〇2. This phenomenon also shows a tight regulation in mammalian egg cells and embryonic stem cells to prevent neuronal differentiation. The mir_3〇2 family complementarily binds to homologous sequences of the transcriptional molecules of the underlying gene' and thereby inhibits their protein translation via RRNA interference. A similar mir_3〇2 family inhibitory effect was found in many different cellular tissues. According to the above evidence, the mir_3〇2 family is likely to play an important role in the maintenance and self-replication of embryonic stem cells. By inhibiting the genes involved in cell development and differentiation, the mir-302 family may be used to transdifferentiate somatic cells into visceral stem cells and maintain the differentiation pluripotency of the cells and the ability of self-replicating embryonic stem cells.
為了測試mir-302的胚胎幹細胞生成與維持功能,本發明使 用一第二型轉錄系統之内含子之微核醣核酸表現系統 (Pol-II-based intronic miRNA expression system)於不同人類體 細胞中表現mir-302家族,供模擬原本内含子之微核醣核酸生 成路徑(native intronic miRNA biogenesis pathway),如圖 1 所 示。内含子之微核醣核酸生成過程與細胞内第二型轉錄系統之 先驅訊息轉錄因子及内含子剪接/切除之間的關係有關,通常 發生於細胞核靠近基因體染色質附近的纖維(Lin β β/. (2〇〇4) Drug Design Reviews 1: 247-255; Ghosh et al. (2000) RKA 6: 1325-1334)。在真核細胞中,具有蛋白轉譯能力的基因轉錄因 子’如訊息核醣核酸係由第二型核醣核酸聚合酶(type-II RNA 10 201009073 polymerases)所生成。通常基因轉錄過程生成先驅訊息核餹核 酸❻re-_A),其包含四個主要部分:五端非轉譯區域 (5’-untranslated region(UTR))、含有蛋白轉譯密碼子之外顯子 (protein-codingexon)、無蛋白轉譯能力之内含子(in1r〇n)及三端 非轉譯區域(3’-UTR)。廣義來說,五端及三端非轉譯區域可視 為特定内含子。内含子佔先驅訊息核醣核酸中無轉錄序列彳艮大 的一部分。每一内含子從30個鹼基到數千個驗基都有,且必 φ 須在訊息核醣核酸成熟前切除。先驅訊息核醣核酸切除内含子 的過程稱為核醣核酸剪接(RNA splicing),通常經由細胞内剪接 體(intracellular spliceosome)剪接。在核醣核酸剪接作用之後, 些許由内含子衍生之核醣核酸片段被進一步處理而形成類微 核釀核酸衍生分子(miRNA-like. derivative molecules),這些分 子能有效地、個別地靜默抑制他們的標的基因。上述靜默抑制 機制係經由類核醣核酸干擾機制(RNAi-like mechanism),此時 ❿ 先驅訊息核酷核酸(pre-mRNA)之外顯子(exon)會接合再一起 而形成成熟的訊息核醣核酸以供蛋白質生合成。 我們已經證實有效的微核醣核酸能由脊椎動物基因中的内 含子生成,此生成機制與小干擾核醣核酸(siRNA)或基因間微 核醣核酸(intergenic miRNA)生成機制不同(Lin β d (2003) Biochem Biophys Res Commun. 310: 754-760; Lin et al. (2005) 356: 32-38)。為了證實這個差異,圖2顯示了細胞内生合 成過程與RNAi機制在小干擾核醣核酸(siRNA)、外顯子之微 11 201009073 核醣核酸(intergenic miRNA)與内含子之微核醣核酸(intr〇nic miRNA)之間的比較。一般推測,siRNA係由兩條完整互補的 核醣核酸所形成,其中這兩條核醣核酸係由同一DNA模板上 相反位置之啟動子(promoter (P))所轉錄而成,在雜合 (hybridized)之後被核醣核酸内切酶(RNasein endoribonucleases, Dicer(俗塞爾))切成約20到25驗基對的雙股核聽核酸。不同 於 siRNA 模式,intergenic miRNA(如 lin-4 及 let-7)包含一長無 編碼前驅核聽核酸轉錄分子(long non-coding precursor RNA transcript(pri-miRNA)) ’此分子係直接由第二型(ρ〇ΐ-π)或第三 型(Pol-III)核醣核酸啟動子所轉錄而成,然而内含子之 pri-miRNA只由第二型啟動子所轉錄而成’並將於核醣核酸剪 接作用被剪接。在細胞核中,pri-miRNA進一步由多希亞 CDms/w-like RNases)(用於形成 intergenic miRNA)或剪接體及 外體(exosomal component)(用於形成 intronic miRNA)而形成類 小夾·脊折先驅物(hairpin-like stem-loop precursor)(又稱為内含 子之微核酷核酸intronic miRNA),之後再被運送至細胞質中以 被miRNA相關之岱塞爾處理而為成熟微核醣核酸。接著,上 述三種形式的核醣核酸最後被整合成核醣核酸誘導靜默複合 體(RNA-induced silencing complex(RISQ),在此複合體中包含 雙股的siRNA或單股的miRNA。岱塞爾與核醣核酸誘導靜默 複合體用於生成siRNA與miRNA的路徑係不同的路徑(Tang, G. (2005) 及bc/zem 5W. 30: 106-114)。是故,miRNA 的效 12 201009073 用’-般而tmiRNA較siRNA為專一並較少不配對,這是因 為m随A只有單股有影響。換句話說,siRNA主要催化訊息 脑核__,而miRNA能誘發絲麵核_降解或抑 制蛋白質生合成。因為内含子的miRNA路徑係被細胞内多重 調控機制所控制,其中多重調控機制包含第二型轉錄機制、 RNA splicing、外體解消(exosome digesti〇r^無義介導降解 (;nonsense_mediated decay (NMD) processing),因此内含子微核 〇 醣核酸之基因靜默效應被認為係所有三種RNAi路徑中最有 效、最專一、最安全的路徑(Lin α/ (2〇〇8) 加 5/osc細ce 13: 2216-2230)。 本發明揭露一種内含子用於基因調控的新功能及其相對應 用方式。如圖3A與圖3B所示’基於内含子之核酿核酸剪接 作用(intronic RNA splicing)與處理機制(processing mechanism),本發明較佳實施例係一第二型基因重組轉錄表現 Θ 系統,此系統包含至少一能經剪接的内含子,此内含子在本發 明當中稱之為办具有抑制標的基因或抑制與 序列高度互補的基因的功能。係與第二型轉錄 系統所轉錄之先驅訊息核醣核酸共同轉錄而形 成,在核醣核酸剪接(RNA splicing)後内含子即被釋放 出來。從而’剪接後之進一步被處理為成熟的基因靜 默劑(例如小夾核醣核酸(small hairpin RNA (shRNA))及微核醣 核酸(miRNA)),該些基因靜默劑能激發RNAi相關的基因靜默 13 201009073 效應。在内含子被剪接移除後’重組基因之外顯子轉錄分子經 連接而形成一成熟的訊息核醣核酸分子’以供轉譯生合成一標 諸蛋白(marker)或功能性蛋白。 如圖3A所示,具體而言包含數個保存性高的核苷 酸片段(consensus nucleotide elements),其包含一五端剪接處 (5'-splice site)、一分支點區(branch point motif; BrP)、一 多嘯咬 區(a poly-pyrimidine tract)以及一三端剪接處(3,_splicesite)。此 外,一類小夾核醣核酸(s_A-like)之先驅微核醣核酸序列係 ❹ 插人SpRNAi今,此先驅微核釀核酸序列插入並位於五端剪接 處與分支點區之間。此部分的办及从心·内含子於核聽核酸剪接 作用時(RNA splicing and processing),能形成一套馬索(1把扯) 結構。此外,•之三端包含一多轉譯停止子區(multipleIn order to test the embryonic stem cell production and maintenance function of mir-302, the present invention uses a Pol-II-based intronic miRNA expression system to express in different human somatic cells. The mir-302 family, which is used to mimic the native intronic miRNA biogenesis pathway, is shown in Figure 1. The intron microRNA production process is related to the relationship between the precursor message transcription factor and intron splicing/resection of the intracellular second transcription system, usually occurring in the nucleus near the chromosomal chromatin (Lin β). β/. (2〇〇4) Drug Design Reviews 1: 247-255; Ghosh et al. (2000) RKA 6: 1325-1334). In eukaryotic cells, a gene transcription factor such as a message ribonucleic acid having a protein translation ability is produced by a type II RNA polymerase (type-II RNA 10 201009073 polymerases). Usually the gene transcription process generates the precursor message 餹 餹 re-_A), which contains four main parts: the 5'-untranslated region (UTR), containing the protein translation codon exon (protein- Illustratoron), introns with no protein translation ability (in1r〇n) and three-terminal non-translated regions (3'-UTR). Broadly speaking, the five-terminal and three-terminal untranslated regions can be considered as specific introns. The intron accounts for a portion of the primordial message that has no transcribed sequence in the ribonucleic acid. Each intron has a base from 30 bases to thousands of test sites, and must be cut off before the message ribonucleic acid matures. The process by which the precursor message RNA excises the intron is called RNA splicing and is usually spliced via intracellular spliceosome. After ribonucleic splicing, a small number of intron-derived ribonucleic acid fragments are further processed to form miRNA-like. derivative molecules, which can effectively and individually suppress their miRNA-like. Target gene. The above silent inhibition mechanism is via an RNAi-like mechanism, in which the exon of the pre-mRNA of the precursor message is joined together to form a mature message ribonucleic acid. For protein synthesis. We have demonstrated that effective microRNAs can be produced by introns in vertebrate genes, a mechanism different from that of small interfering ribonucleic acid (siRNA) or intergenic miRNA (Lin β d (2003). Biochem Biophys Res Commun. 310: 754-760; Lin et al. (2005) 356: 32-38). To confirm this difference, Figure 2 shows the intracellular biosynthesis process and RNAi machinery in small interfering ribonucleic acid (siRNA), exon micro 11 201009073 ribonucleic acid (intergenic miRNA) and intron microRNA (intr〇 Comparison between nic miRNAs). It is generally speculated that the siRNA is formed by two fully complementary ribonucleic acids, which are transcribed from a promoter (Pmo) at the opposite position on the same DNA template, in a hybridized form. It is then cut into two-nucleotide nuclear nucleic acids of about 20 to 25 by the endonuclease (RNasein endoribonucleases, Dicer). Unlike siRNA models, intergenic miRNAs (such as lin-4 and let-7) contain a long non-coding precursor RNA transcript (pri-miRNA). This molecule is directly from the second. A type (ρ〇ΐ-π) or a third type (Pol-III) ribonucleic acid promoter is transcribed, whereas an intron pri-miRNA is only transcribed from a second type promoter and will be ribose Nucleic acid splicing is spliced. In the nucleus, pri-miRNAs are further composed of Doxa CDms/w-like RNases (for the formation of intergenic miRNAs) or splice and exosomal components (for the formation of intronic miRNAs) to form small clips and ridges. A hairpin-like stem-loop precursor (also known as an intron micronucleic acid intronic miRNA), which is then transported to the cytoplasm for processing by the miRNA-associated dextran . Subsequently, the above three forms of ribonucleic acid are finally integrated into an RNA-induced silencing complex (RISQ), in which the double-stranded siRNA or single-stranded miRNA is contained in the complex. The induction of the silent complex is used to generate a different pathway between the siRNA and the miRNA pathway (Tang, G. (2005) and bc/zem 5W. 30: 106-114). Therefore, the miRNA effect 12 201009073 is used as a general tmiRNA is more specific and less unpaired than siRNA, because m has only a single strand with A. In other words, siRNA mainly catalyzes the brain __, while miRNA can induce silk fibroin _ degradation or inhibit protein biosynthesis Because the miRNA pathway of introns is controlled by intracellular multiplex regulation mechanisms, which include a second type of transcriptional machinery, RNA splicing, and exosomal depletion (exosome digesti〇r^ nonsense-mediated degradation (; nonsense_mediated decay (; NMD) processing), therefore the gene silencing effect of intron micronuclear ribonucleic acid is considered to be the most efficient, specific, and safest path among all three RNAi pathways (Lin α/ (2〇〇8) plus 5/osc Fine ce 13: 2216-2230) The present invention discloses a new function of introns for gene regulation and its relative application. As shown in Figure 3A and Figure 3B, intronic RNA splicing (intronic RNA splicing) And a processing mechanism, a preferred embodiment of the invention is a second type of recombinant transcriptional transcriptional Θ system comprising at least one spliced intron, said intron being referred to in the present invention The function of a gene with a suppressor gene or a gene that is highly complementary to a sequence is formed by co-transcription of a ribonucleic acid transcribed with a second-type transcription system, and the intron is ligated after RNA splicing. Released. Thus 'spliced and further processed into mature gene silencers (such as small hairpin RNA (shRNA)) and microribonucleic acid (miRNA), which can stimulate RNAi-related Gene Silence 13 201009073 Effect. After the intron is spliced and removed, 'recombinant gene exon transcription molecules are joined to form a mature message ribonucleic acid molecule' For the translation to synthesize a marker or functional protein. As shown in Figure 3A, specifically comprising a plurality of highly conserved nucleotide fragments comprising a five-terminal splicing site (5'-splice site), a branch point motif (BrP), a poly-pyrimidine tract, and a three-terminal splicing site (3, _splicesite). In addition, a class of small ribonucleic acid (s_A-like) precursor microRNA sequences are inserted into SpRNAi. This pioneer micronuclear nucleic acid sequence is inserted between the five-terminal splicing site and the branching point region. This part of the process and the heart and intron in the nuclear splicing and processing (RNA splicing and processing), can form a set of horses (1 pull) structure. In addition, the three ends contain a multi-translation stop sub-region (multiple
translational stop codon region (T codon)) ’ 以提升 intronic RNA 剪接作用(splicing)與無義介導降解過程的精確性。當此多轉譯 停止子顯現於細胞質中之訊息核醣核酸,此多轉譯停止子能傳 ^ 遞活化無義介導降解路徑之訊息,以供降解細胞中任何異常之 核醣核酸結構。然而,插入办见y:心.之具有高度二級結構的 shRNA與先驅微核醣核酸(pre-miRNA)能個別地被保留至岱塞 爾剪接而形成成熟之siRNA與miRNA。再加上,為了於細胞 中表現,我們利用技術手段將办沿⑷利用限制酶切位 插入一紅色螢光蛋白(red fluorescent protein,抓/户)基因(來自 m咖海葵的突變蛋白),而形成一基因重組之含 14 201009073 分厕/的紅色螢光蛋白之办涵/-及卿基因,其中紅色螢光 蛋白基因之第兩百零八個核苷酸位職限制酶加"作用後會 產生-AG-GN核苦酸之斷點,並於斷點兩端產生三個核魏 突出之結構’ φ細能藉由上精點卿成五端剪接處及三 端剪接處嵌人。因為秘游之欽絲紅㈣正 常表現’不過等内含子剪接後,此紅色螢光蛋白就能恢復正常 表現’因此我們可以利用紅色螢光蛋白在轉染細胞中的表現量 ❹ 來欺内含子之s_/miRNA所釋出的量。鱗紅色螢光蛋 白基因也能提供許多外顯子剪接促進子(ex〇nic splidng enhancer, ESE)能提升核醣核酸的剪接作用(RNA _cing)之正 確與效率。 如圖3B所示之另一實施例中,本發明提供一使用人造合成 核醣核酸剪接與處理元件之遺傳工程方法產生一非天然基 因,例如以人造之五端剪接處、分支點區、多嘧啶區以及三端 © 剪接處而形成人造之(人造内含子),此人造之办_/ 包含至少一嵌入之核醣核酸結構,此結構可係反意核醣核酸 (antisense RNA)或S_A或miRNA之結構。此外,可藉由去 氧核醋核酸合成器(DNA synthesizer)以化學合成製造及連接這 些元件。另一方面這些元件的連接方式亦可用限制酶來連接。 此内含子可直接轉染至細胞中或與整合細胞基因重組 而被第二型轉錄聚合酶系統生合成基因轉錄分子(如 pre-mRNA)。經過核醣核酸剪接(RNA splicing)與訊息核醣核酸 15 201009073 成熟個後,·_人之微核醣嫩結構將經由細胞 内剪接體及無義介導降解機制作用並釋出後,該些結構能經由 高互補性而激化献基因觸分子的槪鶴。鱗,纽基-因中的外顯子能連接以形成成熟之訊息核畴核酸,而表現出該. 基因之功能,例如報導基目轉譯或是以下幾種標諸蛋白:紅色 榮光蛋白、綠色螢光蛋白(green flu〇rescem ρ_ίη)、榮光素 _ferase)、乳糖基因調控組(lac_z)以及它們之衍生物。報導/ 標諸蛋白之存在能有蚊位shRNA/miRNA分转在之位 ❿ 置,尤其在於辨認基因靜默/RNAi效果方面。 此外’藉由連接外顯子所形成之成熟訊息核醣核酸也可能 有助於傳絲目、絲去修棚害或遺失之基目,絨高特定基 因表現。在其他方面,本發明提供一新穎化合物(办以誘 發細胞經由intrcmic RNA splicing機制產生基因靜默分子,此 靜默分子係經由反意基因介導剔除或核聽 核酸干擾效果(RNAi)來抑制特定基因功能。衍生自人造内含子 ❹ 之基因靜默分子包含反意核醣核酸細也邱记j^A)、核 糖酵素(ribozyme)、短臨時核醣核酸(sh〇rt temporary RNA, stRNA)、雙股核酶核酸、小干擾核醋核酸(smau丨他兩咖纟沿认, siRNA)、微小無密碼子之核聽核酸(如丫 non_c〇ding RNA, tncRNA)、短小夾核醣核酸(short hairpin RNA,shRNA)、類小 夾核骑核酸(hairpin_like RNA structure)、微核聽核酸 (microRNA,miRNA)及與核醣核酸干擾(RNAi)有關之前/先驅 16 201009073 核酷核酸結構。使用這些内含子之核醣核酸(重組核苷酸)所衍 生之基因靜默试劑有助於特定基因之靜默效應’這些特定基因 自致病轉殖基因⑦础吨沈化transgenes)、病毒基因(viml genes)、突變基因(mutant genes)、致癌基因(oncogenes)、與疾 病相關小核酶核酸基因(disease_reiated small RNA genes)及任 何具有或不具有蛋白轉譯相關之基因以及以上基因混合之基 因選其一。 © 藉由經第二型轉錄聚合酶表現之含的紅色螢光蛋 白表現糸統expression system),我們已成功地 於人類前列腺癌細胞(prostate cancer LNCaP)、人類子宮頸癌 (human cervical cancer HeLa)以及大鼠神經幹細胞細胞(rat neuronal stem HCN-A94-2 cell) (Lin et al (2006a) Methods Mol BzW· 342: 295-312)產生具有基因靜默效果之成熟shRNA及 miRNA。在斑馬魚(zebrafish)、雞以及小鼠(mouse)體内(Lin β α/. ❹ (2〇〇6b) Mei/wds M?/342: 321-334)亦有相同的效果。我們 已於斑馬魚與許多不同人類細胞株中,針對綠色螢光蛋白與其 他細胞基因轉錄分子的表現,測試過不同的先驅微核醣核酸結 構,並得知較有效之基因靜默微核醣核酸係靠近介於五端剪接 處與分支點區之間序列片段之五端。如圖3C所示,有一顯著 之基因靜默效果發生於轉染針對綠色螢光蛋白之先驅微核醣 核酸(antkEGFP pre-miRNA)之組別(lane4 miR組),然而於其 他實驗組與對照組或控制組並無此效果被偵測到;這些實驗組 17 201009073 與對照組依序(由左到右):1、控制組;2、針對愛滋病病毒蛋 白(月7F-p24)之先驅微核醣核酸的對照組;3、針對反意綠色螢 光蛋白且無小夾結構(antisense 五GFP insert without the hairpin loop structure)之anti組;以及5、反轉先驅微核醣核酸序列之 miR*組’該反轉先驅微核醣核酸序列之miR*組係完全互補於 抗綠色螢光蛋白之先驅微核醣核酸(anti—五 pre-miRNA, miR*)。關於其他非標的基因,例如紅色螢光蛋白以及肌動蛋 白(β-actin)並無靜默現象發生,表示办^^之微核醣核酸介 ❹ 導之核聽核酸干擾具有高度專一性。為了證實核醣核酸剪接 RNA splicing於内含子之核醣核酸干擾(intronic似入丨)的效 果,我們已測試三種不同的办表現系統,如圖3D 顯示(由左到右):1.無内含子之紅色螢光蛋白載體組 你表現系統無任何先驅微核醣核酸);2.具有内含 子之抗綠色螢光蛋白先驅微核醣核酸(intronic anti-EGFP pre-miRNA)之紅色螢光蛋白載體組(办expression ❹ system expressing RGFP with an intronic anti-EGFP pre-miRNA insert) ; 3.具有内含子之抗綠色螢光蛋白先驅微核醣核酸(五端 剪接處缺陷)之紅色螢光蛋白載體組。由北方墨點法(Northern bolting)分析資料顯示’成熟之微核醣核酸(也就是内含子之微 核醣核酸)只有在具有内含子之抗綠色螢光蛋白先驅微核醣核 酸之紅色螢光蛋白載體組形成出來(lane2),此及GF尸 表現系統與圖3C之lane4的表現系統相同,因 18 201009073 此證實需要靠細胞内剪接機制(cellu〗ar处丨A splicing)來形成 intronic miRNA 〇 * 基於上述觀察結果’我們進一步決定較佳之先驅微核醣核 酸(pre-miRNA)結構以供藉由核醣核酸誘導靜默複合體 (RNA_indueed silencing c〇mpiex (RISC))誘發最顯著之基因靜 默效應(Lin β.β/. (2005) Ge從 356: 32-38)。RISC 複合體係一蛋 白核酶核酸複合體(protein-RNA complex),能導致特定基因轉 〇 錄分子降解或經由核醣核酸干擾機制抑制轉譯。對於RISC複Translational stop codon region (T codon)) ' to improve the accuracy of intronic RNA splicing and nonsense-mediated degradation processes. When this multi-translation stop appears in the cytoplasmic message ribonucleic acid, this multi-translating stopr can transmit a message that activates the nonsense-mediated degradation pathway for the degradation of any abnormal ribonucleic acid structure in the cell. However, the shRNA and the precursor microRNA (pre-miRNA), which have a high degree of secondary structure, can be individually retained to the sputum splicing to form mature siRNA and miRNA. In addition, in order to express in the cell, we use technology to insert (4) a restriction enzyme cleavage site into a red fluorescent protein (gravity/household) gene (mute protein from mca anemone). And the formation of a genetically recombined red fluorescent protein containing 14 201009073 toilet / / and the Qing gene, in which the red fluorescent protein gene of the two hundred and eight nucleotide position of the restriction enzyme plus " After that, the breakpoint of -AG-GN nuclear bitter acid will be generated, and three nuclear-protrusion structures will be produced at both ends of the breakpoint. φ Fine energy can be embedded by the upper-end cleavage and the three-end splicing . Because the secret tour of the silk red (four) normal performance 'but after the intron splicing, the red fluorescent protein can resume normal performance' so we can use the red fluorescent protein in the transfected cells The amount released by the s_/miRNA of the sorghum. The scaly red fluorescent protein gene also provides many exon splicing enhancers (ESE) to improve the correctness and efficiency of ribonucleic acid splicing (RNA _cing). In another embodiment, as shown in Figure 3B, the present invention provides a genetic engineering method using synthetic synthetic ribonucleic splicing and processing elements to generate a non-native gene, such as a man-made five-terminal splicing site, a branching point region, and a polypyrimidine. The region and the three-terminal © splicing to form an artificial (artificial intron), the artificial _/ contains at least one embedded ribonucleic acid structure, which may be an antisense RNA or S_A or miRNA structure. In addition, these components can be chemically synthesized and linked by a DNA synthesizer. On the other hand, the connection of these elements can also be connected by a restriction enzyme. This intron can be directly transfected into a cell or recombined with an integrated cell gene to be synthesized by a second type of transcriptional polymerase system to synthesize a gene transcriptional molecule (e.g., pre-mRNA). After RNA splicing and message ribonucleic acid 15 201009073 mature, the human microribose structure will act through the intracellular splice and nonsense-mediated degradation mechanisms, and the structures can pass through Complementary and intensify the cranes that donate gene molecules. The squamous, New Zealand-inducible exons can be joined to form a mature message nucleus nucleic acid, which exhibits the function of the gene, such as reporter translation or the following proteins: red glory protein, green Fluorescent protein (green flu〇rescem ρ_ίη), glover _ferase), lactose gene regulatory group (lac_z) and derivatives thereof. The presence of the reported/marked proteins allows for the presence of mosquito shRNA/miRNA translocations, especially in identifying gene silencing/RNAi effects. In addition, the mature message ribonucleic acid formed by the connection of exons may also contribute to the specific gene expression of the silkworm, silky shed or lost. In other aspects, the present invention provides a novel compound (to induce a cell to produce a gene silencing molecule via an intrcmic RNA splicing mechanism, which inhibits specific gene function via an antisense gene-mediated knockout or nuclear-nuclear interference effect (RNAi) The gene silencing molecule derived from the artificial intron 包含 contains the antisense ribonucleic acid, ribozyme, ribozyme, short ribonucleic acid (stRNA), double-strand ribozyme Nucleic acid, small interfering nucleoside nucleic acid (smau 丨 两 两 ,, siRNA), tiny codon-free nuclear nucleic acid (such as 丫 non_c〇ding RNA, tncRNA), short hairpin RNA (shRNA) , hairpin_like RNA structure, micronucleus listening nucleic acid (microRNA, miRNA) and related to RNA interference (RNAi) before / pioneer 16 201009073 nuclear nucleic acid structure. The gene silencing reagent derived from the ribonucleic acid (recombinant nucleotide) of these introns contributes to the silent effect of specific genes 'the specific genes from the pathogenic transgenic genes 7 to the transgenes), viral genes ( Viml genes), mutant genes, oncogenes, disease-reiated small RNA genes, and any genes with or without protein translation and genes mixed with them One. © By the expression of the red fluorescent protein contained in the second type of transcriptional polymerase, we have successfully used human prostate cancer cells (prostate cancer LNCaP), human cervical cancer (HeLa). And rat neuronal stem cells (HCN-A94-2 cells) (Lin et al (2006a) Methods Mol BzW. 342: 295-312) produce mature shRNAs and miRNAs with gene silencing effects. The same effect was observed in zebrafish, chicken, and mouse (Lin β α/. ❹ (2〇〇6b) Mei/wds M?/342: 321-334). We have tested different precursor microRNAs in zebrafish and many different human cell lines for the expression of green fluorescent protein and other cellular gene transcriptional molecules, and learned that the more efficient gene is silent microRNA The five ends of the sequence segment between the five-end splicing and the branch point region. As shown in Figure 3C, a significant gene silencing effect occurred in the transfection of the green fluorescent protein (antkEGFP pre-miRNA) group (lane4 miR group), but in other experimental groups and control groups or This effect was not detected in the control group; these experimental groups 17 201009073 and the control group were sequentially (from left to right): 1. The control group; 2. The precursor microRNA for the HIV virus (month 7F-p24) Control group; 3, anti group against anti-intentional green fluorescent protein and no splicing structure (antisense GFP insert without the hairpin loop structure); and 5, reverse miR* group of precursor microRNA sequence' The miR* group of the transgenic microRNA sequence is fully complementary to the anti-green fluorescent protein precursor microRNA (anti-five pre-miRNA, miR*). Regarding other non-target genes, such as red fluorescent protein and actin (β-actin), there is no silent phenomenon, indicating that the micronucleic acid-mediated nuclear nucleic acid interference is highly specific. To demonstrate the effect of ribonucleic RNA splicing on intron-induced ribonucleic acid interference (intronic-like enthalpy), we have tested three different performance systems, as shown in Figure 3D (from left to right): 1. No inclusion The red fluorescent protein carrier group of your sub-genus does not have any precursor microRNA; 2. The red fluorescent protein carrier of intronic anti-EGFP pre-miRNA with intron Group expressing (expression expression ❹ system expressing RGFP with an intronic anti-EGFP pre-miRNA insert); 3. Red fluorescent protein carrier group with intron-resistant green fluorescent protein precursor microRNA (five-terminal splicing defect) . Analysis by Northern Bolting showed that 'mature microRNAs (ie, microRNAs in introns) are only red fluorescent proteins with intron-resistant green fluorescent protein precursor microRNAs. The vector group was formed (lane2), and the GF cadaveric expression system was identical to the lane4 expression system of Figure 3C, as 18 201009073. This confirmed the need to rely on the intracellular splicing mechanism (cellu ar splicing) to form the intronic miRNA 〇* Based on the above observations, we further determined the preferred precursor microRNA (pre-miRNA) structure for the most significant gene silencing effect induced by RNA-indueed silencing c〇mpiex (RISC) (Lin β .β/. (2005) Ge from 356: 32-38). The RISC complex, a protein-RNA complex, can cause degradation of specific gene-transfer molecules or inhibition of translation via a ribonucleic acid interference mechanism. For RISC complex
合體之形成,雙股siRNA扮演重要之角色,此雙股siRNA在 功能上是相異的,而且RISC複合體只傾向對其中一股進行反 應。這種_勤每-股五麟基對之齡力献所決定。基 於siRNA之模式,推測m随A及與其互補所形成 之雙股核醣核酸對於RISC複合體之形成也很重要,假如此觀 點為真’應無任何功能傾向性在pre_m麵A的變折(stem l〇叩) β 、结構中顯示。然而我們發現,在斑馬魚中,intronicpre-miRNA 的stem4oop結構方向對於孤C複合體選股並形成miRNA有 影響。 .如圖4A所示,兩個具有不同内含子之微核膽核酸(intronic nuRNA)之表現載體分別命名為 miRNA stemloop-tn^Ai^]及 miRNA stemi⑻麵 (瓜歷*係代表能與成熟miRNA序列互補之miRNA)。這兩 組之先驅微核_酸具有相同的雙股彎折結構(stem-arm 19 201009073 structure) ’該彎折結構能對五GF_P基因第280到第302之核芽 酸序列進行靜默效應。具體而言,miRNA與全長完整的成熟 微核醣核酸序列相同,而miRNA*則與成熟微核醣核酸的序列 互補。經微脂體(liposome)轉染這些載體(6〇 ug * each)進入兩周大的斑馬魚幼胚24小時後(Lin β α/. (2005) 356: 32-38),經由mirVana微核醣核酸分離管柱中之 latex beads將具有靜默效應潛力之微核醣核酸(miRNA)沉澱下 來。經序列比對之後,較有靜默效應之微核醣核酸 ❿ (miR-EGFP(280-302))被揀選並辨識為 miRNA_steml— -miRNA*[2],如圖4B所示的灰色陰影處。因為成熟的微核醣 核酸(miRNA)只有於轉染 miRNA-stemloop-miRNA* [2]之斑馬 魚中被發現,因此推論RISC複合體傾向是與miRNA_stemloop -miRNA* [2]作用而非 miRNA*-stemloop-miRNA[ 1 ]之先驅微 核醣核酸。在此實驗’利用經由肌動蛋白啟動子表達之斑馬魚 (Tg(actin· ΟΑΙν4:υΑ8$φ))來進行實驗’此斑馬魚會一直於各 ❹ 類細胞中表達綠色螢光蛋白。如圖4C所示,於此斑馬魚轉染 办載體後,將使綠色螢光蛋白基因靜默並表達可 為指標蛋白之紅色螢光蛋白。觀察結果發現:胃腸部份的基因 靜默效應較弱於其他組織,推測可能是此部位之核醣核酸酶 (RNase)活性較強之故。圖4D中,西方墨點法(Westernblotting) 可偵測到 miRNA*-stemloop-miRNA[l](l 組)以及 miRNA_stemlo〇p- miRNA* [2] (2組)之紅色螢光蛋白表現,然 20 201009073 而綠色螢光蛋白之基因靜默只有於轉染 miRNA-stemloop-miRNA*[2] (2組)之斑馬魚被發現,也應此呼 應圖 40 因 miRNA*-stemloop-miRNA[l]及 miRNA-stemloop- miRNA打2]之五端stem-arm結構的熱動力穩定力一致,因此 我們推論内含子之先驅微核黯核酸(intr〇nic 之.彎 折結構(stem-loop)可能與RISC複合體形成成熟微核醣核酸 (mature miRNA)的選股有關。俗塞爾於stem-arm的切位決定 ❹ 了成熟微核醣核酸的選股(Lee β α/. ρ〇03) ΛΓ⑽/re 425: 415-419),是故内含子之先驅微核醣核酸的stem_1〇〇p可能決 定了特殊切位的辨認。 因為上述先驅微核畴核酸之變折(stem_i00p)結構太大,對於 分_/-7?6^户載體之表現可能不佳,因此採用轉介核醣核酸 (tRNA)之彎折(l〇op)(5 ’-(A/U)UCCAAGGGGG-3,)(S£Q.ID.N0. 29)來取代原本較大的彎折結構’此較小的彎折(tRNAmet loop) ❿ 被證明能加速微核醣核酸(miRNA)從核内運輸至核外,運輸途 徑可經由Ran-GTP及Exportin-5等細胞核内外運輸機制(Line <3/· (2005) Gene 356: 32-38)。最近’本發明使用一對改良之 pre-mir-302 彎折 l〇op結構(如 N0.1)及 5’-GCCTGGCTTAGC-3,(SEQ.ID.N0.2),它們能提供 同樣快速之先驅微核醋核酸運輸並且不干擾轉介核聽核酸之 運輸。此改良之先驅微核醣核酸l00p係藉由模仿mir_3〇2s之 彎折(short stem-loop)結構而設計,其能於胚胎幹細胞中高度表 21 201009073 達’但於分化細胞中表達程度較低。因此,用此改良之先驅微 核醣核酸loop並不會干擾本身之微核醣核酸的運輸路徑。 關於先驅微核醣核酸之插入處,因為§7见\⑷jGM3重組基 因之内含子插入處的限制酶切位於五端及三端分別是/及 Mw/’此前驅内含子之插入處(intr〇nic insert)能被許多其他專 一性基因之先驅微核醣核酸(pre_miRNA)切除而取代(例如, 抗綠色螢光蛋白及mir-302之先驅微核醣核酸)。藉由改變先驅 微核醣核酸插入處(pre-miRNA insert)而用於對抗或靜默不同 ❿ 基因轉錄分子’因此,此内含子之微核醣核酸產生系統能被應 用於誘發標的基因ζ·« Wiro及m Wvo靜默效應的一種強大工 具。為了確認係正確的插入處(insert)尺寸,具有pre-miRNA 的印尸表現載體(10 ng)可藉由PCR技術並用引子 (primer)(例如,5’-CTCGAGCATG GTGAGCGGCC TGCTGAA-3’(SEQ.ID.N0.23)及 5’-TCTAGAAGTT GGCCTT-CTCG GGCAGGT-3,(SEQ.ID.N0.24))於 94°C(1 min.)、52°C(1 〇 min.)、及70°C(1 min.)複製25個循環週期(cycies)後而大量複 製(插入處)。最後PCR之終產物再經由2%洋菜膠(agarose gel) 層析並利用gel extraction kit(Qiagen,CA)純化並序列確認。 本發明採用一經實驗論證設計的第二型聚合酶(p〇l_H)之 表現系統並利用此系統而發展出用於人類或小 鼠細胞中表達mir-302基因家族。於較佳實施例中,本發明提 供一使用非自然發生之内含子之方法及其化合物,此化合物能 22 201009073 被人類或小鼠細胞處理成類mir_302的核醣核酸分子,以供誘 發細胞發育或分化相關基因的基因靜默效應。上述方法包含下 列步驟:a)提供1)一種細胞,此細胞表現眾多,mir_3〇2s所針 對’發育或分化相關的基因;並提供2)—能表現的化合物 (expression-competent composition),此化合物包含一重組基In the formation of the complex, the double-stranded siRNA plays an important role. The double-stranded siRNA is functionally different, and the RISC complex is only inclined to react to one of the strands. This kind of _ diligence per share of Wu Linji is determined by the age of the contribution. Based on the siRNA model, it is speculated that the double-stranded ribonucleic acid formed by m with A and its complement is also important for the formation of RISC complex. If this is true, there should be no functional tendency in the pre-m surface A. L〇叩) β, displayed in the structure. However, we found that in the zebrafish, the stem4oop structure of the intronicpre-miRNA has an effect on the stock selection of the orphan C complex and the formation of miRNA. As shown in Fig. 4A, two expression vectors of intronic nuRNA with different introns are named miRNA stemloop-tn^Ai^] and miRNA stemi (8) surface (the meridian* represents the ability and maturation). miRNAs with complementary miRNA sequences). The precursor micronucleus-acids of the two groups have the same double-stranded structure (stem-arm 19 201009073 structure). The bent structure can perform a silent effect on the nucleotide 280 to 302 nucleotide sequences of the five GF_P genes. Specifically, the miRNA is identical to the full-length intact mature microribonucleic acid sequence, while the miRNA* is complementary to the sequence of the mature microRNA. Transfection of these vectors (6〇ug * each) via liposome into the two-week old zebrafish embryos 24 hours later (Lin β α/. (2005) 356: 32-38) via mirVana microribose The latex beads in the nucleic acid separation column precipitate microRNAs (miRNAs) with the potential for silent effects. After sequence alignment, the more silent effect of microRNA mi (miR-EGFP (280-302)) was picked and identified as miRNA_steml--miRNA*[2], as shown in the shaded gray in Figure 4B. Because mature microRNAs (miRNAs) are only found in zebrafish transfected with miRNA-stemloop-miRNA* [2], it is concluded that RISC complexes tend to interact with miRNA_stemloop-miRNA* [2] rather than miRNA*- The pioneer microRNA of stemloop-miRNA[1]. In this experiment, the experiment was carried out using a zebrafish (Tg (actin·ΟΑΙν4: υΑ8$φ)) expressed by an actin promoter. This zebrafish has been expressing green fluorescent protein in various scorpion cells. As shown in Fig. 4C, after the zebrafish is transfected with the vector, the green fluorescent protein gene is silenced and the red fluorescent protein which can be the indicator protein is expressed. The observation revealed that the gene silencing effect of the gastrointestinal part was weaker than that of other tissues, and it was speculated that the RNase activity of this part was strong. In Figure 4D, Western blotting can detect the red fluorescent protein expression of miRNA*-stemloop-miRNA[1] (group 1) and miRNA_stemlo〇p-miRNA* [2] (group 2), 20 201009073 The gene silencing of green fluorescent protein is only found in zebrafish transfected with miRNA-stemloop-miRNA*[2] (2 groups), and should also be echoed by Figure 40 due to miRNA*-stemloop-miRNA[l] and The thermodynamic stability of the five-terminal stem-arm structure of miRNA-stemloop-miRNA is 2, so we infer the intron micronuclear nucleic acid (intr〇nic. stem-loop) may be The RISC complex forms a stock selection of mature microRNAs. The cut position of the stem-arm is determined by the selection of mature microRNAs (Lee β α/. ρ〇03) ΛΓ(10)/re 425: 415-419), it is the stem_1〇〇p of the precursor microRNA of the intron that may determine the identification of the special cleavage. Because the structure of the above-mentioned precursor micronuclear domain nucleic acid (stem_i00p) is too large, the performance of the vector of _/-7?6^ may be poor, so the use of transduction ribonucleic acid (tRNA) is bent (l〇op ) (5 '-(A/U)UCCAAGGGGG-3,) (S£Q.ID.N0. 29) to replace the original larger bending structure 'this smaller bend (tRNAmet loop) ❿ proved to be able Accelerate the transport of microRNAs (miRNAs) from the nucleus to the extranuclear, and the transport pathway can be via the intranuclear and extracellular transport mechanisms such as Ran-GTP and Exportin-5 (Line < 3/ (2005) Gene 356: 32-38). Recently, the present invention uses a pair of modified pre-mir-302 bent l〇op structures (such as N0.1) and 5'-GCCTGGCTTAGC-3, (SEQ.ID.N0.2), which provide the same fast The pioneer micronuclear nucleic acid transports and does not interfere with the transport of the transduced nuclear nucleic acid. The improved pioneer microRNA l00p was designed by mimicking the short stem-loop structure of mir_3〇2s, which can be expressed in embryonic stem cells algebra 21 201009073 but is less expressed in differentiated cells. Therefore, the improved pioneering microribonucleic acid loop does not interfere with the transport path of its own microRNA. Regarding the insertion of the precursor microRNA, because the restriction enzyme in the insertion of the intron of the \(4) jGM3 recombinant gene is located at the five-terminal and three-terminal insertions of the / and Mw/' introns (intr) 〇nic insert) can be replaced by the excision of many other specific genes, the precursor microRNA (pre_miRNA) (for example, anti-green fluorescent protein and mir-302 pioneer microRNA). By changing the precursor microRNA insertion to counter or silence different ❿ gene transcriptional molecules' Therefore, the microRNA-generating system of this intron can be applied to the priming gene ζ·« Wiro And a powerful tool for m Wvo silent effects. In order to confirm the correct insert size, a porcine expression vector (10 ng) with pre-miRNA can be used by PCR technology and using a primer (for example, 5'-CTCGAGCATG GTGAGCGGCC TGCTGAA-3' (SEQ. ID.N0.23) and 5'-TCTAGAAGTT GGCCTT-CTCG GGCAGGT-3, (SEQ.ID.N0.24)) at 94 ° C (1 min.), 52 ° C (1 〇 min.), and 70 °C (1 min.) replicates 25 cycles (cycies) and replicates in large quantities (inserts). The final product of the final PCR was further chromatographed via 2% agarose gel and purified using a gel extraction kit (Qiagen, CA) and sequence confirmed. The present invention employs an experimentally demonstrated second type polymerase (p〇l_H) expression system and utilizes this system to develop a family of mir-302 genes for expression in human or mouse cells. In a preferred embodiment, the present invention provides a method of using a non-naturally occurring intron and a compound thereof, which can be treated by a human or mouse cell into a ribo-like ribonucleic acid molecule for induction of cell development 22 201009073 Or the gene silencing effect of differentiation-related genes. The above method comprises the steps of: a) providing 1) a cell which exhibits a plurality of genes, mir_3〇2s for a gene involved in 'development or differentiation; and 2) an expression-competent composition, the compound Containing a recombinant group
因,該基因能於上述細胞中產生具有基因靜默效應之内含子之 刖驅核醣核酸轉錄分子(primary RNA transcript),此分子能從 ❿ 内含子中生成類mir-302的核醣核酸分子(mir-302-like RNA molecule),以供於細胞中經由奶八splicing與相關機制剔除 (knock down)或抑制標的基因;的步驟以上述化合物處理上述 細胞,處理過程係在一定條件下,在此條件的細胞中標的基因 的功能係被抑制。從而細胞被轉型為類胚胎幹細胞,此類細胞 表現胚胎幹細胞標誌(如沾五心及S证以)。該細胞能 於生物體外(加、體内(沅vz.w)、來自體内的體外試驗或間 ❿ 接體内(exWw)等情況下表現標的基因。廣義而言,内含子為 基因中不具绝、碼子的序列(non-coding sequence),其包含全長 的内含子與五端非轉譯區域及三端非轉譯區域。在某些層面, 本發明所設計的類mir_3〇2核醣核酸分子包含mir-302a、 mir-302b、mir-302c 或 mir-302d 的第一段 17 個核苷酸(如 5’-UAAGUGCUUC CAUGUUU-3,(SEQ.ID.N0.3))。所有 mir-302家族的微核醣核酸皆擁有從五端數來相同的17個核 苷酸。在其它實施例中,類mir_3〇2的核醣核酸分子也能設計 23 201009073 在細胞基因中的内含子的區域内,而與之共同表現。一般而 言’内含子插入處的技術包含類質體之轉殖基因轉染 (plasmid-like transgene transfection)、同源基因合併交換 (homologuous recombination)、轉位子傳遞(transposon delivery)、去氧核醣核酸接合(DNA ligation)、插入轉殖基因 (transgene insertion)、跳躍基因嵌^合(jumpiiig gene integration) 及反轉錄病毒感染(retroviral infection)或上述方法的混合方 法。 在另一實施例中,本發明之重組基因表現一先驅訊息核醣 核酸(pre-mRNA)。該重組基因係由外顯子(exon)與内含子 (intron)所組成。外顯子於核醣核酸剪接後能被連接而形成一功 月b性訊息核酶核酸(mRNA)進而轉譯成蛋白,以供辨認内含子 之核醣核酸的釋出,此時内含子被釋出細胞核進而被處理成具 有一具有特定基因靜默功能之基因靜默效應物(gene Silencing effector) ’該基因靜默效應物可為反意核醣核酸(antisense RNA)、微核醣核酸(miRNA)、短小夾核醣核酸/小夾核醣核酸 (shRNA)、siKNA、雙股核醣核酸以及以上核醣核酸之先驅物 (例如,pre-miRNA 與 Piwi 相關核醣核酸(Piwi-interactingRNA (piRNA)))。這些内含子之核醣核酸分子可包含一類髮夾之彎 折結構(hairpin-like stem-loop structure)(約等同於類小夾核醣 核酸),此結構包含一序列,此序列係同源於5,_GCTAAG-CCAGGC -3’(SEQ.ID.N0.1)或是 5,-GCCTGGCTTAGC-3, 201009073 (SEQ.ID.NO.2),該序列能促進核醣核酸分子正確地從内含子 被剪接也能促進該分子由細胞核運輸至細胞質中。而且這些内 含子之核醋核酸分子的彎折結構(stem_arms)包含互補或同源 於特定標的基因之序列。該内含子之核醣核酸分子同源或互補 的序列大小約從15個鹼基對到1500鹼基對之間,較佳係18 個到27個鹼基對左右。這些内含子之核醣核酸分子對於標的 基因序列之互補或同源率約30%到100%之間,較佳為35% 到49%之間。對於類小夾的内含子之核醋核酸 intronicRNA),其互補或同源率約30%到100%之間;而對於 線形内含子之核酶核酸(linear intr〇nic RNA)則係90%到1 〇〇Therefore, the gene can produce a primary RNA transcript of an intron having a gene silencing effect in the above-mentioned cells, and the molecule can generate a mir-302-like ribonucleic acid molecule from the intron ( a mir-302-like RNA molecule for the step of knocking down or inhibiting a target gene in a cell via a milk splicing and related mechanism; the step of treating the cell with the above compound, the treatment being under certain conditions, The function of the target gene in the conditional cell is inhibited. Thus, the cells are transformed into embryonic stem cells, which express embryonic stem cell markers (such as the five hearts and the S syndrome). The cell can express the target gene in vitro (additional, in vivo (沅vz.w), in vitro in vivo or in vivo (exWw). In a broad sense, the intron is in the gene. A non-coding sequence comprising a full-length intron and a five-terminal non-translated region and a three-terminal non-translated region. In some aspects, the mir_3〇2 ribonucleic acid of the present invention is designed. The molecule contains the first 17 nucleotides of mir-302a, mir-302b, mir-302c or mir-302d (eg 5'-UAAGUGCUUC CAUGUUU-3, (SEQ.ID.N0.3)). All mir- The 302 family of microRNAs possess the same 17 nucleotides from the five-terminal number. In other embodiments, the mir_3〇2 ribonucleic acid molecule can also design 23 201009073 intron regions in cellular genes. Internally, and in common with it. In general, the technique of 'intron insertion includes plasmo-like transgene transfection, homologous recombination, transposition (transposon delivery), DNA ligatio n), insertion of transgene insertion, jumpiiig gene integration, and retroviral infection or a hybrid method of the above method. In another embodiment, the recombinant gene of the present invention A precursor message ribonucleic acid (pre-mRNA) is expressed. The recombinant gene consists of an exon and an intron. The exon can be ligated after ribonuclease cleavage to form a dynamite b. The ribozyme nucleic acid (mRNA) is then translated into a protein for the recognition of the release of the ribonucleic acid of the intron, at which time the intron is released from the nucleus and is processed to have a gene silencing effect with a specific gene silencing function. Gene silencing effector 'The gene silencing effector can be antisense RNA, microRNA (miRNA), short ribonucleic acid/small ribonucleic acid (shRNA), siKNA, double-stranded ribonucleic acid The precursor of the above ribonucleic acid (for example, pre-miRNA and Piwi-interacting RNA (piRNA)). The ribonucleic acid molecules of these introns may contain a type of hairpin bend. A hairpin-like stem-loop structure (approximately equivalent to a small ribonucleic acid), this structure comprising a sequence homologous to 5,_GCTAAG-CCAGGC-3' (SEQ.ID.N0.1) Or 5,-GCCTGGCTTAGC-3, 201009073 (SEQ.ID.NO.2), which promotes the correct splicing of the ribonucleic acid molecule from the intron and promotes transport of the molecule from the nucleus to the cytoplasm. Moreover, the bent structure of the nucleic acid molecules of these introns (stem_arms) contains sequences complementary or homologous to a particular target gene. The sequence of the homologous or complementary ribonucleic acid molecule of the intron ranges from about 15 base pairs to about 1500 base pairs, preferably from about 18 to 27 base pairs. The complement or homology of these intron ribonucleic acid molecules to the target gene sequence is between about 30% and 100%, preferably between 35% and 49%. For the intronic RNA of the intron of the small clip, the complement or homology rate is between about 30% and 100%; for the linear intr〇nic RNA of the linear intron 90 % to 1 〇〇
此外,非自然產生(人造的)内含子之五端包含一五端剪接 處(5’-splice site or 5’ clip),其中該五端剪接處係一核苷酸序列 並同源於 5,-GTAAGAGK-3,(SEQ.ID.N0.4)或是 GU(A/G)AG U 序列(例如,5’-GTAAGAGGAT-3, (SEQ.ID.NO. 30)、5,-GTA AGAGT-3’、5’-GTAGAGT-3’及 5’-GTAAGT-3’)。此時,三端 剪接處(3’-splice site or 3, clip)序列係同源於 GWKSCYRCAG (SEQ.ID.N0.5)或 CT(A/G)A(C/T) NG 序列(例如,5,-GATATCC TGCAG-3’(SEQ.ID.N0.31)、5’-GGCTGCAG_3,、5,-CCACAG -3’)。此外,分支點區序列係位於五端與三端剪接處之間,該 分支點區位於一核苷酸序列同源於5 ’-TACTWAY-3,(SEQ.ID. N0.6)(如,5’-TACTAAC-3’及 5,-TACTTAT-3,),該分支點區包 25 201009073 3 一为支點,而該分支點係一腺核苦(adenosine, A)能形成一套 馬索(lariat)結構之内含子核醣核酸,此套馬索(lariat)結構係由 寡腺核苷合成酶(2 ’ -5 ’ -oligoadenylate synthetases)及剪接體協 同作用產生。此外,多嘧啶區係位於分支點區與三端剪接處之 間,其中多嘧啶區是一具有高密度的胸腺嘧啶(Thymine)與胞 嘧咬(Cytosine)之核苷酸序列,多嘧啶區之核苷酸序列同源於 5’-(TY)m(C/-)(T)nS(C/-)-3’(SEQ.ID.N0.7)與 5,-(TC)nNCTAG (G/-)-3’ (SEQ.ID.N0.8)。其中,”m”與”n”係指大於等於一的多 重複序列’較佳m之序列數是一到三之間,而n之序列數是 七到十二之間。”-“係指無任何核苷酸。一些連接核苷酸能用 來連接上述内含子片段。基於37CFR1.822規定(台灣’,核苦酸 及胺基酸序列表記載格式”亦同),W係指腺嘌呤(adenine 或胸腺嘧咬(thymine (T))/尿嘧咬(uracil(U)),K係指鳥嗓吟 (guanine (G))或胸腺嘧啶(T)/尿嘧啶(U),S係指胞嘧啶(〇或鳥 嘌呤(G),Y係指胞嘧咬(〇或胸腺嘧啶(T)/尿嘧啶(U),R係指 腺嘌呤(A)或烏嘌吟(G)以及N係指腺嘌吟(A)、胞嘧咬(〇、鳥 嘌呤(G)或胸腺嘧啶(T)/尿嘧啶(U)或其他。 在本發明之另一實施例中,基因重組核苷酸可被重組併入 表現載體以供基因轉染。表現載體選自DNA轉殖基因(DNA transgene)、質體(plasmids)、跳躍基因(jumping genes)、轉位子 (transposons)、反轉位子(retrotransposons)、反轉錄病毒載體 (retroviral vectors)、慢病毒載體(lentiviral vectors)、腺病毒載體 26 201009073 (adenoviral (AMV) vectors)、腺相關病毒載體(adeno-assodated viral (AAV) vectors)、改性的病毒性肝炎(modified hepatitis-viral (HBV) vectors)、巨細胞病毒相關的病毒載體(Cyt〇megai〇vims (CMV)-associated viral vectors)。於轉染办^^·-及GFP 表現系 統過程中’表現不同内含子之基因靜默效應物的該等載體能用 於達到單一或複數個標的基因之靜默效應。在其他實施例中, 複數個不同基因靜默效應物能自办表現系統之内 ❹ 含子之小夾核醣核酸介子(intronic hairpin RNA insert)衍生,而 使眾多基因靜默。此方法之優勢係藉由使用轉殖基因轉染或病 毒感染而提供一穩定及相對長期之特定基因靜默效應。其中, 本發明經由細胞内核醣核酸剪接及處理機制能產生核醣核酸 干擾相關之基因靜默效應物(RNAi-related.gene silencing effector),該基因靜默效應物包含小干擾核醣核酸(small interfering RNA,siRNA)、微核醣核酸(microRNA(miRNA))及 ❿ 小爽核酶核酸(small hairpin RNA (shRNA))。並由細胞内特定In addition, the five-terminal end of the non-naturally occurring (artificial) intron comprises a 5'-splice site or 5' clip, wherein the five-terminal splicing is a nucleotide sequence and is homologous to 5 , -GTAAGAGK-3, (SEQ.ID.N0.4) or GU(A/G)AG U sequence (eg, 5'-GTAAGAGGAT-3, (SEQ.ID.NO. 30), 5,-GTA AGAGT-3', 5'-GTAGAGT-3' and 5'-GTAAGT-3'). At this point, the 3'-splice site or 3, clip sequence is homologous to the GWKSCYRCAG (SEQ.ID.N0.5) or CT(A/G)A(C/T) NG sequence (eg , 5,-GATATCC TGCAG-3' (SEQ. ID. N0.31), 5'-GGCTGCAG_3, 5, -CCACAG-3'). In addition, the branch point region sequence is located between the five-terminal and three-terminal splicing regions, and the branch point region is located in a nucleotide sequence homologous to 5 '-TACTWAY-3, (SEQ. ID. N0.6) (eg, 5'-TACTAAC-3' and 5,-TACTTAT-3,), the branch point zone package 25 201009073 3 is a fulcrum, and the branch point is an adenosine (A) capable of forming a set of horses ( Lariat) The structure of the intron ribonucleic acid, which is produced by the synergistic action of serotonin synthase (2'-5'-oligoadenylate synthetases) and splices. In addition, the polypyrimidine region is located between the branch point region and the three-terminal splicing region, wherein the polypyrimidine region is a nucleotide sequence having a high density of thymine and Cytosine, and a polypyrimidine region The nucleotide sequence is homologous to 5'-(TY)m(C/-)(T)nS(C/-)-3' (SEQ.ID.N0.7) and 5,-(TC)nNCTAG (G /-)-3' (SEQ.ID.N0.8). Wherein "m" and "n" mean a multiple repeating sequence of greater than or equal to one. Preferably, the number of sequences of m is between one and three, and the number of sequences of n is between seven and twelve. "-" means no nucleotides. Some linked nucleotides can be used to join the above intron fragments. Based on 37 CFR 1.822 (Taiwan ', the format of nucleotide acid and amino acid sequence list is also the same), W refers to adenine (adenine or thymine (T)) / uracil (U) )), K means guanine (G) or thymine (T) / uracil (U), S means cytosine (〇 or guanine (G), Y means cytosine (〇) Or thymine (T) / uracil (U), R refers to adenine (A) or black mites (G) and N refers to adenine (A), cytosine (〇, guanine (G) Or thymine (T) / uracil (U) or others. In another embodiment of the invention, the recombinant nucleotide can be recombinantly incorporated into a performance vector for gene transfection. The expression vector is selected from the group consisting of DNA transfection Genes (DNA transgenes), plastids, jumping genes, transposons, retrotransposons, retroviral vectors, lentiviral vectors, glands Viral vector 26 201009073 (adenoviral (AMV) vectors), adeno-assodated viral (AAV) vectors, modified hepatitis-viral (HBV) vectors, Cytomegalovirus-associated viral vectors (Cyt〇megai〇vims (CMV)-associated viral vectors). These are the gene silencing effectors that express different introns during the transfection process and the GFP expression system. The vector can be used to achieve the silent effect of a single or multiple target genes. In other embodiments, a plurality of different gene silencing effectors can self-organize the intronic hairpin RNA insert of the intron. Derived to silence many genes. The advantage of this method is to provide a stable and relatively long-term specific gene silencing effect by using transgenic gene transfection or viral infection. Among them, the present invention is via the cell nucleus chromosomal splicing and processing mechanism. An RNAi-related.gene silencing effector, which contains small interfering RNA (siRNA), microRNA (miRNA), and sputum Small hairpin RNA (shRNA). Intracellular specific
基因核醣核酸啟動子(promoter)所控制,該些啟動子選自第二 型核醣核酸聚合酶啟動子(Pol-II promoter)、第三型核聽核酸聚 合酶啟動子(Pol-IIIpromoter)及病毒啟動子。該病毒啟動子可 為類第二型核醣核酸聚合酶啟動子(Pol-II-like RNA promoter),其選自細胞巨大病毒(cytomegalovirus (CMV))、逆 轉錄病毒長末端區域(retrovirus long-terminal region ¢1111¾、:B 型肝炎病毒(hepatitis B vims (HBV))、腺病毒(adenovirus 27 201009073 (AMV))及腺相關病毒(adeno-associated virus (AAV))。例如,慢 病毒(lentiviral LTR)啟動子能於每個細胞内提供超過5x1 〇5單 位的先驅訊息核醣核酸。此外,插入一對藥物敏感之抑制子^ drug-sensitive repressor)於這慢病毒啟動子之前端而供控制其 基因靜默效應物的表現速率(expression rate)的方式係可行的 方式之一。此抑制子能被化學藥物或抗生素抑制,這些化學藥 物或抗生素選自G418、四環素(tetracycline)、新黴素 (neomycin)、安比西林(ampicillin)、康黴素(kanamycin)及上述 抗生素之衍生物。 本發明提供一於細胞内產生内含子之核醣核酸(intr〇nic RNA)的新穎方法,以供產生成熟siRNA、miRKA及shRNA, 這些RNA可誘發核醣核酸干擾基因靜默效應 gene silencing effects) 〇 其中,siRNA、miRNA 及 s_A 在細 胞中,能藉由細胞機制的表現與處理本發明先 shRNA之内含子之介子,而產生單一或多重基因靜默效應 物。例如,如之前所述,抗綠色螢光蛋白之先驅微核醣核酸 (pre-miRNA)被異體表現於斑馬魚上,如同圖3A所示,而產 生兩組不同長度的成熟微核釀核酸,如(mir—EGFP 282/300盘 mir-EGFP280-302)。這晴示著,單一办麵z•之介子(insert)能 產生超過一種的基因靜默效應物(gene-silencing effectors)。正 股(sense)或反意(antisense)的DNA構型能產生相同或相異的 基因靜默效應物,以供與標的基因分子互補。在某些例子中, 28 201009073 内含子之基因靜默效應物能與一些標的基因轉錄分子(如 mRNA)雜合,而形成雙股核醣核酸進而驅動核醣核酸干擾 „ (RNAi)效應。因為内含子之基因靜默效應物係由表現載體持續 產生,因此本發明能減輕小型核醣核酸被快速降解所造成之疑 慮。 此外,本發明可供產生幹細胞。本發明潛在應用包含無哺 乳細胞之人類胚胎幹細胞株之維持並避免上述細胞株進行細 〇 胞分化、於體外複製並培養分化之幹細胞株、純化同質性幹細 胞群及利用上述幹細胞進行移植。本發明亦可為用來研究幹細 胞功能及機制的用具或可供改變幹細胞性質以致於用於特定 用途。於不同實施例中,本發明之類胚胎幹細胞可選自正常體 細胞、癌化體細胞、哺乳類(如人類、猴子、大鼠及小鼠)之成 熟幹細胞衍生而得。 ❿ 【實施方式】 為了清楚地描述本發明,文中採用以下特定用語。然而, 本發明並非條於這些特定用語。其應轉絲個較元素均 包含所有技術上的均等物,其可由相似的手段達成相近的目 的0 「核苷酸(Nudeotide)」-詞在此意指—單分子之去氧核釀 核酸(deoxyribotmcleotideXDNA)或核醣核酸(rib〇nude〇tide) (RNA)分子’這些分子包含五碳_em〇se)、鱗酸根⑽〇Sphate) 29 201009073 及驗基(nitrogenous heterocyclic base)。此驗基是經由聽苷鍵 (glycosidic bond)與五碳醣聯接成一核苷(nucleoside),此核苷以 五碳醣三端與五端之位置與磷酸根連接而成微核苷酸。 「募核苷酸(Oligonucleotide)」一詞在此意指一分子包含兩 個以上的DNA或RNA,較佳係超過三個,而通常超過十個。 而其精確的尺寸係取決於其最佳功能狀態。募核苷酸係能以化 學合成、DNA複製、反轉錄及以上方式混合之方式形成。 「核酸(Nucleic Acid)」一詞在此意指核苷酸(Nucleotide)之 聚合體,可為單股或雙股。 「核苷酸相似物(Nucleotide Analog)」一詞在此意指一嘌吟 (purine)或鳴咬(pyrimidine)核苷酸之結構與A、T、C、G或U 不同但相似,而能在核苷酸中取代正常核苷酸。 「核酸化合物(Nucleic Acid Composition)」一詞在此意指一 核酸化合物係關於一種多核苦酸(p〇lynucle〇tide)如DNA或 RNA,其以單股或雙股的形式存在。 「基因(Gene)」一詞在此意指一核酸之序列具有rnA或一 多胜肽(蛋白質)之密碼子,此基因可為RNA或DNA。 「驗基對(Base Pair (bp))」一詞在此意指於雙股DNA分子 中A與T或C與G之配對。在RNA中,U取代T與A配對。 一般來說驗基對係以氫鍵(hydrogen bonding)所連接。 先驅訊息核酷核酸(Precursor messenger RNA (pre-mRNA))」一詞在此意指在真核細胞中藉由第二型反卜丨八聚合 30 201009073 酶(Pol-II)所產生之一基因之則驅RNA轉錄分子(primary ribonucleotide transcripts) , 此過程 為轉錄 (transcription) , 一 先驅訊 息核聽核酸序列包含五端非轉譯區域(5’-end untranslated region)、三端非轉譯區域(3’-end untranslated region)、外顯子 (exon)及内含子(intron) 〇 「内含子(intron)」一詞在此意指一部分之基因轉錄分子所 具有的非轉譯區域之片段如in-frame内含子、五端非轉譯區域 0 及三端非轉譯區域。 「外顯子(exon)」一詞在此意指一部分之基因轉錄分子所具 有蛋白轉譯區域之片段。 「訊息核醣核酸(mRNA)」一詞在此意指經由核内剪接機制 除去内含子後所組成之先驅訊息核醣核酸之外顯子,而其具有 蛋白轉譯密碼之mRNA。 「互補去氧核醋核酸(cDNA)」一詞在此意指一與 參 序列互補之單股DNA,此cDNA無任何内含子序列。 「正股核酸(sense)」一詞在此意指一核酸分子之序列順序 與同源的mRNA相同。此正股核酸構型係被標示為’,+,,、,’s” 或’’sense”。 「反意核酸(antisense)」一詞在此意指一核酸分子之序列順 序與mRNA互補。此反意核酸構型係被標示為,,_,,、,’a” 或’’antisense”,例如’’aDNA” 或’’aRNA”。 「五端(5’-end)」一詞在此意指一連續核苷酸於五碳膽之五 31 201009073 號碳之位置沒有以磷酸二酯鍵(ph〇sph〇diester b〇nd)與下—個 核苷酸之三號碳位置連接之端點謂之五端。有至少一個磷酸根 顯示於端點。 一化(3 -end)」一词在此意指一連續核普酸於五碳醣之三 號碳之位置沒有以磷酸二酯鍵⑽〇Sph〇diester b〇nd)與下一個 核苷酸之五號碳位置連接之端點謂之三端。端點通常為羥基。Controlled by a gene ribonucleic acid promoter selected from the group consisting of a second type ribonucleic acid polymerase promoter (Pol-II promoter), a third type nuclear nucleic acid polymerase promoter (Pol-IIIpromoter), and a virus. Promoter. The viral promoter may be a Pol-II-like RNA promoter selected from the group consisting of a cytomegalovirus (CMV) and a retrovirus long-terminal region (retrovirus long-terminal). Region ¢11113⁄4,: hepatitis B virus (HBV), adenovirus (adenovirus 27 201009073 (AMV)), and adeno-associated virus (AAV). For example, lentiviral LTR The promoter can provide more than 5x1 〇 5 units of the precursor message ribonucleic acid per cell. In addition, a pair of drug-sensitive repressors are inserted at the front of the lentiviral promoter to control the gene silencing. The manner in which the effector expresses the rate is one of the possible ways. The inhibitor can be inhibited by a chemical or antibiotic selected from the group consisting of G418, tetracycline, neomycin, ampicillin, kanamycin, and derivatives of the above antibiotics. . The present invention provides a novel method for producing intron ribonucleic acid (intr〇nic RNA) in a cell for the production of mature siRNA, miRKA and shRNA, which can induce gene silencing effects of ribonucleic acid interference gene silencing effects) siRNA, miRNA and s_A In a cell, a single or multiple gene silencing effector can be produced by the expression of a cellular mechanism and the processing of the meson of the intron of the first shRNA of the present invention. For example, as previously described, the anti-green fluorescent protein precursor microRNA (pre-miRNA) is heterologously expressed on zebrafish, as shown in Figure 3A, resulting in two sets of mature micronucleated nucleic acids of different lengths, such as (mir-EGFP 282/300 disk mir-EGFP280-302). This clearly shows that a single implant can produce more than one gene-silencing effectors. A sense or antisense DNA configuration can produce the same or a different gene silencing effector for complementation with the target gene molecule. In some instances, the gene silencing effector of the intron of 28 201009073 can hybridize with some of the underlying gene transcriptional molecules (eg, mRNA) to form a double-stranded ribonucleic acid that drives the ribonucleic acid interference (RNAi) effect. The gene silencing effector system is continuously produced by the expression vector, and thus the present invention can alleviate the concern caused by rapid degradation of small ribonucleic acid. Furthermore, the present invention can be used to produce stem cells. The potential application of the present invention includes human embryonic stem cells without mammalian cells. The strain maintains and avoids the cell line differentiation of the above cell line, in vitro replication and culture of the differentiated stem cell strain, purification of the homogenous stem cell population, and transplantation using the above stem cells. The present invention may also be used for studying stem cell function and mechanism. Alternatively, the stem cell properties can be altered for specific use. In various embodiments, embryonic stem cells such as the invention can be selected from normal somatic cells, cancerous somatic cells, mammals (eg, humans, monkeys, rats, and mice). The mature stem cells are derived. 实施 Embodiments In order to clearly describe the present invention The following specific terms are used herein. However, the present invention is not intended to be specific to these specific terms. It should be rotated to include all technical equivalents, which can be similarly achieved by similar means. 0 "Nudeotide" - The word here means - a single molecule of deoxyribotmcleotide XDNA or a rib〇nude〇tide (RNA) molecule 'these molecules contain five carbons _em〇se), sulphate (10) 〇Sphate 29 201009073 and nitrogenous heterocyclic base. This test is a nucleoside linked to a five-carbon sugar via a glycosidic bond, which is a micronucleotide linked to the phosphate at the three-terminal and five-terminal positions of the five-carbon sugar. The term "oligonucleotide" as used herein means that a molecule contains more than two DNA or RNA, preferably more than three, and usually more than ten. Its exact size depends on its optimal functional status. The nucleotide system can be formed by chemical synthesis, DNA replication, reverse transcription, and a mixture of the above. The term "nucleic acid" is used herein to mean a polymer of nucleotides, either single or double. The term "Nucleotide Analog" as used herein means that the structure of a purine or pyrimidine nucleotide is different but similar to A, T, C, G or U, but Substitution of normal nucleotides in nucleotides. The term "Nucleic Acid Composition" is used herein to mean a nucleic acid compound relating to a polyphosphate (p〇lynucle〇tide) such as DNA or RNA, which is present in single or double stranded form. The term "gene" as used herein means that the sequence of a nucleic acid has a codon of rnA or a multi-peptide (protein) which may be RNA or DNA. The term "Base Pair (bp)" is used herein to mean the pairing of A with T or C with G in a double stranded DNA molecule. In RNA, U is substituted for T to pair with A. In general, the base pair is connected by hydrogen bonding. The term "precursor messenger RNA (pre-mRNA)" as used herein refers to a gene produced by eukaryotic cells by the second type of anti-dimerization 30 201009073 enzyme (Pol-II). The primary ribonucleotide transcripts, which are transcriptions, a precursor message, the nuclear nucleic acid sequence contains a 5'-end untranslated region, and a three-terminal non-translated region (3' -end untranslated region), exon and intron 〇 "intron" as used herein means a fragment of a non-translated region of a gene transcription molecule such as in- Frame intron, five-terminal non-translated region 0 and three-terminal non-translated region. The term "exon" is used herein to mean a portion of a gene transcription molecule that has a portion of a protein translation region. The term "message ribonucleic acid (mRNA)" as used herein refers to a precursor RNA plasmon exon which consists of an intron after cleavage by a nuclear splicing mechanism, and which has a protein translational code for the mRNA. The term "complementary deoxyribonucleic acid (cDNA)" is used herein to mean a single strand of DNA complementary to a reference sequence which does not have any intron sequences. The term "sense" as used herein means that the sequence of a nucleic acid molecule is identical to that of a homologous mRNA. This positive nucleic acid configuration is designated as ', +,,,, 's' or ''sense'. The term "antisense" as used herein means that the sequence of a nucleic acid molecule is complementary to the mRNA. This anti-nucleic acid configuration is designated as, _,,,, 'a' or ''antisense', such as ''a DNA'' or ''aRNA''. The term "5'-end" is used herein to mean that a contiguous nucleotide is not in the position of carbon at the carbon of the five carbons, No. 31, 201009073, and is not a phosphodiester bond (ph〇sph〇diester b〇nd). The end point of the carbon number of the next nucleotide is called the five ends. There is at least one phosphate displayed at the endpoint. The term "3 -end" is used herein to mean that a continuous nucleotide is not in the position of the carbon of the five carbon sugars, and that the phosphodiester bond (10) 〇Sph〇diester b〇nd) and the next nucleotide The end of the fifth carbon position connection is called the three ends. The endpoint is typically a hydroxyl group.
「模板(Template)」一詞在此意指一能經核醣核酸聚合酶複 製之核酸分子,根據不同的核醣核酸聚合酶,模板係可為單 股、雙股、部分雙股。合成之複製核酸互補於模版,其中至少 雙股中之一股互補或部分互補。RNA與DNA皆由五端到三端 的方向合成。核酸的兩股通常結合(align)在一起以形成雙股。 「核酸模板(Nucleic Acid Template).」一詞在此意指一雙股 DNA、雙股RNA、DNA-RNA雜合雙股或單股DNA或單股 RNA °The term "template" as used herein refers to a nucleic acid molecule that can be replicated by a ribonucleic acid polymerase. The template system can be single-stranded, double-stranded, or partially double-stranded depending on the ribonucleic acid polymerase. The synthetic replicating nucleic acid is complementary to a template wherein at least one of the double strands is complementary or partially complementary. Both RNA and DNA are synthesized from the five-terminal to the three-terminal direction. The two strands of nucleic acid are usually aligned together to form a double strand. The term "Nucleic Acid Template". herein means a double-stranded DNA, double-stranded RNA, DNA-RNA hybrid double-stranded or single-stranded DNA or single-stranded RNA.
「一致(Conserved)」一詞在此意指一核苷酸序列是與前驅 序列一致。 「互補(Complemetary or complementarity 〇r complementation)」一詞在此意指多核苷酸之間鹼基配對的方 式,例如序列”AGT”係互補於序列”TCA”或”TCU”。互補可以 係兩股DNA之間、DNA與RNA之間、兩股RNA之間。互 補能是部分或完全。部分互補係只有某些核苷酸鹼基配對;然 而完全互補則是全部核苷酸鹼基皆配對。而互補之程度對於兩 32 201009073 股雜合之效率重要影響。互補對於複t(amplificati〇n)反應很重 要’在偵測核酸的接合(binding)也重要。互補率係關於一條單 股核酸中非配對(mismatch)的鹼基與全部驗基數量的比率,因 此50%的互補率就是一半的鹼基非配對,一半的鹼基配對。即 使是鹼基數量不同的雙股也能配對。在此情況下,互補發生於 較長的一股的部分鹼基配對於較短的一股。 「同源(homologous or homology)」一詞在此意指一多核苷 酸序列與一基因或mRNA之序列相似。如,一核酸序列可能 部分或完全與一特定基因或mRNA之序列同源。同源可能也 表示相似核苷酸數量與全部核苷酸數量的比率。 「互補鹼基(Complemetary base)」一詞在此意指當DNA或 RNA形成雙股構型時’配對之核苷酸。 「 ^ 互補核苷酸序列(Complemetary Nucleotide Sequence)」一 詞在此意指一單股RNA或DNA之核苷酸序列足夠專一互補 於另一股,其中係以氫鍵力量來形成互補。 「雜合(Hybirdize and Hybridization)」一詞在此意指核苦酸 序列經由鹼基互補所形成雙股的情況。而雜合有時在引子 (primer)對特定核酸序列(如模板)進行互補後可提供DNA聚合 酶進行DNA複製初始步驟。有一非隨機且專一的交互作用在 兩條互補多核苷酸之間。 「核醣核酸干擾(RNA interference (RNAi))」一詞在此意指 在真核細胞中一經由RNA小片段(例如’微核醣核酸 33 201009073 及小干擾核醣核酸(siRNA))驅動之「後轉錄基因靜默機制」。 11些RNA小片段可當成基因靜默效應物進而干擾與其互補之 細胞内特定基因的表現(轉錄或轉譯)。 「微核醣核酸(Micr〇RNA(miRNA))」一詞在此意指一能與 . 特定基因轉錄分子互補之單股核醣核酸(RNA^miRNA通常 係長約17到27個核苷酸之間’並能經由11111^入與1111^之 間的互補直接降解細胞中之訊息核醣核酸或抑制特定基因之 蛋白轉譯。細胞本身miRNA能在所有真核細胞中發現,當成 ❿ 一防衛病毒感染之重要機制,並調控動植物生長發育基因的表 現。 「先驅微核醣核酸(Pre—miRNA)」一詞在此意指一具有小夾 結構之單股核醣校酸,此Pre-miRNA包含彎折結構區域 (stem-arm and stem-loop region)用來與 R^aselll 内切酶交互作 用而產生一基因靜默效應物(gene siiencing effect〇r)(如 miRNA) °此miRNAs能抑制與miRNA互補標的基因。 Pre-miRNA的彎折結構區域能與雙股的特定基因轉錄分子形 成完全或部分雜合,此時彎折結構區域與雙股的一端形成一圓 形或一髮夾似的彎折結構。 「小干擾核醣核酸(small interfering RNA(siRNA))」一詞在 此意指一短雙股核醣核酸,其長約18到25個鹼基配對之核苷 酸,其能將與其完整互補的基因轉錄分子降解。 「小夾核酷核酸(small or short hairpin RNA(shRNA))」一詞 34 201009073 在此意指一具有一部分或完全互補之彎折結構序列之一單股 核醣核酸,彎折結構序列經非配對核苷酸形成類髮夾結構。許 多微核醣核酸(miRNA)係自shRNA先驅物所衍生,此shRNA 先驅物又稱為先驅微核醣核酸^pre_miRNA)。 「載體(Vector)」一詞在此意指一具有能移動並於不同遺傳 環境中表現的之重組核酸分子(如rDNA)。一般來說,此重組 核酸分子係連接成一環型。此載體係能於細胞中自動複製,因 〇 此於其中的片段也會複製。一種較佳形式之載體為離合染色小 體(episome)能於染色體外自我複製^較佳的載體能自動複製並 表現所攜帶的遺傳物質。其中具有表現特定多胜肽之基因之載 體為表現載體(expressionvector),具體來說,載體亦可經由反 轉錄酶形成mRNA來重組cDNA。 「作用子(Cistron)」一詞在此意指一核苷酸序列具有胺基酸 轉譯的密碼子,且其序列上及下端各有DNA表現控制區。 籲 「啟動子听刪㈣」一詞在此意指-能經聚合酶辨認之核 酸而能啟動轉錄反應。本發明中啟動子亦可為聚合酶接合處、 促進子(Enhancer)與其它能啟動聚合酶反應的序列。 「抗體(Antibody)」一詞在此意指一具有與受體接合之一致 性胺基酸序列之多胜肽或蛋白分子。 雖然本發明之實施例係由圖式所描述,必需指出的是,已 揭露之實施例並未關本發明之範圍。相反地,包含於申請專 利範圍之精神及範圍之修改及均等設置均包含於本發明之範 35 201009073 圍内。本發明係關於一種新化合物及方法,該方法藉由内含子 衍生之核醣核酸使真核細胞遺傳特性改變。這種遺傳特性改變 是藉由一内含子之基因靜默機制而產生,重點在於此機制係藉 由轉染一包含至少一能RNA splicillg剪接之内含子(命名為 . <57^40之重組基因進入目標細胞或有機組織中yA能攜 帶内含子之核醣核酸之介子如加咖:^八心坤’經由細胞内 核酷核酸之剪接與處理之機制而釋出該内含子之核醣核酸之 介子,並經由RNAi/後轉錄基因靜默(p0st-transcriptional gene @ silencing (PTGS))靜默效應以互補方式抑制與内含子之核醣核 酸之介子互補率尚的基因轉錄分子。一般來說,如圖4及圖5 所示’當重組基因利用化學方式或脂質體(lip0S0me)轉染或病 毒感染進入真核細胞後,該内含子之核醣核酸之介子(intr〇nic RNA insert)經由第二型核醣核酸聚合酶系統轉錄,並由核醣核 酸之努接與處理之機制如剪接體(spliceosome)、外體(exosomes) 與無義介導降解系統等作用後而釋出。在核醣核酸之剪接期 ❹ 間,内含子之核醣核酸(intronic RNA)形成一套馬索核醣核酸 (lariat RNA)並進一步處理成基因靜默效應物(gene silendng effectors) ’ 如短暫時核醋核酸(short-temporary RNA(stRNA»、 反意核醣核酸(antisense RNA)、小干擾核醣核酸(siRNA)、小 夾核醣核酸(shRNA)、微核醣核酸(miRNA)、Piwi交互作用核 醣核酸(piRNA)及這些核醣核酸之先驅物與衍生物以及上述核 醣核酸混合之核醣核酸選其一。之後,這些基因靜默效應物將 36 201009073 經由RISC複合體及核醣核酸基因靜默效應(RNAi-induced initiator of transcriptional silencing (RITS))而進行降解它們之標 的基因轉錄分子或抑制標的基因之蛋白轉譯。 為了模擬細胞内先驅訊息核醣核酸(pre-mRNA)剪接及處理 機制,我們使用細胞内剪接體、外體與NMD系統來催化内含 子移除並處理表現系統。經由一連串細胞内剪 接體組成物於办似⑷的snRNP辨識區域(如snRNPs Ul, U2 ❹ 及U4/U6U5 tri-snRNP)組合後,被釋出以進一步形成 基因靜默效應物。將人造snRNP辨識區域併入办並將該 併入重組表現系統之方法將分別於實施例一及 二揭露。 設計、建構及評估能誘發内含子核醣核酸某因靜默敔龐之 1二型轉錄聚合酶之紅色螢光蛋白之砉規.糸 魏 〇 用於驅使細胞内核醣核酸剪接與作用導致基因靜默效應機 制於體内(in vivo)已經被證實,本發明藉使用第二型轉錄聚合 酶(Pol-II)之重組基因載體系統(稱為供表現内 含子之基因靜默效應物(intronic gene silencing effectors)如圖 3A與3B所示,此表現系統具有一人造的能剪 接之内含子,這些基因靜默效應物如miRNA與類夾 shRNA(hairpin-like shRNA)。將办利用基因工程方法及 數條合成DNA連接(ligation)方式併入紅色螢光蛋白基因 37 201009073 (i?GFP),如實施例一及實施例二所揭露。办•包含先驅 miRNA或shRNA介子,這些介子經由核醣核酸之剪接與處理 之機制而產生成熟的miRNA或shRNA基因靜默效應物。然 而在其他實施例中’經由同樣之精神與原理’由第一型核醣核 酸^^合轉系統(用於先驅核醋體核醋核酸ribosomal precursor RNA)也可以產生功能相同之基因靜默效應物(gene siiencing effector)。此外能用來產生之核醣核酸轉錄分子包含 訊息核醣核酸(mRNA)、異質核核醣核酸(hnRjsiA)、核醣體核 @ 醣核酸(rRNA)、轉介核醣核酸_a、snoRNA、小胞核核醣 核酸snRNA、先驅微核糖核酸(pre_mj^NA)、病毒核醣核酸 (viral RNA)以及上述核醣核酸之衍生物及先驅物。 如實施例1與2及圖3A所揭露,知被併入紅色螢光 蛋白(red flUOrescent pr〇tein,及GF尸)基因(來自丑你 的HcRedl突變的色彩蛋白)而形成一基因重組之含紅色螢光 蛋白之SpRNAi(SPmAi-RGFP)基m结填。钽爲SpRNAH欲入 ❹ 造成紅色螢光蛋白無法正常表現,不過等内含子被剪接後,此 紅色螢光蛋白就能恢復正常表現,我們可以利用紅色螢光波長 570mn所偵測到之紅色螢光蛋白表現量來判定内含子之訊息 核酷核酸(mRNA)的成熟。办構建是基於先驅訊息 核醣核酸之結構特性。人造内含子)的主要單元包含數 個snRNP辨識區域及連接件(linker)如五端剪接處、三端剪接 處、分支點區(branch point motif (BrP))(用於辨識剪接體)、多 38 201009073 响啶區((PPT)用來與剪接體交互作用)以及連接件(linker),以供 連接母一早元及限制酶切位。如圖3B所示,本發明之具有靜 默效應物之SpRNAi(人造內含子)從五端到三端包含五端剪接 處、反意内含子之介子(anti intronic insert)(可經剪接或處理後 而形成基因靜默效應物如類mir-302基因靜默效應物 (mir-302-like gene silencing effector))、分支點區(BrP)、多嘴咬 區(PPT)及三端剪接處(其可供剪接體組合)。此外,一些轉譯終 ❹ 止子(translational termination codons (T codon))係位於靠近 之三端剪接處之連接件序列。 一般來說’五端剪接處可微核普酸序列,該序列包含或同 源於 5’-GTAAGAGK-3,(SEQ.ID.N0.4)或是 GU(A/G)AGU 序 列(例如.,5’-GTAAGAGGAT-3,(SEQ.ID.NO.30)、 5’-GTAAGAGT-3’、5’-GTAGAGT-3’及 5’-GTAAGT-3,)。三端 剪接處序列可包含或同源於GWKSCYRCAG(SEQ.ID.N0.5)或 ❹ CT(A/G)A(C/T)NG 序列(例如,5’-GATATCCTGCAG-3, (SEQ.ID.N0.31)、5,-GGCTGCAG-3,及 5,-CCACAG-3,)。此 外’分支點序列係位於五端與三端剪接處之間,該分支點區序 列包含或同源於 5,-TACTWAY-3,(SEQ.ID.N0.6)(例如, 5’-TACTAAC-3’及5’-TACTTAT-3’)。該分支點區序列之分支點 核苷酸係一腺核苷(adenosine,A),其能形成一套馬索(㈣站)内 含子核醣核酸結構(2’-5,方式連接),其藉由2,-5,寡腺核酸合成 酶(2’-5’-olig〇adenylate synthetases)及剪接體在大部分的剪接内 39 201009073 含子中形成。此外,多做區位於分支祕與三端剪接處之 間,其中多嘧啶區具有許多胸腺嘧啶(Thymine)與胞嘧啶 (Cytosine)之核苷酸序列,多嘧啶區之核苷酸序列同源於The term "conserved" is used herein to mean that a nucleotide sequence is identical to a precursor sequence. The term "Complemetary or complementarity 〇r complementation" is used herein to mean a method of base pairing between polynucleotides, for example, the sequence "AGT" is complementary to the sequence "TCA" or "TCU". Complementation can be between two strands of DNA, between DNA and RNA, between two strands of RNA. Mutual complement can be partial or complete. Partial complements have only certain nucleotide base pairings; however, complete complementation means that all nucleotide bases are paired. The degree of complementarity has an important impact on the efficiency of the hybridization of the two 32 201009073 shares. Complementation is important for complex t (amplificati〇n) reactions. It is also important to detect binding of nucleic acids. The complementarity rate is the ratio of the number of mismatched bases to the total number of all the bases in a single strand of nucleic acid, so the 50% complementarity is half of the base unpaired and half of the base pairing. Even double strands with different base numbers can be paired. In this case, the complement occurs in the longer base of the partial base pair for the shorter one. The term "homologous or homology" as used herein means that a polynucleotide sequence is similar to the sequence of a gene or mRNA. For example, a nucleic acid sequence may be partially or completely homologous to the sequence of a particular gene or mRNA. Homology may also indicate the ratio of the number of similar nucleotides to the total number of nucleotides. The term "Complemetary base" is used herein to mean a paired nucleotide when DNA or RNA forms a double-strand configuration. The term "Complemetary Nucleotide Sequence" as used herein means that the nucleotide sequence of a single strand of RNA or DNA is sufficiently complementary to another strand, in which hydrogen bonding forces are used to form a complement. The term "Hybirdize and Hybridization" is used herein to mean the case where the nucleotide sequence is double-stranded by base complementation. Hybridization sometimes provides a DNA polymerase for the initial step of DNA replication after the primer complements a particular nucleic acid sequence (e. g., a template). There is a non-random and specific interaction between the two complementary polynucleotides. The term "RNA interference (RNAi)" as used herein means "post-transcription" driven by small RNA fragments (eg, 'microRNA33 201009073 and small interfering ribonucleic acid (siRNA)) in eukaryotic cells. Gene silencing mechanism." These small RNA fragments can be used as gene silencing effectors to interfere with the expression (transcription or translation) of specific genes in their complementary cells. The term "microcrRNA (miRNA)" is used herein to mean a single-stranded ribonucleic acid (RNA miRNA typically between about 17 and 27 nucleotides in length) that is complementary to a particular gene transcriptional molecule. It can directly degrade the message ribonucleic acid in the cell or inhibit the translation of the specific gene through the complementation between 11111^1111 and 1111^. The miRNA of the cell itself can be found in all eukaryotic cells, and it is an important mechanism for preventing virulence virus infection. And regulate the performance of genes for growth and development of animals and plants. The term "pre-miRNA" refers to a single-stranded ribose acid with a small sandwich structure containing a bent structure region (stem) -arm and stem-loop region) are used to interact with R^aselll endonuclease to generate a gene siiencing effector (such as miRNA). This miRNAs can inhibit genes complementary to miRNAs. Pre- The bent structure region of the miRNA can form a complete or partial hybrid with the double-stranded specific gene transcription molecule, and the bent structure region forms a circular or a hairpin-like bending structure with one end of the double strand. nuclear The term "small interfering RNA (siRNA)" as used herein, refers to a short double-stranded ribonucleic acid having a length of about 18 to 25 base pairing nucleotides that is capable of degrading a gene transcription molecule that is fully complementary thereto. The term "small or short hairpin RNA (shRNA)" 34 201009073 herein means a single-stranded ribonucleic acid having a partially or fully complementary sequence of bent structures, the sequence of the bent structure being unpaired Nucleotide-forming hairpin structures. Many microRNAs (miRNAs) are derived from shRNA precursors, also known as precursor microRNAs [pre_miRNAs]. The term "Vector" is used herein to mean a recombinant nucleic acid molecule (e.g., rDNA) that is capable of movement and expression in a different genetic environment. Generally, the recombinant nucleic acid molecules are joined in a loop form. This vector is capable of being automatically replicated in cells, as the fragments in it are also replicated. A preferred form of vector is that the episome can replicate extrachromosomally. A preferred vector automatically replicates and expresses the genetic material carried. A vector in which a gene expressing a specific multi-peptide is expressed is an expression vector, and specifically, the vector can also recombine cDNA by forming a mRNA via a reverse transcriptase. The term "Cistron" is used herein to mean a nucleotide sequence having an amino acid-translated codon and having a DNA expression control region at the top and bottom of each sequence. The term "promoter (4)" is used herein to mean a transcriptional reaction that can be detected by a polymerase-identified nucleic acid. The promoter of the present invention may also be a polymerase junction, an enhancer and other sequences capable of initiating a polymerase reaction. The term "antibody" as used herein means a multi-peptide or protein molecule having a consensus amino acid sequence joined to a receptor. While the embodiments of the present invention have been described in the drawings, it is to be understood that the disclosed embodiments are not intended to On the contrary, modifications and equivalents of the spirit and scope of the invention are included in the scope of the invention. The present invention relates to a novel compound and method for altering the genetic properties of eukaryotic cells by intron-derived ribonucleic acids. This genetic change is produced by a gene silencing mechanism of an intron, with a focus on transducing an intron containing at least one RNA splicillg splicing (named <57^40) The recombinant gene enters the target cell or organic tissue. The yA can carry the intron ribonucleic acid meson such as Jiajia: ^八心坤' releases the ribonucleic acid of the intron via the mechanism of splicing and processing of the cellular nucleus a meson, and a gene transcriptional molecule that complements the intron of the ribonucleic acid of the intron by a silencing effect of the RNAi/post-transcriptional gene @ silencing (PTGS). In general, such as Figure 4 and Figure 5 show that when the recombinant gene is transfected by chemical means or liposome (lip0Sme) or virally infected into eukaryotic cells, the intron ribonuclease RNA insert is passed through the second The ribonuclease polymerase system transcribes and is released by the action of ribonucleic acid and processing such as spliceosome, exosomes and nonsense-mediated degradation systems. During the splicing period of the nucleic acid, the intronic RNA of the intron forms a set of lariat RNA and is further processed into gene silendng effectors, such as short-lived nucleoside nucleic acid (short). -temporary RNA (stRNA», antisense RNA, small interfering ribonucleic acid (siRNA), small ribonucleic acid (shRNA), microRNA (miRNA), Piwi interaction ribonucleic acid (piRNA) and these ribose The nucleic acid precursor and the derivative and the ribonucleic acid mixed ribonucleic acid are selected. Thereafter, the gene silencing effector will pass 36 201009073 via the RISC complex and the RNAi-induced initiator of transcriptional silencing (RITS). In order to mimic the translation of their target gene transcriptional or inhibitory proteins, in order to mimic the intracellular precursor message ribonucleic acid (pre-mRNA) splicing and processing mechanisms, we use intracellular splices, exosomes and NMD systems to catalyze The intron removes and processes the expression system. It is identified by a series of intracellular splice compositions in the snRNP (4) Regions (eg, snRNPs Ul, U2 ❹ and U4/U6U5 tri-snRNP) are combined to be released to further form gene silencing effectors. The integration of the artificial snRNP recognition region and the incorporation of the recombinant expression system will be It is disclosed in the first and second embodiments. Design, construct, and evaluate the regulation of red fluorescent protein that can induce the intron ribonucleic acid (D2) transcriptional polymerase. The use of 糸 〇 〇 驱 驱 细胞 细胞 细胞 细胞 细胞 细胞 细胞 细胞 细胞 细胞 内核 内核 内核 内核 内核 内核 内核 内核 内核 内核The mechanism has been demonstrated in vivo, and the present invention utilizes a recombinant gene vector system using a second type of transcription polymerase (Pol-II) (referred to as intronic gene silencing effectors). As shown in Figures 3A and 3B, the expression system has an artificial splicing intron, such as miRNA and hairpin-like shRNA, which will utilize genetic engineering methods and several The synthetic DNA ligation method incorporates the red fluorescent protein gene 37 201009073 (i?GFP), as disclosed in Example 1 and Example 2. • Contains a precursor miRNA or shRNA meson, which is spliced via ribonucleic acid The mechanism of processing produces a mature miRNA or shRNA gene silencing effector. However, in other embodiments, the first type of ribonucleic acid is transferred to the system via the same spirit and principle ( The ribosomal precursor RNA can also produce a gene siiencing effector with the same function. In addition, the ribonucleic acid transcription molecule can be used to generate a message ribonucleic acid (mRNA), heterogeneous ribonucleic acid. (hnRjsiA), ribosome nucleus @ 糖核核(rRNA), ribonucleic acid _a, snoRNA, small nuclear RNA sRNA, precursor microRNA (pre_mj^NA), viral ribonucleic acid (viral RNA) and the above ribose Derivatives and precursors of nucleic acids. As disclosed in Examples 1 and 2 and Figure 3A, it is known to incorporate red fluorescent protein (red flUOrescent pr〇tein, and GF cadaver) genes (color proteins from ugly HcRedl mutations) And form a recombinant red fluorescent protein-containing SpRNAi (SPmAi-RGFP)-based m-filler. The sputum is SpRNAH, which causes the red fluorescent protein to fail to perform normally, but after the intron is spliced, the red Fluorescent proteins can return to normal performance, and we can use the red fluorescent protein expression detected by the red fluorescent wavelength of 570mn to determine the maturation of the intron message nucleic acid (mRNA). The construction is based on the structural characteristics of the precursor message ribonucleic acid. The main unit of the artificial intron contains several snRNP recognition regions and linkers such as five-terminal splicing, three-terminal splicing, branch point motif (branch point motif (branch point motif) BrP)) (for identification of splices), multiple 38 201009073 Cyclic region ((PPT) for interaction with splices) and linkers for ligation of maternal early and restriction enzyme cleavage sites. As shown in FIG. 3B, the SpRNAi (artificial intron) having a silent effector of the present invention comprises a five-terminal splicing, an anti intronic insert from the five-terminal to the three-terminal (can be spliced or After treatment, a gene silencing effector such as a mir-302-like gene silencing effector, a branch point region (BrP), a multi-mouth bite region (PPT), and a three-terminal splicing site (which can be formed) For the combination of shears). In addition, some translational termination codons (T codon) are located in the sequence of connectors near the three-terminal splicing. Generally, the 'five-terminal splicing site can be a micronucleotide sequence containing or homologous to 5'-GTAAGAGK-3, (SEQ.ID.N0.4) or GU(A/G)AGU sequences (eg ., 5'-GTAAGAGGAT-3, (SEQ. ID. NO. 30), 5'-GTAAGAGT-3', 5'-GTAGAGT-3' and 5'-GTAAGT-3,). The tri-terminal splicing sequence may comprise or be homologous to a GWKSCYRCAG (SEQ. ID. N0.5) or ❹ CT (A/G) A (C/T) NG sequence (eg, 5'-GATATCCTGCAG-3, (SEQ. ID.N0.31), 5, -GGCTGCAG-3, and 5, -CCACAG-3,). Furthermore, the 'branches point sequence is located between the five-terminal and three-terminal splicing, the branch point region sequence contains or is homologous to 5,-TACTWAY-3, (SEQ.ID.N0.6) (eg, 5'-TACTAAC) -3' and 5'-TACTTAT-3'). The branching point nucleotide of the branch point region sequence is an adenosine (A), which can form a set of (a) station intron ribonucleic acid structure (2'-5, mode linkage), By 2,-5, 2'-5'-olig〇adenylate synthetases and splices are formed in most of the splicing 39 201009073. In addition, the multiple region is located between the branch and the three-terminal splicing region, wherein the polypyrimidine region has a plurality of nucleotide sequences of Thymine and Cytosine, and the nucleotide sequence of the polypyrimidine region is homologous to
5 _(TY)m(C/-)(T)nS(C/-)-3’(SEQ.ID.N0.7)與 5’-(TC)nNCTAG (G/-)-3’(SEQ.ID.N0.8)。,,m”與,,n”係指大於等於一之多重複序 列,較佳m之序列數是一到三之間而n之序列數是七到十二 之間。”一 “係指無任何核苷酸。全部内含子之單元是藉由一此 連接件(linker)核苷酸來連接,基於使用符號及公式以供表達核 ❹ 苷酸與胺基酸序列之37CFR1.822規定,W係指腺嘌呤(adenine (A))或胸腺嘧啶(thymine (T))/尿嘧啶(uracil(U)),K係指鳥嗓吟 (guanine(G))或胸腺嘧咬/尿嘧啶,s係指胞嘧啶(〇或鳥嗓呤, Y係指胞嘧啶或胸腺嘧咬/尿嘧啶,R係指腺嘌呤或鳥嘌呤以 及N係指腺嗓吟、胞癌咬、鳥嗓吟或胸腺痛咬/尿嘲咬。對於 上述剪接體辨識單元(spliceomomal recognition components), 去氧胸腺核苷酸(deoxythymidine)可由尿核酸(uridine)取代。 ❹ 為了確定剪接後之之介子(insert)之功能。許多寡核 苷酸序列經由基因工程方式併入重組及GFP之内含子 介子區域。這些反意内含子介子區域包含數種限制酶切位,其 中這些限制酶係選自乂加//、Jcc/、4/?///瓜、乂炉/、却a//ZJ、5 _(TY)m(C/-)(T)nS(C/-)-3'(SEQ.ID.N0.7) and 5'-(TC)nNCTAG (G/-)-3' (SEQ .ID.N0.8). , m" and, n" means a repeating sequence of more than one, preferably the number of sequences of m is between one and three and the number of sequences of n is between seven and twelve. "One" means no nucleotides. The units of all introns are linked by a single nucleotide of the linker, based on the use of symbols and formulas for expression of the nucleotide and amino acid sequence of 37 CFR 1.822, and W is adenine. (adenine (A)) or thymine (T) / uracil (U), K means guanine (G) or thymidine / uracil, s means cytosine (〇 or guanine, Y refers to cytosine or thymidine / uracil, R refers to adenine or guanine and N refers to adenine, cell carcinoma bite, guanine or thymus bite / urinary For the above spliceomomal recognition components, deoxythymidine may be replaced by uridine. ❹ In order to determine the function of the spliced insert, many oligonucleotides. The sequence is genetically engineered into the recombination and intron meson regions of GFP. These anti-intron meson regions contain several restriction enzyme cleavage sites, wherein these restriction enzymes are selected from 乂 plus / /, Jcc /, 4 / ?/// melon, 乂 furnace /, but a / / ZJ,
Asel、Asp7181、BamHI、BbeI、BclI/II、BglII、BsmI、Bsp 1201、 BspHI/LUllI/1201、BsrI/BI/GI、BssHII/SI、BstBI/Ul/XI、ClaI、Asel, Asp7181, BamHI, BbeI, BclI/II, BglII, BsmI, Bsp 1201, BspHI/LUllI/1201, BsrI/BI/GI, BssHII/SI, BstBI/Ul/XI, ClaI,
Csp6I、DpnI、DraI/II、EagI、Eel 13611、EcoRI/RW47III、EheI、 40 201009073Csp6I, DpnI, DraI/II, EagI, Eel 13611, EcoRI/RW47III, EheI, 40 201009073
FspI、Haelll、Hhal、HinPI、Hindlll、Hinfl、ΗραΙ/ΙΙ、KasI、 Kpnl、Maell/III、Mfel、Mlul、MscI、Msel、NaeI、NarI、NcoI、 Ndel、NgoM、NotI、NruI、NsiI、PmlI、PpulOI、PstI、PvuI/II、 Rsal、SacI/II、Sail、Sm3AI、Smal、SnaBI、SphI、SspI、StuI、 7^:/、7^/、Ιδβ/以及以上限制酶混合之限制酶。 其中這些内含子之寡核普酸介子(intronic oligonucleotide insert) 是DNA模板,此模板可供轉錄成具有相當多的二級結構之轉 〇 錄分子’上述分子選自套馬索核醣梭酸、短暫時(short- temporary) 核 醣核酸 (stRNA) 、 反意核 聽核酸 (antisense RNA) 、 小干擾核醣核酸(siRNA)、小夾核醣核酸(shRNA)、微核醣核 酸(miRNA)、Piwi交互作用核醣核酸(piRNA)、核糖酵素 (ribozyme)及這些核醣核酸之先驅物或衍生物,其可為正股或 反意的形式或具有兩種形式,以及上述核醣核酸之混合物。 為了基因傳送之方便以誘發特定細胞活化,本發明之較佳 Ο 之基因重組結構办被併入表現載體,該載體可選 自DNA轉殖基因(DNA transgene)、質體(plasmid)、轉位子 (transposon)、反轉位子(retrotransposon)、跳躍基因(jumping)、 病毒載體及上述載體之混合載體。該載體藉由基因轉染方法進 入特定細胞或組織,這些基因轉染方法選自脂質體轉染法 (liposomal transfection)、化學轉染法(chemical transfection)、電 穿孔法(electroporation)、轉位子 DNA 重組法 (transposon-mediated DNA recombination)、跳躍基因併入法 201009073 (jumping gene insertion)、病毒感染法(viral infection)、微注射 法(micro-injection)、基因搶法(gene-gun penetration)以及以上方 法混合之方法。此載體進一步包含至少一病毒或第二型核醣核 酸聚合酶(Pol-II)或第三型核醣核酸聚合酶(Pol-ΠΙ)之啟動子以 表現尸。再者,上述載體可包含Kozak轉譯起始 處(Kozak consensus translation initiation site)以增加在真核細胞 中之轉譯效率、多重SV40之多腺苷酸化作用信號 (polyadenylation signals)於*之下游區域以供重 組基因轉錄分子三端的進一步處理、pUC複製起始子(origin of replication)以中於原核細胞中大量複製、至少兩個限制酶切位 用於併合办入載體、選擇性(可有或可不有)之 SV40複製起始子用於在哺乳細胞中表達SV40 T抗原、及選 擇性(可有或可不有)之早期啟動子(early promotor)用於在能複 製的原核細胞中具有表現至少一抗生素的抗藥性。抗生素抗藥 性基因的表現可用來篩選是否順利轉染或感染標的細胞的指 標。上述抗生素抗藥性基因可對抗選自青黴素G (penicillin G)、安比西林(ampicillin)、新徽素(neomycin)、巴龍徽素 (paromycin)、康黴素(kanamycin)、鏈黴素(streptomycin)、紅黴 素(erythromycin)、斯派克黴素(spectromycin)、霍火黴素 (phophomycin)、四環素(tetracycline)、利福黴素(rifapicin)、兩 性黴素B(amphotericin B)、健他黴素(gentamycin)、氣黴素 (chloramphenicol)、頭孢黴素(cephalothin)、泰黴素(tylosin)以 42 201009073 及以上抗生素混合之抗生素。 办载體已經於(Tg(actin-GAL4:UAS-gfj)))株之 斑馬魚體内測試過,證實可抑制綠色螢光蛋白基因表現。如實 施例三及六與圖3C所示,抗綠色螢光蛋白(anti-五之先驅 微核醣核酸介子之質體,此質體經由脂質體轉 染後(第四列(lane 4))顯示出很顯著之綠色螢光蛋白的基因靜 默效應(約大於80%之蛋白被抑制),然而於其他實驗組與對照 〇 組中並無任何靜默效應被偵測到;這些實驗組與對照組依序 (由左到右)為1、控制組(blank vector control,Ctl) ; 2、針對愛 滋病病毒蛋白;之先驅微核醣核酸(pre-miRNA)的 對照組。3、針對反意綠色螢光蛋白且無小夾結構介子(antisense EGFP insert without the hairpin loop structure)之 anti 組以及 5、 反轉先驅微核醣核酸序列之miR*組,其中反轉先驅微核醣核 酸序列完全互補於抗綠色螢光蛋白之先驅微核醋核酸 ❹ (anti-五GFP pre-miRNA,miR*)。對於非專一基因,如紅色螢光 蛋白及肌動蛋白(actin),發現並無靜默效應發生,表示内含子 之微核醣核酸介入之核醣核酸干擾效應(intr〇nic miRNA-mediated RNA interference (RNAi))具有高度專一性。 此外’如圖3D所示,藉由北方墨點法(Northernbolting)分析, 顯示有效用之内含子之核酷核酸(intronic RNA)只在具·有内含 子之抗綠色螢光蛋白先驅微核醣核酸之紅色螢光蛋白載體組 生成出來(中間第二列),在不具有内含子之紅 43 201009073 色螢光蛋白組(intrcm彻抓FP).(左邊第—列)或缺乏五端剪 接處之及GFP組中並無此現象發生。此時紅色螢光蛋 白之外顯子可被連接起來形成成熟核醣核酸以進行表現具有 -FspI, Haelll, Hhal, HinPI, Hindlll, Hinfl, ΗραΙ/ΙΙ, KasI, Kpnl, Maell/III, Mfel, Mlul, MscI, Msel, NaeI, NarI, NcoI, Ndel, NgoM, NotI, NruI, NsiI, PmlI, PpulOI, PstI, PvuI/II, Rsal, SacI/II, Sail, Sm3AI, Smal, SnaBI, SphI, SspI, StuI, 7^:/, 7^/, Ιδβ/ and a restriction enzyme mixed with the above restriction enzymes. The intronic oligonucleotide insert of these introns is a DNA template which can be transcribed into a transgenic molecule having a considerable number of secondary structures. The above molecule is selected from the group consisting of snail ribose fumarate. Short-temporary ribonucleic acid (stRNA), antisense RNA, small interfering ribonucleic acid (siRNA), small ribonucleic acid (shRNA), microRNA (miRNA), Piwi interaction ribose Nucleic acids (piRNA), ribozymes, and precursors or derivatives of these ribonucleic acids, which may be in the form of either a positive or negative form or in two forms, as well as mixtures of the above ribonucleic acids. For the convenience of gene delivery to induce specific cell activation, the preferred recombinant structure of the present invention is incorporated into an expression vector which may be selected from the group consisting of a DNA transgene, a plasmid, a transposon. (transposon), retrotransposon, jumping, viral vector, and a mixed vector of the above vectors. The vector is introduced into a specific cell or tissue by gene transfection, and the gene transfection method is selected from the group consisting of liposomal transfection, chemical transfection, electroporation, transposon DNA. Reposon-mediated DNA recombination, jumping gene insertion 201009073 (jumping gene insertion), viral infection, micro-injection, gene-gun penetration, and more Method of mixing. The vector further comprises a promoter of at least one virus or a second type ribonucleotide polymerase (Pol-II) or a third type ribonucleic acid polymerase (Pol-ΠΙ) to express the corpse. Furthermore, the vector may comprise a Kozak consensus translation initiation site to increase translation efficiency in eukaryotic cells, multiple polyadenylation signals of SV40 in the downstream region of * Further processing of the three ends of the recombinant gene transcriptional molecule, pUC origin of replication to a large number of copies in prokaryotic cells, at least two restriction enzyme cleavage sites for conjugation into vectors, selectivity (may or may not The SV40 replication promoter is used to express the SV40 T antigen in mammalian cells, and the selective (may or may not be) early promotor is used to exhibit at least one antibiotic in replicable prokaryotic cells. Resistance. The performance of antibiotic resistance genes can be used to screen for indicators of successful transfection or infection of target cells. The above antibiotic resistance gene can be countered from penicillin G, ampicillin, neomycin, paromycin, kanamycin, streptomycin. , erythromycin, spectromycin, phophomycin, tetracycline, rifapicin, amphotericin B, gentamicin (gentamycin), chloramphenicol, cephalothin, and tylosin are antibiotics mixed with antibiotics of 42 201009073 and above. The vector has been tested in the zebrafish of the (Tg (actin-GAL4: UAS-gfj)) strain and has been shown to inhibit the expression of the green fluorescent protein gene. As shown in Examples 3 and 6 and Figure 3C, the anti-green fluorescent protein (the plastid of the anti-five pioneer microribonucleic acid meson, which is displayed after transfection by liposome (lane 4)) A significant gene silencing effect of green fluorescent protein (more than 80% of the protein was inhibited), however, no silent effects were detected in the other experimental groups and the control group; these experimental groups and the control group were The order (from left to right) is 1. control group (blank vector control, Ctl); 2. for AIDS virus protein; the precursor of micro-ribonucleic acid (pre-miRNA) control group. 3. against anti-intentional green fluorescent protein And the anti group of the antisense EGFP insert without the hairpin loop structure and the miR* group of the inverted precursor microRNA sequence, wherein the inverted precursor microRNA sequence is completely complementary to the anti-green fluorescent protein Pioneer micro-nuclear acid ❹ (anti-five GFP pre-miRNA, miR*). For non-specific genes, such as red fluorescent protein and actin, no silent effects were found, indicating introns. Microribonuclease intervention The intrinsic miRNA-mediated RNA interference (RNAi) is highly specific. In addition, as shown in Figure 3D, the Northern blotting analysis shows the effective use of the intron nucleus. Intronic RNA is produced only in the red fluorescent protein carrier group with the intron-resistant green fluorescent protein precursor microRNA, (second column in the middle), in the absence of introns 43 201009073 The fluorescein group (intrcm FP). (left column - column) or lack of five-terminal splicing and GFP group did not occur. At this time, red fluorescent protein exons can be joined to form Mature ribonucleic acid for performance -
功能的紅色螢光蛋白。 _ 先前實驗建立内含子之微核醣核酸(intronic miRNA)能提 供一種化合物與方法,其可於體内咖生基因靜默效 應。為了進一步評估内含子之微核醣核酸之基因靜默效應之效 率以及決疋較佳的内含子之微核酷核酸之結構,以供產生最佳 ® 的基因靜默效應。根據研究,在細胞内的核醣核酸靜默(RNAi) 相關基因靜默效應機制(如RISC)對於成熟的微核醣核酸的特 定-股具有結構上的偏好。RISC為蛋自__賊複合體,此 複合體經由RNAi機制對於標的基因轉錄分子的降解或標的 基因的轉譯抑制或PTGS機制皆有影響。 選擇以斑馬魚做為實驗制,在實射發現先職獅核 ◎ 酸之弯折結構(stem-loop)決定了见父複合體與成熟微核醣核 酸序列之組合’此組合與習知的組合之複合體不 同(Lm ei.a/· (2005) Gewe 356: 32-38)。siRNA 雙股的形成於 siRNA-RISC複合體中粉演重要之角色,siRNA的雙股功能並 不相同,只有一股會與RISC複合體組合。此偏好現象是由於 siRNA雙股五端之鹼基對之動態熱穩定性(therm〇dynamic stability of each 5’-end base-pairing)所決定。基於 siRNA 模式, 44 201009073 miRNA及其互補之miRNA(又稱miRNA,兩者之間的雙股形 成被認為係組成miRNA-RISC複合體關鍵性之一步。假如此 模式係正確的話’將無偏好特定一股之現象出現在先驅微核疏 核酸的變折結構上。然而,實驗發現丨血〇niCpre-m说NA之蠻 折結構對於miRNA-RISC複合體的組成選股上具有影響。 如實施例一與二揭露方式,利用建構完成之尸 miRNA 之办載體以及 miRNA*-stemloop-miRNA ❹ ⑴以及 miRNA-stemloop-miRNA*[2](miRNA*代表係與成熟 微核醣核酸序列互補之微核醣核酸)這兩個不同之先驅微核醣 核酸’經DNA合成器合成後’個別併入預先準備好之 及GFP載體中。這兩組的先驅微核醣核酸包含相同之雙股變折 結構(double-sttandstem-arm region),該彎折結構能對五基 因第280到第302之核苷酸序列進行靜默效應。因為办狀办 及GFP載體中經由五端及三端的_pvw/及灿限制酶切位將内 © 含子之介子併入。上述介子能輕易被許多其他抗不同基因的介 子(例如,anti-丑GFP,mir-3〇2先驅微核醣核酸)所取代。藉由 此可將介子取代成其他抗不同基因轉錄分子的介子的 方式’此内含子之微核醣核酸表現系統能提供一於體内之發育 微核醣核酸遺傳應用之重要工具。 為了決定先驅微核醣核酸結構上的偏好性,先經由mirVana 微核醣核酸分離管柱(Ambion,Austin,TX)分離後,再藉由latex beads將具有斑馬魚中具有靜默效應潛力之微核聽核駿沉殿下 45 201009073 來。其中一全長微核醣核酸,miR_EGFP(280-302),在 miRNA_stemloop_miRNA*[2]結構中,被證實具有靜默效應, 如圖4A及圖4B(灰色陰影序列)所示。因為此有效之成熟微核 聽核酸只有在斑馬魚轉染miRKA-stemloop-miRNA* [2]中,被 發現有效’因此推測miRNA-RISC複合體對於miRNA_ stemloop-miRNA*[2]而非[1]有結構上之偏好性。如圖4C所 示,利用經由肌動蛋白(beta-actin)啟動子表達之斑馬魚 Γ^(&(Λίη-ΟΑΙΑυΑ8·^φ))來進行實驗以展現視覺上標的基因 靜默效應與miRNA表現之關係,此斑馬魚會一直於各類細胞 中表達綠色螢光蛋白。於此斑馬魚轉染抗 載體並表達一可當為指標蛋白之紅色螢光蛋白,可利用指標蛋 白當成微核醣核酸在細胞中生成的指標。上述載體利用Functional red fluorescent protein. _ Previous experiments to establish intronic miRNAs in introns provide a compound and method that can be used to silence genes in vivo. In order to further evaluate the efficiency of the gene silencing effect of the microRNA of the intron and the structure of the micronucleic acid of the preferred intron, the gene silencing effect of the optimal ® is produced. According to the study, the RNA silencing (RNAi)-related gene silencing effect mechanism (such as RISC) in cells has a structural preference for the specific-strand of mature microRNA. RISC is an egg-to-thief complex that affects the degradation of the underlying gene transcription molecule or the translational inhibition of the target gene or the PTGS mechanism via the RNAi mechanism. The zebrafish was chosen as the experimental system. The spot-loop of the lion's nucleus was determined by the actual shot. The combination of the parental complex and the mature microRNA sequence was determined. The complex is different (Lm ei.a/. (2005) Gewe 356: 32-38). The formation of siRNA double strands plays an important role in the siRNA-RISC complex. The double-strand function of siRNA is not the same, only one will be combined with the RISC complex. This preference is due to the thermodynamic stability of each 5'-end base-pairing of the siRNA. Based on siRNA model, 44 201009073 miRNA and its complementary miRNA (also known as miRNA, the double-strand formation between the two is considered to be one of the key steps in the composition of the miRNA-RISC complex. If the pattern is correct then there will be no preference specific A phenomenon occurs in the deformed structure of the pioneer micronuclear acid-cleaving nucleic acid. However, it has been found that the niCpre-m of the blood stasis has an influence on the composition selection of the miRNA-RISC complex. The first and second disclosure methods utilize the constructed cadaveric miRNA vector and miRNA*-stemloop-miRNA ❹ (1) and miRNA-stemloop-miRNA*[2] (miRNA* represents a microRNA complementary to the mature microribonucleic acid sequence The two different precursor microRNAs are 'integrated into a pre-prepared and GFP vector after synthesis by a DNA synthesizer. The precursor microRNAs of these two groups contain the same double-stranded fold structure (double-sttandstem) -arm region), this bent structure can silence the nucleotide sequence of 280th to 302th of the five genes, because the _pvw/can restriction enzyme is cut through the five-terminal and three-terminal The meson is incorporated into the meson. The above meson can be easily replaced by many other mesons that are resistant to different genes (for example, anti-ugly GFP, mir-3〇2 pioneer microRNA), whereby the meson can be replaced. The way of other mesons against different gene transcriptional molecules' microRNA-expressing system of this intron can provide an important tool for the development of microRNA in vivo. In order to determine the structural preference of the pioneer microRNA First, it is separated by mirVana microribonucleic acid separation column (Ambion, Austin, TX), and then with the latex beads, it has the potential of silent effect in the zebrafish. Ribonucleic acid, miR_EGFP (280-302), has been shown to have a silent effect in the miRNA_stemloop_miRNA*[2] structure, as shown in Figure 4A and Figure 4B (gray shaded sequence). Because this effective mature micronucleus is only available in The zebrafish transfected miRKA-stemloop-miRNA* [2] was found to be effective 'so it is speculated that the miRNA-RISC complex has a structural preference for miRNA_ stemloop-miRNA*[2] rather than [1]. As shown in Figure 4C, experiments were performed using zebrafish Γ^ (&(Λίη-ΟΑΙΑυΑ8·^φ)) expressed by the actin-activated promoter to visualize the supervised gene silencing effect and miRNA expression. Relationship, this zebrafish will always express green fluorescent protein in various cells. The zebrafish is transfected with an anti-vector and expresses a red fluorescent protein which can be used as an indicator protein, and can be used as an indicator of the production of microRNA in cells. Use of the above carrier
Pu<3ene eationie liposomal reagent (Roche,In)轉染办 載體進入斑馬魚胚胎後,發現所有載體能在轉染%小 時後完全進入斑馬魚胚胎中,除了骨骼及魚鱗部分以外。 該紅色螢光蛋白之指標蛋白係在被轉染之斑馬魚中被偵測 到,然而綠色螢光蛋白(EGFP)之靜默效應只在被轉染 miRNA-steml00p_miRNA*[2]之先驅微核醣核酸之斑馬魚組別 (miR組)中被觀察到。如圖4D所示,西方墨點分析法定量性 地確認基因靜默效應,在P]結構所轉染之斑馬魚有大於百分 之八十五的基因抑制。然而基因抑制效應於腸道(〇1)係較其他 組織要低,此一現象可能與腸道中較高RNase活性有關。因 201009073 為[丨]與[2]之五端之熱穩定度為相同,因此推測此先驅微核醣 . 核酸之彎折結構係與RISC複合體組合成熟微核醣核酸的選股 有關。而岱塞爾(Dicer)於彎折結構(stem-loop)的切位已知可決 定成熟微核醣核酸的選股,因而先驅微核醣核酸之彎折結構可 能扮演決定辨識特殊切位的角色。因此基於不同微核醣核酸之 彎折結構之多樣性,本發明利用一組改良之pre_mir_3〇2彎折 (如 5’-GCTAAGCCAGGC-3,(SEQ.ID.N0.1)及 5,-GCCTGGCT ❺ TAGC-3’(SEQ.ID.N0.2))與RISC複合體最佳化地組合以發揮 本發明之效用。Pu<3ene eationie liposomal reagent (Roche, In) Transfection Service The vector entered the zebrafish embryo and found that all vectors were able to completely enter the zebrafish embryos after % of transfection, except for the bone and scales. The indicator protein of the red fluorescent protein was detected in the transfected zebrafish, whereas the silent effect of green fluorescent protein (EGFP) was only in the precursor microRNA which was transfected with miRNA-steml00p_miRNA*[2]. It was observed in the zebrafish group (miR group). As shown in Fig. 4D, Western blot analysis quantitatively confirmed the gene silencing effect, and the zebrafish transfected with the P] structure had greater than 85 percent gene suppression. However, the gene suppression effect in the intestine (〇1) is lower than in other tissues, and this phenomenon may be related to higher RNase activity in the intestine. Since 201009073 is the same as the thermal stability of the five ends of [丨] and [2], it is speculated that this pioneer microribose. The bent structure of nucleic acid is related to the stock selection of mature microribonucleic acid combined with RISC complex. Dicer's cut position in the stem-loop is known to determine the stock selection of mature microRNAs, so the bent structure of the pioneer microRNA may play a role in determining the special cut position. Therefore, based on the diversity of the bending structures of different microribonucleic acids, the present invention utilizes a modified set of pre_mir_3〇2 bends (eg, 5'-GCTAAGCCAGGC-3, (SEQ. ID. N0.1) and 5, -GCCTGGCT ❺ TAGC-3' (SEQ. ID. N0.2)) is optimally combined with the RISC complex to exert the utility of the present invention.
Mir-302之於人類初胚表細胞OidESCV人 類前列腺癌細胞PC3輿人類初胚黑色素瘤細胞Colo細胞之蜱 染作用 基於上述實驗,將設計好的 mir-302a-mir_302b-mir-302c-mir-302d 之先驅微核醣核酸介子 參 或重新設計的mir-302先驅微核醣核酸介子(如類小夾序列,其 包含 5’-UAAGUGCUUC CAUGUUUUAG UGU-3, (SEQ.ID.N0.9))併入所設計之載體中,以供於 hpESC、PC3及Colo細胞中,靜默發育及分化的相關基因。 mir-302a、mir-302b、mir-302c 及 mir-302d 的成熟序列分別為 5,-UAAGUGCUUC CAUGUUUUGG UGA-3, (SEQ.ID.NO.10)、5’-UAAGUGCUUC CAUGUUUUAG UAG-3, (SEQ.ID.NO. 11)、5,-UAAGUGCUUC CAUGUUUCAG UGG-3, 47 201009073 (SEQ.ID.NO.12)及 5,-UAAGUGCUUC CAUGUUUGAG UGU -3’(SEQ.ID.NO.13)。這些類mir-302基因靜默效應物之同源物 在前端共十七個核苷酸(100%同源)中分享一致的五端區域,這 十七個核苷酸與 5’-UAAGUGCUUC CAUGUUU-3,(SEQ. ID.N0.3)的序列相同。在這些mir-302同源序列中,胸腺喊咬 (T)能用來取代尿嘧啶(U)。 在這些實驗中,mir-302a-mir-302b-mir-302c-mir-302d 之先 驅微核醣核酸經轉染入hpESC及PC3細胞,而重新設計的 mir-302同源序列(SEQ.ID.NO.9)則轉染入Colo細胞中。在 mir-302轉染後’所有的細胞株的型態(mojphoiogy(下部圖面)) 則改變,從紡錘狀或.變形蟲狀改變置較圓胖的外型,顯示這些 細胞可能喪失移動(migration)的能力且其細胞增生速率很低, 此時如同幹細胞成長速率(圖5A至圖5C)。流式細胞儀(上部 圖面)的細胞DNA含量(DNAcontent)(Y軸)對應不同細胞周期 (X軸)所顯示有絲分裂的細胞群減少超過,證實這些 mir-302轉染細胞之細胞增生速率變慢,而上述細胞群係由 DNA含量所決定。第一峰(左)與第二峰(右)分別顯示為g〇/gi 與有絲分裂Μ期的細胞群占整體細胞群的相對數量。在 rmr-302轉染後’有絲分裂的細胞群在hpES(:細胞中從36.1% 降低至H).9% ;在PC3細胞中從38.4%降低至12 6% ;在c〇i〇 細胞中從36.5%降低至1L5%。然而,當轉染無办漏-娜户 ,細胞形態 48 201009073 或細胞增生皆無明顯地改變。上述mir-gft)先驅微核醣核酸係 設計為抑制螢火蟲的綠色螢光蛋白,其與人類或小鼠的基因序 列並無任何同源一致性。基於上述發現,mir_3〇2同源物的基 因轉殖表現能將人類初胚細胞及癌化細胞轉型為更類似胚胎 幹細胞的型態及增生速率,如同先前iPS細胞所發現的改變 (Okita et al., (2007) Nature 448: 313-317; Wemig et al, (2007) 448: 318-324)。 ❹ 篮樣體(embryoid body)形成、胚胎幹細胞指標蛋白表現、 基因體DNA去甲基化及mir-302韓殖表規.於 CoMColo+mirGCm及PC3(PC3+mir-302)細胞中所造成之細腧 移動箄作用評估 為了證實mir-302轉染細胞的類胚胎幹細胞性質,本發明 使用胚樣體形成、胚胎幹細胞指標蛋白表現、基因體去曱基化 及細胞移動現象的減少來進行評估。mir-302轉染細胞有著很 〇 高的細胞叢聚性(high density cell culture confluence (>80%-90%))並傾向於形成上述胚樣體之緊密的細胞叢 (colonies)如同原生人類胚胎幹細胞所衍生的胚樣體(如圖 6A)。然而,若無適當的贺爾蒙或生長因子導引,這些胚樣體 於再次培養時將相互分散並分化成類神經元細胞(如右下 圖)為了證實胚胎幹細胞及胚樣體細胞的遺傳特性,進一步 評估這些胚胎幹細胞的指標蛋白表現。如圖6B所示,mir_3〇2 轉染之Colo細胞(Colo+mir-302)顯著地表現出一系列胚胎幹細 49 201009073 胞標準的指標蛋白,如〇ct3/4、SSEA-3、SSEA-4及Sox2等, 然而並無上述胚胎幹細胞的指標蛋白在一般的C〇l〇細胞中或 轉染空載體的 Colo 細胞(colo cells transfected with an empty vector)中、轉染mir-g§)微核糖核酸載體的Colo 細胞(Colo+mir-gQj)或轉染mir-434-5p微核醣核酸載體的Colo 細胞(Colo+mir-434-5p)等細胞中並無被偵測到的跡象。 mir-434-5p的序列並不與mir_3〇2同源。因為Colo細胞係已分 化的人類黑色素瘤細胞株,因此結果顯示11^-3〇2-办^^·-及GFP載體的轉染能使c〇l〇細胞再度導向胚胎幹細胞的狀 態’此一狀態與真正的胚胎幹細胞相似。 〇ct3/4(或稱〇ct-3或Oct-4)係POU轉錄因子的一種,其於 分化全能胚胎幹細胞及生殖細胞表現的量很高(Sch〇ler扣α/., (1989) EMBO J. 8: 2543-2550; Rosner et al., (1990) Nature 345: 686-692)。〇ct3/4的表現量對於維持幹細胞自我更新及分化多 能性扮演重要的角色。〇ct3/4的抑制調控導致胚胎幹細胞的分 化進入不同的發育過程。SSEA蛋白包含SSEA-1、3及4起初 係由單株抗體所辨識’此單株抗體能辨識在鼠科胚胎細胞初期 著床階段表面及畸形癌細胞表面之乳糖醣脂體,但卻無法在上 述細胞分化後的衍生細胞被抗體辨識(S〇lter β α/.,(1978) Proc. Wi/. 知·· t/以75: 5565-5569)。未分化之初期胚胎幹細 胞、人類胚胎癌細胞(hEC)及胚胎幹細胞皆表現出SSEA-3及 SSEA-4 但並無 SSEA-l(Thomson β 乂,(1998)公282: 50 201009073 1145- 1147)。在印子生成過程中SSEA_3及ssea 4係生成於 _子、又神及早期分裂的胚胎細胞之細胞膜表面(Shevinsky 以”(1982) &㈣:齡狗。S()x2在維持分化全能性上松演 核心轉錄分子,但此功能並非專一於胚胎幹細胞中(Boyer—, (2005) CW/122: 947-956)。因此,基於對於胚胎幹細胞指標蛋 白的知識,經mir-302轉染之Cok)細胞具有表現所有上述胚 胎幹細胞指標蛋白及胚胎幹細胞的特性。 ® 此外,分化多能性幹細胞具有另一獨特性質的後修飾改 變’如基因體去曱基化(Hochedlinger ei or/., (2006) Atowre 441: 1061 -1067)。為了轉分化已經分化的體細胞進入胚胎幹細胞階 段,許多胚胎基因需要經由再激化以至於抑制發育及分化相關 訊號或基因。DNA甲基化對於調控上述基因的表現或不表現 扮演重要的角色。因為上游啟動子區域的曱基化通常干擾眾多 轉錄分子對於基因表現的組合,去甲基化過程必須啟動以供重 〇 新活化胚胎基因,如Oct3/4、SSEA-3、SSEA-4及Sox2。為 了评估Colo+mir-302細胞及Colo細胞的曱基化程度,首先運 用(DNA isolation kit, Roche,IN)分離上述細胞的基因體。並用 切位為CCGG的限制酶Hpall將分離之基因體作用,HpaII對 於CpG曱基化具有敏感性,並只切沒有甲基化的ccGG處, 但無法切有曱基化的CCGG處。如圖6C所示,切解作用後之 基因體片段,類胚胎幹細胞Colo+mir-302細胞的片段較一般 Colo細胞的片段要小,暗示轉染mir_3〇2的Colo細胞確實有 51 201009073 較尚程度的去曱基化發生。此外,Colo細胞及Colo+mir-302 細胞的基因體之原始尺寸大小幾乎相同,故可證實上述結論。 圖6D進一步顯示〇ct3/4基因啟動子區域甲基化形態上的 改變’尤其係在hpESC、PC3及Colo細胞與轉染mir-302的 上述細胞之間改變很明顯。為了證實這些區域的曱基化,本實 驗利用重亞硫酸鹽(bisulfite)來分離基因體DNA(CpGenome DNA modification kit, Chemicon,CA),重亞硫酸鹽可將未曱基 化的胞嘧啶轉變為尿嘧啶,之後利用兩條前向引子(primer) 5’-GTTGTTTTGT TTTGGTTTTG GATAT-3’(SEQ.ID.N0.36)及 5’-ATTGTTTTGT TTTGGTTTTG GATTTA-3,(SEQ.ID.N0.37) 以及一條反向引子(reverse primer)5’-GTAGAAGTGC CTCTGCCTTC C-3’(SEQ.ID.N0.38)及聚合酶連鎖反應 (polymerase chain reaction (PCR))(long template PCR extension kit,Roche,IN)分離Oct3/4之五端上游啟動子區域。細胞基因 體(100 ng)先與引子(共150pmole)及lxPCR緩衝液混合,加熱 至94°C至四分鐘後立即放置冰上冷卻。而後,經25個PCR 循環,其條件如下:92°C、1分鐘;55°C、1分鐘;以及70。(:、 5分鐘。而後,藉PCR純化套組(Qiagen,CA)收集PCR反應產 物,此PCR產物與切ACGT序列的多重限制酶,這些限制酶 包含 dc//(AACGTT)、刀w沙/(CACGTC)、Pw//(CACGTG)、 5>w5/(TACGTA)及母tyC^W/RACGT),每種 5 單位(5U each) 均勻混合。因為在此區域中無曱基化的ACGT處可經由重亞 52 201009073 硫酸鹽(bisulfite)反應轉化為AUGT處,而AUGT處無法被上 述限制酶切動。如圖6D所示,至少四種曱基化的ACGT處, 在轉染mir-302的hpESC、PC3及Colo細胞中,被轉化成去 曱基化的ACGT處。經mir-302轉染所造成〇奶/^基因啟動 子區域的去曱基化可能係由mir-302轉染細胞如c〇l〇+mir-302 中,Oct3/4基因表現的再度活化所造成。 除此之外,細胞移動的抑制通常在mir-302所轉染的癌化 ❹ 細胞中被觀察到。一般而言,胚胎幹細胞傾向於停留於一處並 形成原位胚樣體(embryoidbody/wszYw),這可能可以解釋為何 PC3及Colo細胞在mir-302轉染之後會喪失移動能力。如圖 6E所示’當PC3細胞置於PC3+mir-302細胞旁時,我們能清 楚觀察到癌化的PC3細胞沿著PC3+mir-302細胞之一邊快速 移動約30秒。黑色箭頭指示PC3細胞移動的方向。此實驗結 果暗示一種mir-302轉染於癌細胞中的潛在治療應用,這不單 φ 可以使癌細胞轉化成有用的幹細胞亦可降低癌細胞轉移的可 能性,更有優勢的是,因為mir-302轉染的癌細胞仍然可與病 人的免疫系統相容’如上所述的類胚胎幹細胞的分化多能性細 胞能被用來移植治療而無任何免疫排斥的反應。 利用miRNA基因晶分妍辨識棘殖基因mir-302砉規 為了證實在轉染細胞中轉殖mir-302基因的表現量,我們 使用 miRNA 基因晶片分析(miRNA microarray analysis)。在約 70%的匯流,從每株細胞中經mz>Vana™ miRNA分離套組 53 201009073 (Ambion,Inc.,Austin, TX)所分離的小核醣核酸。所分離的小核 醣核酸經純化並定量後使用1%曱醛-洋菜膠電泳法及光譜儀分 析(spectrophotometer measurement)(Bio-Rad,Hercules,CA)以 及送至 LC Sciences(San Diego, CA)以供進一步 miRNA 生物 晶片分析。在Cy3及Cy5的強度圖片中,訊號的強度增加由 第1級至第65535級’其相對應的色彩改變由藍轉綠到黃至 紅。在Cy5/Cy3的圖片比率來看,當Cy3強度高於Cy5時, 顏色為綠色,當Cy3與Cy5的強度相同時,顏色為黃色,以 及當Cy5強度較Cy3高時,顏色為紅色。如圖7A所示,Cy3 為細胞沒有任何處理(如Colo),而Cy5為細胞有經mir-302轉 染(如Colo+mir-302)。在Cy5/Cy3的圖片比率(最右),在 及GFP-mirJO〗轉染後,全部的.mir-302家族(白圈)都 高度表現。因為mir-302家族基因及重新設計的mir-302試劑 有約91%的同源性,這顯示重新設計的mir-302試劑能當成 mir-302成員,並代替mir-302的原本功能。圖7B顯示在 Colo+mir-302細胞中,不同的表現量之miRNA的條列。 基於如圖7A所示的結果,我們也可以發現mir-302表現量 的增加能增加前驅mir-302的表現以及其他微核醣核酸,例如 mir-92, mir-93, mir-200c, mir-367, mir-371, mir-372, mir-373, mir-374以及全部的mir-520家族成員。經由miRBase::Sequence programfhtto://microma.sanger.ac.uk/)及這些 mir 的標的基因 分析證實mir-302家族可針對超過400種標的基因,這暗示這 201009073 些微核醣核酸可能對於維持幹細胞的分化多能性及再生性扮 演重要的角色。他們的標的基因包含但不限於RAB/RAS相關 的致癌基因成員、ECT相關的致癌基因、多種型態腺癌基因 (pleiomorphic adenoma genes)、E2F 轉錄分子、Cydin D 結合 類 Myb 轉錄仝子(cyclin D binding Myb-like transeription factors)、HMG-box轉錄分子、沖3轉錄因子、類CP2轉錄因 子(CP2-like proteins transcription factor)、NFkB 活化蛋白基 ❹ 因、cyclm 相伴激酶(cyclin-dpendent kinases (CDK))、ΜΑΡΚ 相關激酶、SNF相關激酶、肌凝蛋白支鍵激酶扣^血light chain kinases)、TNF-alpha 誘發蛋白基因(TNF_alpha-induce protein genes)、DAZ-相關蛋白基因(DAZ-associated protein genes)、LIM 相關 homeobox 基因(LIM-associated homeobox genes)、DEAD/H box 蛋白基因(DEAD/H box protein genes)、 forkhead box 蛋白基因(forkhead box protein genes)、BMP 調控 ❹ 子(BMP regulator)、Rho/Rac鳥嘌呤核苷酸交換因子(Rho/Rac guanine nucleotide exchange factor)、IGF 受體(IGF receptor)、 endothelin 受體(endothelin receptor)、左右決定因子(left-right determination factors)、細胞週期素(cyclins)、p53 誘發核蛋白 基因(p53-inducible nuclear protein gens)、類 RBl(RB-like 1)、 RB接合蛋白基因(RB binding protein genes)、Max接合蛋白基 因(Max-binding protein genes)、c-MIR 細胞免疫辨識模組 (c-MIR cellular modulator of immune recognition)、Bd2-like 細 55 201009073 胞)周亡處進子(Bcl2-like apoptosis facilitator)、連接蛋白 (protocadherins)、結合蛋白(integrin β4/β8)、抑制子_bin)、 婀克力(ankyrins)、SENP1、NUFIP2、FGF9/19、SMAD2、 CXCR4、EIF2C、PCAF、MECP2、組織蛋白乙醯轉化酶 MYST3 (histone acetyltransferase MYST3)、細胞核蛋白 RNP H3(nuclear RNPH3)以及許多核受體及因子。這些所有基因皆與胚胎發育 及癌化生成相關。 Μ甩基因晶片分析辨識胚胎幹細胞標誌、表規. ❹ 在共同表現胚胎幹細胞標誌蛋白與轉殖mir_3〇2基因的相 關性已經被證實,我們利用基因晶片分析來搜尋在細胞内 mir-302轉染前及後,基因體範圍内的基因表現改變在mir_3〇2 轉染細胞及其他人類胚胎幹細胞之間。Afiymetrix基因晶片 (GeneChip U133A&B arrays,Santa Clara,CA)被用來評估在 Colo+mir-302及其他人類胚胎幹細胞之間超過32668個人類 基因表現型態,如HuEC8及H9。從每個測試細胞株所分離的 ❹ 全部核醣核酸經 RNeasy spin column(Qiagen,Valencia, CA)收 集。為了認實背景的不同標的’我們重覆生物晶片測試並使用 相同Colo+mir302樣本及選出兩百個基因,這些基因在其中一 邊有顯現出來。如圖8A所示,這些選擇基因(白點)的表現量 改變全都小於Colo+mir-302的一倍,顯示這些背景值的雜訊 係相當小的。基於這些預先選擇的基因並用一倍的改變量當成 篩選標準(threshold),我們能計算在兩組比較基因的相對係數 56 201009073 (correlation coefficiency (CC))。32668 個人類基因表現型態在 相比較的樣本之間的相對係數比率具有相似的比例。在如此的 相對係數比率,如圖8A所示的結果證實Colo+mir-302細胞之 基因表現型態與hES HuEC8及H9細胞之間具有88%及86%的 相似性,然而只有53%的相對係數係顯示於Colo與 Col〇+mir-302細胞之間。這證實办相關的mir-302 轉染改變至少15354個細胞基因的表現形態,這些可能與癌化 ❹ Colo細胞轉化成類胚胎幹細胞c〇l〇+mir-302細胞相關。 許多在Colo與Colo+mir-302細胞之間主要不同表現程度的 基因列表顯示於圖8B。如H9及HuEC8細胞,Colo+mir-302 細胞表現胚胎幹細胞及生殖細胞的細胞標諸蛋白(如 SSEA-4, Utfl,0ct4, Sox2, Pulimio-2 反 Nanog')表現i板高。然 而’ Klf4並不表現於Colo+mir-302細胞中,顯示與們細胞 有些許不同(如圖6B所示)。此外,許多癌症標誌(cancer ❹ marker)、發育訊號(developmental signal)及細胞增長因子(ceu proliferating facotr)被發現顯著地在πώ-302轉染細胞中受到抑 制’如同未分化細胞(undifferentiated round cell)的型態及如圖5 所示之較慢的細胞複製的現象被觀察到。縱上所述,這些發現 指出mir-302轉染的方法能遺傳地轉化已分化的c〇1〇細胞株 而成具有類胚胎幹細胞的Colo+mir-302細胞株,而與分化多 能性的H9及HuEC8幹細胞相似。 利用各種荷爾蒙及生長因子導弓丨_細胞分化 57 201009073 就定義上來說’分化多能性幹細胞能分化成許多細胞型 態,這些形態與從胚胎外胚層、中胚層及内胚層衍生的組織細 胞相似。舉例來說,在無哺乳細胞的條件下(feeder_ftee)利用活 體外(沩V办如)的赫爾蒙及生長因子進行處理,本發明已經可成 - 功的導引c〇lo+mir-302細胞的分化成三種不同細胞形態如圖 9A到9C所示。首先,在無哺乳細胞的條件下,用雄激素 (androgen)與雙水化睪固 _(dihydrotestosterone(DHT 50 ng/ml>> 處理Colo+mir-302細胞六小時後,移植上述細胞(約105個細 鲁 胞)入六周大雌性免疫喪失米黃色 小鼠的子宮中,一周之後生成一類精原細胞的孢囊在移植處 (圖9A中間)。接者’運用轉形生長因子点ι(打 factory31(TGF-/31 l〇〇ng/mi))處理ι:2小時後,移植處理後的 細胞進入六周大雌性免疫喪失(immunocompromisedpciD米 黃色小鼠的子宮中,這些細胞分化成類纖維母細胞的型態並開 始分泌膠原蛋白,在一周内,這些細胞占據了子宮大部分的區❹ 域(圖 9B)。隶後’用骨轉形蛋白 4(bone morphogenetic protein 4 (BMP4 100 ng/ml))處理Colo+mir-302細胞12小時後,再用異 種皮移植(xenograft)方式將處理後的細胞移植到六周大免疫喪 失SCID米黃色小鼠的肝臟中’上述細胞會分化成類軟骨細 胞,其周圍有些許鈣化沉澱(圖9C)。藉由用無胸腺淋巴小鼠 (thymic nude mice)當成一種體内模擬移殖治療的環境。這些實 驗證實本發明之mir-302之轉染方法可產生新穎的胚胎幹細胞 58 201009073 株’这些細胞株可在無哺乳細胞的體外環境中,經導引並生成 ' 不敝織細胞賴。耻,本㈣不只能轉化或轉形以分化的 • 體_喊_胎幹細胞的分化錄性_,而且亦可在無哺 乳細胞的培養環境下維持幹細胞的分化多能性及自我複製的 能力。 因此,本發明藉由利用内含子的mir-302表現載體提供一 種新穎的幹細胞生成方法,具體來說,由初胚體細胞株及癌細 〇 胞株所衍生的生成方法。因為内含子之微核醣核酸相關基因靜 默路徑與許多細胞内的調控機制協調反應,這些機制包含基因 轉錄因子、核醣核酸剪接(RNA splicing)、外體解消及無義介 導降解。内含子的微核醣核酸之基因靜默效應被認為最有效、 最專一、最安全於所有三種已知的RNAi路徑。基於全部的優 勢,本發明之内含子的mir_3〇2試劑的使用提供一種簡單、有 效及安全的基因使用方法,其不只可供轉化體細胞成類胚胎幹 〇 細胞的分化多能性細胞,亦可在無哺乳細胞的培養條件下維持 胚胎幹細胞的分化多能性,因此可避免如同先前的iPS幹細胞 方法將四種巨大轉錄因子基因以令人厭煩的反轉錄病毒轉染 入單一細胞。如圖10所示,基於mir-302所誘發生成之胚胎 幹細胞(mir-302-induced embryonic stem cell),這暗示 SSEA-1 在mir-302誘發的細胞(Colo+mir-302)細胞中有一定程度的表 現;然而在Klf4則無此表現。 本發明之化合物: 59 201009073 -種可供誘發内含子之核醣核酸相關的基因靜默效應之重 組核酶核酸化合物包含: a) 至少-内含子,其中該内含子由複數個外顯子包圍,這 些外顯子能齡細納RNAsplieing料顯子切除並 由處理機制接著作用;以及 b) 複數個外顯子,其中該外顯子能連接成一基因而具有特 定功能。 上述的重組核醣核酸化合物,進一步包含 a) 至少一限制酶切位,其中該限制酶切位可用於併合該重 組核醣核酸化合物於一表現載體中’以供表現該重組 核醣核酸化合物的前驅核醣核酸轉錄分子於哺乳細胞 中;以及 b) 複數個轉錄及轉譯終止處 termination sites),其中該轉錄及轉譯終止處可被用來 製造該重組核醣核酸化合物的核醣核酸轉錄分子的正 確尺寸。 上述重組核醣核酸化合物的内含子進一步包含: a) —基因靜默效應物的介子,其互補或同源於至少一標的 基因; b) —五端剪接處; c) 一三端剪接處; d) —可供剪接體辨識的分支點區域; 201009073 e) —可供剪接體接合的多嘧啶區; Q複數個可供連接主要元件的連接件。 基因靜默效應物之介子包含一核苷酸序列,其同源於 5’-UAAGUGCUUC CAUGUUU-3’(SEQ.ID.N0.3) ’ 該五端剪接 處係一核苷酸序列並同源於5’-GTAAGAGK-3’(SEQ.ID.N0.4) 或是 GU(A/G)AG U 序列(例如,5,-GTAAGAGGAT-3, ❹ (SEQ.ID.NO. 30)、5,-GTA AGAGT-3,、5,-GTAGAGT-3,及 5’-01^01'-3’)。此時,三端煎接處(3’>^1^3如(^3’(;邱)序 列係同源於 GWKSCYRCAG (SEQ.ID.N0.5)或 CT(A/G)A(C/T) NG 序列(例如,5’-GATATCC TGCAG-3,(SEQ.ID.N0.31)、 5 ’-GGCTGCAG-3 ’、5 ’-CCACAG -3 ’)。此外,分支點區序列係 位於五端與二端剪接處之間,該分支點區位於一核苷酸序列同 源於 5’-TACTWAY_3’(SEQ.ID. N0.6)(如,5,-TACTAAC-3,及 Φ 5’-TACTTAT-3’)。此外’多嘧啶區係位於分支點區與三端剪接 處之間,其中多嘧啶區是一具有高密度的胸腺嘧啶(Thymine) 與胞嘧啶(Cytosine)之核苷酸序列,多嘧啶區之核苷酸序列同 源於 5 -(TY)m(C/-)(T)nS(C/-)_3’ (SEQ.ID.N0.7)與 5’-(TC)nNCTAG (G/-)-3’(SEQ.ID.N0.8)。其中,”m”與,,n”係 指大於等於一的多重複序列,較佳m之序列數是一到三之間, 而η之序列數是蝴十二之” “係指無任何核魏。一些 連接核苷酸能用來連接上勒含子片段。基於37CFR1 822規 61 201009073 定(台灣”核苷酸及胺基酸序列表記載格式,,亦同),w係指腺嗓 呤(adenine (A))或胸腺嘧啶(thymine (T))/尿嘧啶扭acil^j)),κ 係指鳥嗓吟(guanine (G))或胸腺嘴咬(Τ)/尿喷咬(υ),s係指胞 ’啶(C)或鳥嘌呤(G),Y係指胞嘧啶(C)或胸腺嘧啶(τ)/尿嘧咬 ⑼’ R係指腺嗓呤(A)或鳥嘯呤(G)以及N係指腺嗓呤⑷、胞 嘧啶(C)、鳥嘌呤(G)或胸腺嘧啶(T)/尿嘧啶(U)或其他。對於上 魄所有剪接體辨識元件中,deoxythymidine(T)核普酸係可用尿 嘧咬(U)來取代。 本發明之方法: 一種在哺乳細胞中用於誘發内含子mir-302相關的基因靜 默效應之轉殖基因方法,其包含下列步驟: a) 建構一重組核醣核酸化合物,其包含具有mir_3〇2相關 基因靜默效應物之至少一内含子,該基因靜默效應物 由外顯子環繞,其中内含子能經切除後而與外顯子分 離,以供進一步mir-302基因靜默效應; b) 將該重組核醣核酸化合物併入一表現載體中;以及 c) 轉殖該載體進入複數個哺乳細胞中,其中該細胞產生許 多上述核醣核酸化合物的前驅核醣核酸轉錄分子,其 中細胞的剪接體將内含子經剪接作用後從前驅核醣核 酸轉錄分子中分離出來,以至於提供mir_3〇2相關的 基因靜默效應,其係針對與mir_3〇2基因靜默效應物 序列同源或互補的序列基因。 62 201009073 本發明已由上述相關實施例加以描述,然而上述實施例僅 ^ 為實施本發明之範例。必需指出的是,已揭露之實施例並未限 . 制本發明之範圍。相反地,包含於申請專利範圍之精神及範圍 之修改及均等設置均包含於本發明之範圍内。 以下實驗設計為舉例說明,但並不限制本發明之範圍。對 所有熟習本領域之人士來說’可於不脫離本發明的精神和範圍 内’對此做合理的變化。 實施例一違構包含知奶沾之重組基因 用於產生三種不同办内含子之合成核酸序列,該序列包 含正股、反意或小夾五GFP介子(hairpin-EGFP insert),如下所 示:N1-正股(sense),5,-GTAAGAGGAT CCGATCGCAG GAGCGCACCA TCTTCTTCAA GA-3’(SEQ.ID.NO.14); N1-反 意,5’-CGCGTCTTGA AGAAGATGGT GCGCTCCTGC ❹ GATCGGATCC TCTTAC-3,(SEQ.ID.NO.15); N2-正股,Mir-302 is stained by human primary embryonic cell OidESCV human prostate cancer cell PC3 舆 human primordial melanoma cell Colo cell based on the above experiment, will be designed mir-302a-mir_302b-mir-302c-mir-302d The precursor of the microRNA promoter or redesigned mir-302 precursor microribonucleic acid meson (such as the small clip sequence, which contains 5'-UAAGUGCUUC CAUGUUUUAG UGU-3, (SEQ.ID.N0.9)) Among the vectors, genes related to silent development and differentiation in hpESC, PC3 and Colo cells. The mature sequences of mir-302a, mir-302b, mir-302c and mir-302d are 5,-UAAGUGCUUC CAUGUUUUGG UGA-3, (SEQ.ID.NO.10), 5'-UAAGUGCUUC CAUGUUUUAG UAG-3, (SEQ .ID.NO. 11), 5,-UAAGUGCUUC CAUGUUUCAG UGG-3, 47 201009073 (SEQ.ID.NO.12) and 5,-UAAGUGCUUC CAUGUUUGAG UGU-3' (SEQ.ID.NO.13). These mir-302 gene silencing effector homologs share a consensus five-terminal region in the anterior 17-nucleotide (100% homology), which is a 17-nucleotide with 5'-UAAGUGCUUC CAUGUUU- 3. The sequence of (SEQ. ID. N0.3) is the same. In these mir-302 homologous sequences, the thymus gland (T) can be used to replace uracil (U). In these experiments, the precursor microRNA of mir-302a-mir-302b-mir-302c-mir-302d was transfected into hpESC and PC3 cells, and the redesigned mir-302 homologous sequence (SEQ.ID.NO) .9) Transfected into Colo cells. After mir-302 transfection, the pattern of all cell lines (mojphoiogy (lower surface)) changed, changing from a spindle-shaped or amoeba-like shape to a chubby appearance, indicating that these cells may lose movement ( The ability to migrate and its cell proliferation rate is very low, at this time as the growth rate of stem cells (Fig. 5A to Fig. 5C). The cellular DNA content (Y-axis) of the flow cytometer (upper panel) corresponds to a decrease in the mitotic cell population shown by different cell cycles (X-axis), confirming the rate of cell proliferation of these mir-302 transfected cells. Slow, and the above cell population is determined by the DNA content. The first peak (left) and the second peak (right) are shown as the relative number of g〇/gi and mitotic ticks in the whole cell population. After rmr-302 transfection, the 'mitotic cell population decreased from 36.1% to H in hpES (:6) to 9%; from 38.4% to 12 6% in PC3 cells; from c〇i〇 cells 36.5% is reduced to 1L5%. However, when transfection was not done - Nahu, cell morphology 48 201009073 or cell proliferation did not change significantly. The above mir-gft) precursor microRNA is designed to inhibit the firefly's green fluorescent protein, which has no homology to the human or mouse gene sequence. Based on the above findings, gene transfer of mir_3〇2 homologues can transform human blast cells and cancerous cells into more similar embryonic stem cell types and proliferation rates, as found in previous iPS cells (Okita et al (2007) Nature 448: 313-317; Wemig et al, (2007) 448: 318-324).形成 Embryoid body formation, embryonic stem cell indicator protein expression, genomic DNA demethylation and mir-302 Korean colonization. In CoMColo+mirGCm and PC3 (PC3+mir-302) cells Fine 腧 箄 箄 评估 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了 为了The mir-302 transfected cells have a high density of cell culture confluence (>80%-90%) and tend to form tight cell clusters of the above embryoid bodies like native humans. Embryonic stem cells derived from embryonic stem cells (Fig. 6A). However, without proper hormone or growth factor guidance, these embryoid bodies will disperse and differentiate into neuron-like cells when cultured again (as shown in the lower right panel) in order to confirm the inheritance of embryonic stem cells and embryoid-like somatic cells. Characteristics to further evaluate the indicator protein performance of these embryonic stem cells. As shown in Figure 6B, mir_3〇2 transfected Colo cells (Colo+mir-302) significantly exhibited a series of indicator proteins of embryonic stem 49 201009073 cells, such as 〇ct3/4, SSEA-3, SSEA- 4 and Sox2, etc., however, there is no indicator protein of the above embryonic stem cells in the general C〇l cells or in the colo cells transfected with an empty vector, transfected with mir-g § micro There were no detectable signs in cells such as Colo cells (Colo+mir-gQj) of ribonucleic acid vector or Colo cells (Colo+mir-434-5p) transfected with mir-434-5p microribonucleic acid vector. The sequence of mir-434-5p is not homologous to mir_3〇2. Because the Colo cell line has differentiated human melanoma cell lines, the results show that transfection of 11^-3〇2-run^^·- and GFP vectors can redirect c〇l〇 cells to embryonic stem cells again. The state is similar to real embryonic stem cells. 〇ct3/4 (or 〇ct-3 or Oct-4) is a kind of POU transcription factor, which is highly expressed in differentiated pluripotent embryonic stem cells and germ cells (Sch〇ler deduction α/., (1989) EMBO J. 8: 2543-2550; Rosner et al., (1990) Nature 345: 686-692). The performance of 〇ct3/4 plays an important role in maintaining stem cell self-renewal and differentiation pluripotency. Inhibition regulation of 〇ct3/4 results in the differentiation of embryonic stem cells into different developmental processes. The SSEA protein contains SSEA-1, 3 and 4 initially identified by monoclonal antibodies. This monoclonal antibody recognizes the lactose glycolipid on the surface of the initial implantation stage of murine embryonic cells and on the surface of abnormal cancer cells, but it cannot The differentiated cells after the above cell differentiation are recognized by the antibody (S〇lter β α/., (1978) Proc. Wi/. 知 t· at 75: 5565-5569). Undifferentiated early embryonic stem cells, human embryonic carcinoma cells (hEC) and embryonic stem cells all exhibit SSEA-3 and SSEA-4 but no SSEA-1 (Thomson β 乂, (1998) 282: 50 201009073 1145-1147) . During the production of imprints, SSEA_3 and ssea 4 are produced on the cell membrane surface of _, sac, and early dividing embryonic cells (Shevinsky (1982) & (4): age dog. S()x2 is loose on maintaining differentiation pluripotency The core transcriptional molecule, but this function is not specific to embryonic stem cells (Boyer-, (2005) CW/122: 947-956). Therefore, based on the knowledge of embryonic stem cell indicator proteins, chrom-302 transfected Cok) Cells have the property of expressing all of the above-described embryonic stem cell indicator proteins and embryonic stem cells. ® In addition, differentiated pluripotent stem cells have another unique property of post-modification changes, such as genomic de-mercapitation (Hochedlinger ei or/., (2006) Atowre 441: 1061 -1067). In order to transdifferentiate differentiated somatic cells into the embryonic stem cell stage, many embryonic genes need to be re-intensified to inhibit developmental and differentiation-related signals or genes. DNA methylation regulates the expression of these genes or Does not play an important role because the thiolation of the upstream promoter region often interferes with the combination of numerous transcriptional molecules for gene expression, the demethylation process Must be activated to regenerate newly activated embryonic genes such as Oct3/4, SSEA-3, SSEA-4 and Sox2. To assess the degree of thiolation of Colo+mir-302 cells and Colo cells, first use (DNA isolation kit, Roche, IN) isolating the genome of the above cells, and using the restriction enzyme Hpall, which is a CCGG cleavage, to isolate the genomic body. HpaII is sensitive to CpG thiolation and only cuts the ccGG without methylation, but cannot The thiolated CCGG was cut. As shown in Fig. 6C, the fragment of the gene fragment after excision, the fragment of the embryonic stem cell Colo+mir-302 cell was smaller than that of the general Colo cell, suggesting that the transfected mir_3〇2 The Colo cells do have a de-demethylation of 51 201009073. In addition, the original size of the genomes of Colo cells and Colo+mir-302 cells is almost the same, so the above conclusion can be confirmed. Figure 6D further shows 〇ct3 The morphological changes in the methylation domain of the /4 gene promoter region are particularly evident in the changes between hpESC, PC3 and Colo cells and the above cells transfected with mir-302. To confirm the thiolation of these regions, this experiment utilized Heavy sulfite (bisulfite) to isolate the genomic DNA (CpGenome DNA modification kit, Chemicon, CA), bisulfite can convert unpurified cytosine to uracil, then use two forward primers 5'- GTTGTTTTGT TTTGGTTTTG GATAT-3' (SEQ.ID.N0.36) and 5'-ATTGTTTTGT TTTGGTTTTG GATTTA-3, (SEQ.ID.N0.37) and a reverse primer 5'-GTAGAAGTGC CTCTGCCTTC C- 3' (SEQ. ID. N0.38) and polymerase chain reaction (PCR) (long template PCR extension kit, Roche, IN) were used to isolate the five-terminal upstream promoter region of Oct3/4. The cell genome (100 ng) was first mixed with the primer (150 pmole) and lxPCR buffer, and heated to 94 ° C for four minutes and then placed on ice for cooling. Then, after 25 PCR cycles, the conditions were as follows: 92 ° C, 1 minute; 55 ° C, 1 minute; and 70. (:, 5 minutes. Then, the PCR reaction product (Qiagen, CA) was used to collect the PCR reaction product, the PCR product and the multiple restriction enzymes of the cut ACGT sequence. These restriction enzymes include dc//(AACGTT), knife w/ (CACGTC), Pw//(CACGTG), 5>w5/(TACGTA) and parent tyC^W/RACGT), each 5 units (5U each) are uniformly mixed. Since the ACGT which is not thiolated in this region can be converted to AUGT via the bisulfite reaction, the AUGT cannot be cleaved by the above restriction enzyme. As shown in Figure 6D, at least four thiolated ACGTs were transformed into demethylated ACGTs in hpESC, PC3 and Colo cells transfected with mir-302. The demethylation of the 〇// gene promoter region by mir-302 transfection may be reproduced by mir-302 transfected cells such as c〇l〇+mir-302, and the reactivation of Oct3/4 gene expression. Caused. In addition, inhibition of cell migration is usually observed in cancerated sputum cells transfected with mir-302. In general, embryonic stem cells tend to stay in one place and form an in situ embryoid body (embryoidbody/wszYw), which may explain why PC3 and Colo cells lose mobility after mir-302 transfection. As shown in Fig. 6E, when PC3 cells were placed next to PC3+mir-302 cells, we were able to clearly observe that the cancerated PC3 cells rapidly moved along one side of PC3+mir-302 cells for about 30 seconds. Black arrows indicate the direction in which PC3 cells move. The results of this experiment suggest a potential therapeutic application of mir-302 transfection in cancer cells, which can not only convert cancer cells into useful stem cells, but also reduce the possibility of cancer cell metastasis, and more advantageous because of mir- The 302 transfected cancer cells are still compatible with the patient's immune system. The differentiated pluripotent cells of the embryonic stem cells described above can be used for transplantation therapy without any immune rejection reaction. Identification of the porcine gene mir-302 by miRNA gene crystallization 为了 In order to confirm the amount of mir-302 gene transfected in transfected cells, we used miRNA microarray analysis. Small RNAs isolated from each cell by mz>VanaTM miRNA isolation kit 53 201009073 (Ambion, Inc., Austin, TX) at approximately 70% confluence. The isolated picorucleic acid was purified and quantified using 1% furfural-cabbage electrophoresis and spectrophotometer measurement (Bio-Rad, Hercules, CA) and sent to LC Sciences (San Diego, CA). For further miRNA biochip analysis. In the intensity pictures of Cy3 and Cy5, the intensity of the signal increases from level 1 to level 65535' and the corresponding color change changes from blue to green to yellow to red. In the picture ratio of Cy5/Cy3, when the intensity of Cy3 is higher than that of Cy5, the color is green, when the intensity of Cy3 and Cy5 is the same, the color is yellow, and when the intensity of Cy5 is higher than that of Cy3, the color is red. As shown in Fig. 7A, Cy3 is a cell without any treatment (e.g., Colo), and Cy5 is a cell transfected with mir-302 (e.g., Colo+mir-302). In the picture ratio of Cy5/Cy3 (far right), all of the .mir-302 families (white circles) were highly expressed after transfection with GFP-mirJO. Because the mir-302 family gene and the redesigned mir-302 reagent have about 91% homology, this shows that the redesigned mir-302 reagent acts as a mir-302 member and replaces the original function of mir-302. Figure 7B shows a list of different amounts of miRNA in Colo+mir-302 cells. Based on the results shown in Figure 7A, we can also find that the increase in the amount of mir-302 can increase the performance of the precursor mir-302 as well as other microRNAs, such as mir-92, mir-93, mir-200c, mir-367. , mir-371, mir-372, mir-373, mir-374 and all members of the mir-520 family. The miRBase::Sequence programfhtto://microma.sanger.ac.uk/) and the target gene analysis of these mirs confirmed that the mir-302 family can target more than 400 target genes, suggesting that this 201009073 microRNA may be responsible for maintaining stem cells. Differentiation pluripotency and regenerative play an important role. Their target genes include, but are not limited to, RAB/RAS-associated oncogene members, ECT-related oncogenes, pleiomorphic adenoma genes, E2F transcriptional molecules, Cydin D-binding Myb transcriptional nucleons (cyclin D) Binding of myb-like transeripation factors, HMG-box transcriptional molecules, rushing 3 transcription factors, CP2-like proteins transcription factor, NFkB-activated protein-based genes, cyclin-dpendent kinases (CDK) ), ΜΑΡΚ related kinases, SNF-related kinases, muscle chain kinases, TNF-alpha-induce protein genes, DAZ-associated protein genes LIM-associated homeobox genes, DEAD/H box protein genes, forkhead box protein genes, BMP regulatory scorpions (BMP regulators), Rho/ Rac/Rac guanine nucleotide exchange factor, IGF receptor, endothelin (endothelin receptor), left-right determination factors, cyclins, p53-inducible nuclear protein gens, RB1-like 1 gene, RB-binding protein gene (RB binding protein genes), Max-binding protein genes, c-MIR cellular modulator of immune recognition, Bd2-like fine 55 201009073 Bcl2-like apoptosis facilitator, protocadherins, binding protein (integrin β4/β8), inhibitor _bin), ankyrins, SENP1, NUFIP2, FGF9/19, SMAD2, CXCR4, EIF2C , PCAF, MECP2, histone acetyltransferase MYST3, nuclear RNPH3, and many nuclear receptors and factors. All of these genes are involved in embryonic development and cancer formation. Μ甩 Gene chip analysis identifies embryonic stem cell markers and gauges. ❹ The correlation between the expression of the embryonic stem cell marker protein and the transgenic mir_3〇2 gene has been confirmed. We used gene chip analysis to search for intracellular mir-302 transfection. Before and after, gene expression changes within the genome range between mir_3〇2 transfected cells and other human embryonic stem cells. Afiymetrix gene chips (GeneChip U133A & B arrays, Santa Clara, CA) were used to assess more than 32,668 human gene expression patterns between Colo+mir-302 and other human embryonic stem cells, such as HuEC8 and H9. All ribonucleic acids isolated from each test cell line were collected by RNeasy spin column (Qiagen, Valencia, CA). In order to recognize the different backgrounds of the background, we repeated the biochip test and used the same Colo+mir302 sample and selected two hundred genes, which appeared on one side. As shown in Fig. 8A, the expression changes of these selection genes (white spots) were all less than twice that of Colo+mir-302, and the noise lines showing these background values were quite small. Based on these pre-selected genes and using a one-fold change as a threshold, we can calculate the relative coefficient of the comparison genes in the two groups 56 201009073 (correlation coefficiency (CC)). The 32668 human gene expression pattern has a similar ratio of relative coefficient ratios between the compared samples. At such a relative coefficient ratio, the results shown in Fig. 8A confirmed that the gene expression pattern of Colo+mir-302 cells was 88% and 86% similar to that of hES HuEC8 and H9 cells, whereas only 53% of the relatives were The coefficient is shown between Colo and Col〇+mir-302 cells. This confirms that the relevant mir-302 transfection changes the expression of at least 15354 cellular genes, which may be associated with the transformation of cancerous ❹ Colo cells into embryonic stem cell c〇l〇+mir-302 cells. A list of many of the major differences in performance between Colo and Colo+mir-302 cells is shown in Figure 8B. For example, in H9 and HuEC8 cells, Colo+mir-302 cells express embryonic stem cells and germ cell cell-associated proteins (eg, SSEA-4, Utfl, Oct4, Sox2, Pulimio-2 anti-Nanog'). However, 'Klf4 does not appear in Colo+mir-302 cells, showing a slight difference from our cells (as shown in Figure 6B). In addition, many cancer markers, developmental signals, and cue proliferating facots were found to be significantly inhibited in πώ-302 transfected cells as 'undifferentiated round cells' The pattern and the phenomenon of slower cell replication as shown in Figure 5 were observed. In summary, these findings indicate that the mir-302 transfection method can genetically transform a differentiated c〇1〇 cell line into a Colo+mir-302 cell line with embryonic stem cells, and differentiated pluripotent H9 and HuEC8 stem cells are similar. Using various hormones and growth factors to induce 丨 cell differentiation 57 201009073 By definition, 'differentiated pluripotent stem cells can differentiate into many cell types, which are similar to those derived from embryonic ectoderm, mesoderm and endoderm. . For example, in the absence of mammalian cells (feeder_ftee) using in vitro (沩V), Helmon and growth factors, the present invention can already be achieved - c〇lo+mir-302 Differentiation of cells into three different cell morphology is shown in Figures 9A through 9C. First, in the absence of mammalian cells, the above-mentioned cells were transplanted with androgen and dihydrated sputum _ (dihydrotestosterone (DHT 50 ng/ml>>> after six hours of treatment with Colo+mir-302 cells). 105 cells were inserted into the uterus of a six-week-old female immunodeficient beige mouse. One week later, a type of spermatogonia was produced at the transplant site (in the middle of Figure 9A). The recipient's use of the transforming growth factor (factory31 (TGF-/31 l〇〇ng/mi)) treatment: 2 hours, the transplanted cells entered the six-week-old female immune loss (immunocompromisedpciD beige mice, the cells differentiated into The type of fibroblasts began to secrete collagen, and within a week, these cells occupied most of the uterus in the uterus (Fig. 9B). After using 'bone morphogenetic protein 4 (BMP4 100 ng) /ml)) After treatment of Colo+mir-302 cells for 12 hours, the treated cells were transplanted into the liver of a six-week-old immunodeficient SCID beige mouse by xenograft. Chondrocytes, some around Calcified precipitation (Fig. 9C). By using thymic nude mice as an environment for mimicking colonization therapy in vivo, these experiments confirmed that the mir-302 transfection method of the present invention can produce novel embryos. Stem cells 58 201009073 strain 'These cell lines can be guided and produced in the in vitro environment without mammalian cells. 'No woven cell ray. Shame, this (four) can not only transform or transform to differentiate. Body _ shouting - fetal stem cells Differentiated traits, and can also maintain the differentiation pluripotency and self-replication ability of stem cells in a culture environment without mammalian cells. Therefore, the present invention provides a novel novel by using the mir-302 expression vector of introns. A method for producing stem cells, specifically, a method for producing a cell line derived from an embryo and a cell line of a cancer cell. These mechanisms are coordinated by the silent pathway of the microRNA-related gene of the intron and many intracellular regulatory mechanisms. Contains gene transcription factors, RNA splicing, exosome elimination, and nonsense-mediated degradation. The gene silencing effect of microRNAs in introns is considered to be the most Effective, most specific, and safest for all three known RNAi pathways. Based on all advantages, the use of the intron mir_3〇2 reagent of the present invention provides a simple, effective and safe method of gene use that is not only available Transforming somatic cells into differentiated pluripotent cells of embryonic stem cells can also maintain the differentiation pluripotency of embryonic stem cells in culture conditions without mammalian cells, thus avoiding four large transcription factors as in the previous iPS stem cell method. The gene is transfected into a single cell with an annoying retrovirus. As shown in Figure 10, based on mir-302-induced embryonic stem cells, this suggests that SSEA-1 is present in mir-302-induced cells (Colo+mir-302) cells. Degree of performance; however, there is no such performance in Klf4. Compounds of the invention: 59 201009073 - A recombinant ribozyme nucleic acid compound for inducing a ribonucleic acid-related gene silencing effect of an intron comprises: a) at least an intron, wherein the intron consists of a plurality of exons Surrounded by these exons, the fine-nose RNAsplieing exon is excised and manipulated by a processing mechanism; and b) a plurality of exons, wherein the exons can be joined to form a gene with specific functions. The above recombinant ribonucleic acid compound further comprising a) at least one restriction enzyme cleavage site, wherein the restriction enzyme cleavage site can be used to combine the recombinant ribonucleic acid compound in a expression vector for providing a precursor ribonucleic acid of the recombinant ribonucleic acid compound The transcriptional molecule is in the mammalian cell; and b) a plurality of transcriptional and translational termination sites, wherein the transcription and translation termination can be used to make the correct size of the ribonucleic acid transcription molecule of the recombinant ribonucleic acid compound. The intron of the above recombinant ribonucleic acid compound further comprises: a) a meson of a gene silencing effector complementary or homologous to at least one of the underlying genes; b) a five-terminal splicing; c) a three-terminal splicing; d ) - a branch point region for identification of the splice body; 201009073 e) - a polypyrimidine region for splice engagement; Q a plurality of connectors for connecting the main components. The gene silencing effector meson comprises a nucleotide sequence homologous to 5'-UAAGUGCUUC CAUGUUU-3' (SEQ.ID.N0.3)'. The five-terminal splicing is a nucleotide sequence and is homologous to 5'-GTAAGAGK-3' (SEQ.ID.N0.4) or GU(A/G)AG U sequence (for example, 5,-GTAAGAGGAT-3, ❹ (SEQ.ID.NO. 30), 5, -GTA AGAGT-3,, 5, -GTAGAGT-3, and 5'-01^01'-3'). At this time, the three-terminal frying joint (3'>^1^3 such as (^3' (; Qiu) sequence is homologous to GWKSCYRCAG (SEQ.ID.N0.5) or CT(A/G)A ( C/T) NG sequence (eg, 5'-GATATCC TGCAG-3, (SEQ.ID.N0.31), 5 '-GGCTGCAG-3 ', 5 '-CCACAG -3 '). In addition, the branch point region sequence The line is located between the five-terminal and the two-terminal splicing region, wherein the branching point region is located in a nucleotide sequence homologous to 5'-TACTWAY_3' (SEQ. ID. N0.6) (eg, 5, -TACTAAC-3, and Φ 5'-TACTTAT-3'). In addition, the 'polypyrimidine region is located between the branch point region and the three-terminal splicing region, wherein the polypyrimidine region is a high density of Thymine and Cytosine. Nucleotide sequence, the nucleotide sequence of the polypyrimidine region is homologous to 5-(TY)m(C/-)(T)nS(C/-)_3' (SEQ.ID.N0.7) and 5' -(TC)nNCTAG (G/-)-3' (SEQ.ID.N0.8), wherein "m" and ", n" refer to a multiple repeat sequence of one or more, preferably the number of sequences of m is Between one and three, and the sequence number of η is a butterfly twelve "" means that there is no nuclear Wei. Some connecting nucleotides can be used to link the Lezi fragment. Based on 37 CFR1 822 regulation 61 2010 09073 (Taiwan) nucleotide and amino acid sequence table format, same as), w refers to adenine (adenine (A)) or thymine (thymine (T)) / uracil twist acil ^ j )), κ refers to guanine (G) or thymus bite (Τ) / urinary sputum (υ), s refers to the cell 'pyridine (C) or guanine (G), Y refers to the cell Pyrimidine (C) or thymine (τ) / uridine (9) 'R refers to adenine (A) or bird sputum (G) and N refers to adenine (4), cytosine (C), guanine ( G) or thymine (T) / uracil (U) or other. For all splicing recognition elements of the upper sputum, the deoxythymidine (T) nucleoside acid system can be replaced by urinary pyridine bite (U). Method of the invention: A method for transgenic genes for inducing intron mir-302-related gene silencing effects in mammalian cells, comprising the steps of: a) constructing a recombinant ribonucleic acid compound comprising mir_3〇2 At least one intron of the related gene silencing effector, the gene silencing effector is surrounded by an exon, wherein the intron can be excised and separated from the exon for further mir-302 gene silencing effect; b) Incorporating the recombinant ribonucleic acid compound into a performance vector; and c) transducing the vector into a plurality of mammalian cells, wherein the cell produces a precursor ribonucleic acid transcription molecule of a plurality of the above ribonucleic acid compounds, wherein the splicing of the cells is within The splicing of the sera from the precursor ribonucleic acid transcriptional molecule provides a mir_3〇2-related gene silencing effect against a sequence gene homologous or complementary to the mir_3〇2 gene silencing effector sequence. 62 201009073 The present invention has been described by the above-described related embodiments, but the above embodiments are merely examples for implementing the present invention. It must be noted that the disclosed embodiments are not intended to limit the scope of the invention. On the contrary, modifications and equivalents of the spirit and scope of the invention are included in the scope of the invention. The following experimental design is illustrative, but does not limit the scope of the invention. Reasonable changes can be made to those skilled in the art without departing from the spirit and scope of the invention. Example 1 is a construction of a synthetic nucleic acid sequence comprising a recombinant milk gene for the production of three different introns, the sequence comprising a positive-stranded, anti-sense or small-pin GFP meson (hairpin-EGFP insert), as shown below :N1-sense,5,-GTAAGAGGAT CCGATCGCAG GAGCGCACCA TCTTCTTCAA GA-3' (SEQ.ID.NO.14); N1-reverse, 5'-CGCGTCTTGA AGAAGATGGT GCGCTCCTGC ❹ GATCGGATCC TCTTAC-3, (SEQ. ID.NO.15); N2-positive stock,
5,-GTAAGAGGAT CCGATCGCTT GAAGAAGATG GTGCGCTCCT GA-3, (SEQ.ID.NO. 16); N2_ 反意,5,-GTAAGAGGAT CCGATCGCTT GAAGAAGATG GTGCGCTCCT GA-3, (SEQ.ID.NO. 16); N2_
5,-CGCGTCAGGA GCGCACCATC TTCTTCAAGC5,-CGCGTCAGGA GCGCACCATC TTCTTCAAGC
GATCGGATCC TCTTAC-3,(SEQ.ID.NO.17); N3-正股, 5,_GTAAGAGGAT CCGATCGCAG GAGCGCACCA TCTTCTTCAA GTTAACTTGA AGAAGATGGT GCGCTCCTGA-3’ (SEQ.ID.NO.18); N3-反意(antisense), 63 201009073GATCGGATCC TCTTAC-3, (SEQ.ID.NO.17); N3-正股, 5,_GTAAGAGGAT CCGATCGCAG GAGCGCACCA TCTTCTTCAA GTTAACTTGA AGAAGATGGT GCGCTCCTGA-3' (SEQ.ID.NO.18); N3-antisense (antisense), 63 201009073
5,-CGCGTCAGGA GCGCACCATC TTCTTCAAGT5,-CGCGTCAGGA GCGCACCATC TTCTTCAAGT
TAACTTGAAG AAGATGGTGC GCTCCTGCGATAACTTGAAG AAGATGGTGC GCTCCTGCGA
TCGGATCCTC TTAC-3,(SEQ.ID.NO. 19); N4-正股(sense), 5,-CGCGTTACTA ACTGGTACCT CTTCTTTTTTTCGGATCCTC TTAC-3, (SEQ.ID.NO. 19); N4-sense, 5,-CGCGTTACTA ACTGGTACCT CTTCTTTTTT
TTTTTGATAT CCTGCAG-3’ (SEQ.ID.NO.20); N4-反意, 5,-GTCCTGCAGG ATATCAAAAA AAAAAGAAGA GGTACCAGTT AGTAA-3’(SEQ.ID.NO.21)。從 SEQ.ID.NO.14 到SEQ.ID.NO.21的所有序列在該等序列的五端皆有填酸化。 此外,兩外顯子片段係經由Dra//限制酶切紅色螢光及GPP基 因(SEQ.ID.NO.22)之第208個核苷酸處所產生,且該片段之五 端進一步經T4 DNA聚合酶作用而生成平整端(blunt end)。此 處所指的及GFP為在第69個胺基酸處嵌入一額外的天門冬胺 酸(aspartate)之新穎的紅光色偏(red_shiited)的螢光蛋白基因, 該螢光蛋白(HcRedl)係由海蔡//e妙 Biosciences,CA)所衍生而來。修飾後的紅色螢光蛋白具有較少 的變性以及幾乎兩倍遠紅外線螢光強度之紅色螢光57〇nm波 長射線。本發明利用載體(BE) Bi〇sciences,CA) 與瓜及限制酶切開並用2%洋菜膠(agar〇se gd)電泳 純化全長769鹼基對_之及GFP基因片段與3934bp之無 尸之空載體並純化之(gel extracti〇nkit,伽卿,CA)。 將Nl-正股與脉反意、Ν2·正股與N2_反意、N3_正股與 64 201009073 N3_反意及N4-正股與N4-反意序列(1:1)的雜合,個別加熱每 個互補序列到94°C(2分鐘),於lxPCR緩衝液(如50mM Tris-HCl,pH 9.2 at 25〇C,16mM (NH4)2S04, 1.75mM MgCl2)加 熱70°C(l〇分鐘)。接著立刻個別逐漸冷卻(一小時期間從50°C 到 10°C)N1+N4、N2+N4、Ν3+Ν4(1··1)之雜合混合而實施 m、 N2、N3雜合到N4連續性連接(sequential ligation)。之後用T4 DNA接合酶(ligase)及相對應之缓衝液中在12°C再作用12小 ❹ 時使其接合,而獲得心·内含子以供插入πσπ外顯子之TTTTTGATAT CCTGCAG-3' (SEQ.ID.NO.20); N4-reverse, 5,-GTCCTGCAGG ATATCAAAAA AAAAAGAAGA GGTACCAGTT AGTAA-3' (SEQ.ID.NO.21). All sequences from SEQ. ID. NO. 14 to SEQ. ID. NO. 21 were acidified at the five ends of the sequences. In addition, the two exon fragments were generated by Dra// restriction enzyme cleavage of red fluorescence and the 208th nucleotide of the GPP gene (SEQ.ID.NO.22), and the five ends of the fragment were further passed through T4 DNA. The polymerase acts to generate a blunt end. As used herein, and GFP is a novel red-shiited fluorescent protein gene (HcRedl) that is embedded with an additional aspartate at the 69th amino acid. Derived from Hai Cai//e wonderful Biosciences, CA). The modified red fluorescent protein has less denaturation and nearly twice the far-infrared fluorescence intensity of the red fluorescent 57 〇 nm wavelength ray. The present invention utilizes a carrier (BE) Bi〇sciences, CA) to cut with a melon and a restriction enzyme and purify a full-length 769 base pair with a 2% agarose (g) electrophoresis and a GFP gene fragment and a 3934 bp corpse. The vector is empty and purified (gel extracti〇nkit, gamma, CA). Mixing Nl-positive strands with veins, Ν2·positive strands and N2_reverse, N3_positive strands with 64 201009073 N3_ anti-sense and N4-positive strands with N4-reverse sequence (1:1) Individually heat each complementary sequence to 94 ° C (2 minutes), heat 70 ° C in lxPCR buffer (such as 50 mM Tris-HCl, pH 9.2 at 25 ° C, 16 mM (NH4) 2S04, 1.75 mM MgCl2) 〇 minutes). Immediately afterwards, individual cooling (one-hour period from 50 ° C to 10 ° C), hybridization of N1+N4, N2+N4, Ν3+Ν4 (1··1), and m, N2, N3 hybridization to N4 Sequential ligation. Then, the T4 DNA ligase and the corresponding buffer were incubated at 12 ° C for 12 hours to obtain a cardiac intron for insertion of the πσπ exon.
Dra//切位處。在及GF_P外顯子片段被加入反應(1:1:1)後,Τ4 DNA接合酶及相對應之緩衝液經相對應調整再一次進行連接 反應12小時(12°〇。為了建構正確大小尺寸的重組办餅」/接 入及GFP 基因(recombinant 5)?及A^-inserted 及GFP gene),10 ng 之接合核苷酸(ligated nucleotide)序列經PCR技術及一對 及特定引子(primers) 5,-CTCGAGCATG GTGAGCGGCC ❿ TGCTGAA-3, (SEQ.ID.NO.23)與 5,-TCTAGAAGTT GGCCTTCTCG GGCAGGT-3’(SEQ.ID.NO.24)在 PCR 條件於 94°C(1分鐘)、52°C(1分鐘)、68°C(2分鐘)而進行30次重覆反 應。而後’利用2%洋菜膠(agarose gel)分離出PCR之產物, 約 900bp 大小之核督酸序列經 Gel Extraction kit(Qiagen, CA) 所純化出來。此900bp大小之》?m^inserted gene,可 供進一步用序列比對(sequencing)確認之。較佳而言,在缺乏 内含子介子的情況下’ 内含子的正股序列為 65 201009073Dra / / cut position. After the GF_P exon fragment was added to the reaction (1:1:1), the Τ4 DNA ligase and the corresponding buffer were further adjusted for the corresponding reaction for 12 hours (12°〇). In order to construct the correct size Recombination cake/access and GFP gene (recombinant 5)? and A^-inserted and GFP gene), 10 ng of ligated nucleotide sequence by PCR technology and a pair of specific primers 5,-CTCGAGCATG GTGAGCGGCC ❿ TGCTGAA-3, (SEQ.ID.NO.23) and 5,-TCTAGAAGTT GGCCTTCTCG GGCAGGT-3' (SEQ.ID.NO.24) under PCR conditions at 94 ° C (1 min), The reaction was repeated 30 times at 52 ° C (1 minute) and 68 ° C (2 minutes). Then, the PCR product was isolated using 2% agarose gel, and the nucleotide sequence of about 900 bp was purified by Gel Extraction kit (Qiagen, CA). This 900 bp size "m^inserted gene" can be further confirmed by sequence sequencing. Preferably, in the absence of an intron meson, the positive strand sequence of the intron is 65 201009073
5'-GTAAGTGGTC CGATCGTCGC GACGCGTCAT5'-GTAAGTGGTC CGATCGTCGC GACGCGTCAT
TACTAACTAT CAATATCTTA ATCCTGTCCC TTTTTTTTCC ACAGTAGGAC CTTCGTGCA-3' (SEQ.ID.NO.25),而办厕/ 内含子的反意序列為5'-TGCACGAAGG TCCTACTGTG GAAAAAAAAG GGACAGGATT AAGATATTGA TAGTTAGTAA TGACGCGTCG CGACGATCGG ACCACTTACJ (SEQ.ID.NO.26)。 在另一實施例中,重組办轉殖基因能經併 夺皿」/(由SEQ.ID.NO.25及SEQ.ID.NO.26雜合)入及外 顯子的Dra//之限制酶切位。而之後的實驗流程如前所述。用 於測試重新設計的mir-302先驅miRNA介子之及 轉殖基因建構載體係由這種方式形成。 因為重組SpRNAi-RGFP基因分別在五端及三端具有沿以 與;限制酶切位,其能輕易地經由^^^與恐以限制酶切 位併入載體中。此載體必須為有機組織或次有機組 織(suborganism),該些組織選自DNA轉殖基因、質體 (plasmids)、跳躍基因伽卿㈣genes)、轉位子(tramp〇s〇ns)及 病毒載體(retroviral vectors)。此外’因為位於内含子之該介子 分別在五端及三端經户如/及限制酶切位併入内含子,因 此本發明也能利用同樣的限制酶切位將其他不同介子接入载 體以替換之。U(inserteci sequenee insert)較佳為類小失 201009073 之基因靜默效應物(hairpin-like gene silencing effector),該基因 靜默效應物具有能標定(target)特定基因的高度互補性序列,這 些特定基因選自綠色螢光蛋白基因、螢光素基因 (luciferasegenes)、乳糖控制組(lac_z)基因、病毒基因、細菌基 因、植物基因、動物及人類基因等序列以進行靜默。這些靜默 效應物介子(insert)與其標的基因序列之互補或同源率約3〇% 到100%之間,對hairpin-shRNA介子(insert)較佳為35%到49 參 %,對正股-RNA與反意-RNA介子而言,較佳之序列互補率 範圍為90%到100%。 复施例二__建構包含岛见\%·之重組|因(SvRNAi-RGFP) 進入表現裁體(Expression-competent Vftntnr) 因為重組》尸基因分別於五端及三端具有^ 與恐以的限制酶切位,其能利用該等切位將重組基因接入載 ❹ 體。本發明將重組基因與3934bp之 載體以l:16(w/w)混合,並從65。(:降溫到15°C超 過50分鐘,之後加入T4接合酶及其緩衝液混合12它(12小 時)以進行接合。所形成的办表現載體能利用 五.co" DH5aLB(50ug/ml 康黴素(kanamycinXSigma Chemical, St· Louis, Mo))進行大量複製。並利用PCR技術及其及GFP特 定引子(SEQ.ID.NO.23)及(SEQ.ID.NO.24)於 94°C(1 分鐘)、68 °C (2分鐘)並進行30次循環反應而序列比對以確認為具有特定 67 201009073 重組基因的菌株(positive clone)。為了將重組基因併入病毒載 體,相同的接合程序也能實施於瓜〇/ZY2>a/-linearized/7ZjVCZ2 反轉錄病毒載體(BD)以外的載體。因為介子分別於五端及三端 經Pvw/及Mm/限制酶切位連接於内,因此本發明能 利用該等切位去除或以重新設計的mir-302介子取代 antkEGFP shRNA介子。該重新設計的mir-302介子序列包含 同源的 5’-UAAGUGCUUC CAUGUUU-3’(SEQ.ID.N0.3)區 域,如相似於 5’-UAAGUGCUUC CAUGUUUUAG UGU_3, (SEQ.ID.N0.9)、5’_UAAGUGCUUC CAUGUUUUGGUGA-3, (SEQ.ID.NO.10)'5?-UAAGUGCUUC CAUGUUUUAG UAG-35 (SEQ.ID.NO.ll)、5’-UAAGUGCUUC CAUGUUUCAG UGG-3, (SEQ.ID.NO.12)或· 5,-UAAGUGCUUC CAUGUUUGAG UGU-3,(SEQ.ID.NO.13) 〇 ❹ 合成核酸序列可用來產生許多不同内含子包含 mir-302家族先驅微核醣核酸叢聚(mir_3〇2 familial pre-miRNA cluster)或重新設計的mir_302介子,示例如下:mir-302a-正股,TACTAACTAT CAATATCTTA ATCCTGTCCC TTTTTTTTCC ACAGTAGGAC CTTCGTGCA-3' (SEQ.ID.NO.25), and the reverse sequence of the toilet/intron is 5'-TGCACGAAGG TCCTACTGTG GAAAAAAAAG GGACAGGATT AAGATATTGA TAGTTAGTAA TGACGCGTCG CGACGATCGG ACCACTTACJ (SEQ.ID.NO. 26). In another embodiment, the recombinant transgenic gene can be fused to and/or restricted by Dra// of the exon and (except for SEQ.ID.NO.25 and SEQ.ID.NO.26) Enzyme cleavage position. The subsequent experimental process is as described above. The mir-302 pioneer miRNA meson used to test the redesign and the transfer gene construct vector were formed in this manner. Since the recombinant SpRNAi-RGFP gene has a cleavage at the five-terminal and three-terminal ends, respectively, and restriction enzyme cleavage, it can be easily incorporated into the vector via restriction enzyme restriction. The vector must be an organic tissue or a suborganism selected from the group consisting of DNA transgenes, plasmids, jumping genes, genes, transposons (tramp〇s〇ns), and viral vectors ( Retroviral vectors). In addition, since the meson located in the intron is incorporated into the intron at the five-terminal and three-terminal translocations, respectively, and the restriction enzyme sites, the present invention can also use the same restriction enzyme cleavage site to access other different mesons. The carrier is replaced. U(inserteci sequenee insert) is preferably a hairpin-like gene silencing effector, which has a highly complementary sequence capable of targeting a specific gene, and these specific genes are selected. Sequences are silenced from the sequence of green fluorescent protein gene, luciferasegenes, lactose control group (lac_z) gene, viral gene, bacterial gene, plant gene, animal and human gene. These silent effector mesons have a complementarity or homology rate of about 3〇% to 100% with their target gene sequence, and preferably 35% to 49% for hairpin-shRNA mesons. For RNA and anti-intention-RNA mesons, the preferred sequence complementarity ranges from 90% to 100%. Recombination Example 2 __Construction includes the reorganization of the island see \%·(SvRNAi-RGFP) into the expression-competent Vftntnr because the recombination corpse gene has ^ and the fear at the five-terminal and three-terminal A restriction enzyme cleavage site that allows the recombinant gene to be introduced into the steroid using these cleavage sites. The present invention mixes the recombinant gene with a 3934 bp vector at a ratio of 1:16 (w/w) and from 65. (: Cool down to 15 ° C for more than 50 minutes, then add T4 ligase and its buffer to mix it (12 hours) for bonding. The resulting performance vector can utilize five.co" DH5aLB (50ug/ml Mass (kanamycin XSigma Chemical, St. Louis, Mo)) was subjected to large-scale replication using PCR technology and its GFP-specific primers (SEQ.ID.NO.23) and (SEQ.ID.NO.24) at 94 °C ( 1 minute), 68 °C (2 minutes) and 30 cycles of reaction were sequenced to confirm that it was a positive clone with a specific 67 201009073 recombinant gene. In order to incorporate the recombinant gene into the viral vector, the same ligation procedure It can also be carried out on a vector other than the guar/ZY2>a/-linearized/7ZjVCZ2 retroviral vector (BD). Since the mesons are respectively ligated at the five-terminal and three-terminal positions by the Pvw/ and Mm/restriction sites, The present invention can utilize these cleavage removals or replace the anktEGFP shRNA meson with a redesigned mir-302 meson. The redesigned mir-302 meson sequence contains the homologous 5'-UAAGUGCUUC CAUGUUU-3' (SEQ.ID.N0). .3) Area, such as similar to 5'-UAAGUGCUUC CAUGUUUUAG UGU_3, (SEQ.ID.N0.9 ), 5'_UAAGUGCUUC CAUGUUUUGGUGA-3, (SEQ.ID.NO.10) '5?-UAAGUGCUUC CAUGUUUUAG UAG-35 (SEQ.ID.NO.ll), 5'-UAAGUGCUUC CAUGUUUCAG UGG-3, (SEQ.ID .NO.12) or · 5,-UAAGUGCUUC CAUGUUUGAG UGU-3, (SEQ.ID.NO.13) 〇❹ Synthetic nucleic acid sequences can be used to generate a number of different introns containing mir-302 family precursor microribonucleic acid clusters ( Mir_3〇2 familial pre-miRNA cluster) or redesigned mir_302 meson, examples are as follows: mir-302a-positive strand,
5,-GTCCGATCGT5,-GTCCGATCGT
GTACTTGCTTGTACTTGCTT
CTTCCATGTT C-3’(SEQ.ID.N0.39);CTTCCATGTT C-3' (SEQ.ID.N0.39);
TCCATCACCATCCATCACCA
CTTTAGTTTCCTTTAGTTTC
CCCACCACTT TGAAACTAAA TTGGTGATGG mir-302a-反意, AAACATGGAA AAAGCAAGTACCCACCACTT TGAAACTAAA TTGGTGATGG mir-302a-Reverse, AAACATGGAA AAAGCAAGTA
AAACGTGGATAAACGTGGAT
GAAGTAAGTGGAAGTAAGTG
ATCTCGAGCTATCTCGAGCT
5,-GAGCTCGAGA5,-GAGCTCGAGA
GCACTTACTTGCACTTACTT
CATCCACGTT 68 201009073CATCCACGTT 68 201009073
TAAGTGGTGG mir-302b-正股 AACTTTAACA TTGAAAGTAATAAGTGGTGG mir-302b-正股 AACTTTAACA TTGAAAGTAA
GACGATCGGA C-3 ’(SEQ.ID.NO.40); ,5’_ATCTCGAGCT CGCTCCCTTC TGGAAGTGCT TTCTGTGACTGACGATCGGA C-3 ' (SEQ.ID.NO.40); , 5'_ATCTCGAGCT CGCTCCCTTC TGGAAGTGCT TTCTGTGACT
GTGCTTCCAT GTTTTAGTAG GAGTCGCTAG CGCTA-3’(SEQ.ID.N0.41); mir-302b-反意,GTGCTTCCAT GTTTTAGTAG GAGTCGCTAG CGCTA-3' (SEQ.ID.N0.41); mir-302b-reverse,
GAGAT-3’(SEQ.ID.N0.42); mir-302c-正股,GAGAT-3' (SEQ.ID.N0.42); mir-302c-positive strand,
5,-TAGCGCTAGC5,-TAGCGCTAGC
AGCACTTACTAGCACTTACT
TTCCATGTTATTCCATGTTA
ACCTTTGCTTACCTTTGCTT
TGTGAAACAGTGTGAAACAG
GACTCCTACTGACTCCTACT
TTCAAAGTCATTCAAAGTCA
AAGTTGAAGGAAGTTGAAGG
TAACATGGAGTAACATGGAG
AAGTAAGTCGAAGTAAGTCG
AAAACATGGAAAAACATGGA
CAGAAAGCACCAGAAAGCAC
GAGCGAGCTCGAGCGAGCTC
5,-CGCTAGCGCT5,-CGCTAGCGCT
GTACCTGCTGGTACCTGCTG
TTCATGTTTCTTCATGTTTC
AGTGGAGGCG TCTAGACAT-3, (SEQ.ID.NO.43); mir_302c_ 反意,5’-ATGTCTAGAC GCCTCCACTG AAACATGAAC ❹ TCGACGCGTC AT_3’ (SEQ.ID.NO.45);AGTGGAGGCG TCTAGACAT-3, (SEQ.ID.NO.43); mir_302c_, 5'-ATGTCTAGAC GCCTCCACTG AAACATGAAC TC TCGACGCGTC AT_3' (SEQ.ID.NO.45);
GACTTACTTCGACTTACTTC
TCCATGTTAA (SEQ.ID.NO.44);TCCATGTTAA (SEQ.ID.NO.44);
TAACACTCAATAACACTCAA
GCCAGGCTAA 5,-ATGACGCGTCGCCAGGCTAA 5,-ATGACGCGTC
ACTTAGCCTGACTTAGCCTG
TGTTTCACAC AGCAAAGGTA mir-302d-正股, ACATGGAAGC GTGCTTCCATTGTTTCACAC AGCAAAGGTA mir-302d-正股, ACATGGAAGC GTGCTTCCAT
GAACACTCAAGAACACTCAA
GCTTAGCTAAGCTTAGCTAA
AGCAGGTACC GCGCTAGCG-3, 5,_CGTCTAGACA ACTTAGCTAA GTTTGAGTGT mir-302d-反意, ACATGGAAGC GTGCTTCCAT GTTTGAGTGT TATGTCTAGA CG-3, (SEQ.ID.NO.46); and 69 201009073AGCAGGTACC GCGCTAGCG-3, 5, _CGTCTAGACA ACTTAGCTAA GTTTGAGTGT mir-302d-reverse, ACATGGAAGC GTGCTTCCAT GTTTGAGTGT TATGTCTAGA CG-3, (SEQ.ID.NO.46); and 69 201009073
miR-302s-正股,5’-GTCCGATCGT CATAAGTGCT TCCATGTTTT AGTGTGCTAA GCCAGGCACAmiR-302s-正股,5'-GTCCGATCGT CATAAGTGCT TCCATGTTTT AGTGTGCTAA GCCAGGCACA
CTAAAACATG GAAGCACTTA TCGACGCGTC AT-3, (SEQ.ID.NO.27); mir-302s-反意,5,-ATGACGCGTCCTAAAACATG GAAGCACTTA TCGACGCGTC AT-3, (SEQ.ID.NO.27); mir-302s-reverse, 5,-ATGACGCGTC
GATAAGTGCT TCCATGTTTT AGTGTGCCTGGATAAGTGCT TCCATGTTTT AGTGTGCCTG
GCTTAGCACA CTAAAACATG GAAGCACTTA TGACGATCGGAC-3’(SEQ.ID.N0.28)。GCTTAGCACA CTAAAACATG GAAGCACTTA TGACGATCGGAC-3' (SEQ. ID. N0.28).
Mir-302家族先驅微核醣核酸叢聚可分別經mir_3〇2a_正股 與mir-302a-反意雜合、mir-302b-正股與mir-302b-反意雜合、 mir-302c-正股與mir-302c-反意雜合及mir-302d-正股與 mir-302d-反意雜合而形成。接著,mir_302a、mir_3〇2b、mir-302c 反 分别經 pvui/XhoI,Xhol/Nhel,Nhel/Xbal 反 等限制酶切開並經洋菜膠萃取過濾管柱(gd extraction filter column)(Qiagen,CA)於 35 微升之高壓滅菌二次 水(autoclaved ddHe)萃取之。立刻接著,所收集的雜合經T4 DNA接合轉(Roche,20U)互相接合而形成mir-302家族微核醣 核酸介子叢聚,此外這些雜合核醣核酸可進一步經由 PVW//MM/等限制酶切位併入表現載體。包含 mir_302家族微核醣核酸介子叢聚之办重組基因 被併入反轉錄病毒載體,此載體具有表面抗 原,此抗原可供轉殖性感染hpESC與PC3細胞。為了形成人 工重新設計的mir-302先驅微核醣核酸介子,本發明雜合 201009073 (SEQ.ID.NO.27)與(SEQJD.NO.28)兩條合成序列,而後以 Pvw//Mw/等限制酶切開並以T4 DNA接合酶(20U)將此雜合序 列接合於表現办載體。此重組基因包 含一重新設計的mir-302先驅微核醣核酸,其可供於Colo細 胞的轉殖性DNA重組。成功轉染的細胞可經分離及24小時 後收集以供繼代培養’並利用抗RGFP的單株抗體及細胞流式 儀(Clontech, Palo Alto, CA)來收集上述細胞。 參 mir-302先驅微核醣核酸叢聚及mir-302表現載體如上述方 式形成後可於五.co/z· DH5aLB(50微克/毫升康黴素)進行 厂質體載體的大量複製或(1〇〇微克/毫升安比西 林)進行〆M:Z2反轉錄載體的大量複製。大量複製的 表現載體經 mini-prep 或 maxi-prep plasmid extraction kit(Qiagen,CA)分離及純化,詳細流程詳見使用說 明。對於反轉錄載體而言,本發明可利用包裝細胞株 ❹ (packaging cell line)GP2-293(Qiagen,CA)以供製造具有感染但 卻無法複製的病毒。經感染之GP2-293細胞於lxDMEM(碳吸 附的10%胎牛血清(FBS)、4 mM L-麵醯胺酸、1 mM丙酮酸 鈉、100微克/毫升硫酸鍵絲菌素、50微克/毫升新黴素(sigma Chemical, MO))培養液中於37°C及5%的二氧化碳中培養。經 GP2-293細胞產生的病毒數量在轉染之前測定至少為1〇6cfil/ 毫升。 71 201009073 實施例三沅V办〇轉辖忖轉平 對以反轉錄病毒載體轉染入hpESC及PC3細胞株而言,、 斑馬魚幼苗及老鼠皮膚,首先將具有^或 mir_302家族叢聚先驅微核醣核酸介子之分似⑷及⑺ϊρ . /?ΖΛ02反轉錄表現載體於pVSV_G共同轉染的Gp2 293細胞 (Clontech,CA)。在培養於37°C、5%的二氧化碳36個小時後, GP2-293細胞的培養液(每1〇毫升)經由過濾(0.25微米的孔徑) 並直接個別地傳送於hpESC及PC3細胞培養液中。因為該培 ❹ 養液中含有很高的該反轉錄病毒載體劑量,因此全部的測試細 胞皆轉殖性地經載體所感染並於24小時内開始表現内含子的 介子及RGFP。為了轉殖性傳遞重新設計的人造mir_3〇2先驅 微核醣核酸進入Colo細胞中,本發明首先混合預先準備好的 知餅办及研尸轉殖基因(每細胞培養皿中60微克(pg)溶於1〇 毫升中),該轉殖基因包含實施例二的預先設計之mir-302先驅 微核糖核酸介子,與FuGene試劑(Roche, IN)混合而依使用手 ^ 冊操作。接著,混合物用於Colo細胞培養24小時。因為轉殖 基因也包含類轉位子序列,其同源於特定不具有密碼子的人類 基因體區域,而後經由細胞流式儀及抗RGFP的單株抗體 (Clontech,CA)收集成功轉殖性轉染的細胞,以供繼代培養。 實施例四北方專點法分析(Northern Blot Analysis) RNA(20pg 全部 RNA 或 2ug poly[A+]RNA)經由 1% 甲搭- 72 201009073 洋菜膠(fonnaidehyde-agarose gels)電泳分離後利用毛細現象將 RNA 吸附於尼龍膜上(Schleicher & Schuell,Keene, NH)。能互 補於連接之5端外顯子與先前設計之先驅微核醣核酸介 子(pre-miRNA insert)之間之 75 bp 連接序列(junction sequence) 之合成探針(probe)經 Prime-It II kit(Stratagene,La Jolla,CA)所 標定(labeled) ’ 並藉由隨機引子延長(ran(jom primer extension) 技術,使用[32P]-dATP(>3000 Ci/mM,Amersham International, ❹ Arlington Heights,IL)及所純化之 i〇 bp-cutoff Micro Bio-Spin chromatography columns (Bio-Rad,Hercules, CA)來標定序列。 序列的雜合係藉由混合50 %去離子曱醯胺(deionized formamide)(pH 7.0, 5x Denhardfs solution, 0.5% SDS, 4 x SSPE and 250 mg/mL denatured salmon sperm DNA fragments (18 hr, 42°C))而實施。尼龍膜於 2x SSC,0.1% SDS (15 min, 25°C)的條 件下洗滌兩次並以0.2 x SSC,0.1% SDS (45 min,37°C)的條件 ® 洗條一次後,進行(自動)放射攝影術(autoradiography)。 實施例五十二烷某碏酸鈉聚丙醯胺膠體電泳(SDS-PAGE) 及西方專點法分折(Western Blot Analysis) 對特定蛋白之免疫轉印法(immunoblotting),於培養液經去 除後之分離細胞經過冰的食鹽填酸緩衝液(phosphate buffered saline(PBS))潤拭,並用CelLytic-M細胞溶解萃取劑 (lysis/extraction. reagent)(Sigma, MO)並依據使用說明補充蛋白 73 201009073 酶抑制劑(protease inhibitors)如 Leupeptin、TLCK、TAME 及 PMSF。之後細胞至於室溫中以搖晃器(shaker)搖晃15分鐘後 將細胞刮入試管中後,用l2000xg之轉速離心5分鐘將細胞殘 潰沉殿,並將具有蛋白質之細胞萃取液收集並儲存在_7〇〇c以 待使用。並利用 SOFmax software package 在 E-max microplate 測疋器(reader)(Molecular Devices,Sunny vale,C A)將蛋白定 量。每30pg之細胞萃取液被加入SDS_PAGE樣品緩衝液 (sample buffer)(有還原或未還原50mM DTT)並將上述樣本煮 彿3分鐘,再將樣本注入8%聚丙酿胺膠(polyacrylamide gels),同時將 2~3 μΐ 蛋白標示(protein marker)(Bio-Rad)注入其 中。而 SDS-polyacrylamide gel 電泳(electrophoresis)是依據標 準程序來實施(Molecular Cloning, 3rdED)。蛋白層析後經由電 轉潰(electroblotting)法將蛋白質吸附在硝化纖維膜 (nitrocellulose membrane)而用 Odyssey blocking reagent(Li-C〇r Biosciences,Lincoln,NB)在室溫作用1〜2小時。本發明利用抗 體(primary antibody)直接對特定蛋白(EGFP (1:5,000; JL-8, BD), RGFP (1:10,000; BD), Oct3/4 (1:500; Santa Crutz) , SSEA-3 (1:500; Santa Crutz), SSEA-4(1:500; Santa Crutz) , Sox2(l:1000; Santa Crutz),Klf4(l :200; Santa Crutz))標定,於 4°C 作用整晚, 以供評估蛋白表現量。接著用TBS-T緩衝液洗三次,並再以 抗體(secondary antibody)作用此 nitrocellulose membrane(goat anti-mouse IgG conjugate with Alexa Fluor 680 reactive dye 201009073 (1:2,000; Molecular Probes)),室溫作用一小時後再用 TBS-Τ 緩 衝液洗三次後進行呈像並用Li-Cor Odyssey Infrared Imager及 Odyssey Softearev.lO(Li-Cor)紀錄影像。 實施例六 斑馬魚中内含子之核醣核酸基因靜默敎廒 (Intronic RNA-mediated Gene Silencing) 將此株Τ§(ύ^/«-ΟΑ]ϋ4:υΑ8$φ)斑馬魚幼魚養在具有i〇mi ❹ 0·2χ無血清(semm-jfree)RPMI 1640培養液之容器中以待轉 染。藉由輕巧地溶解 60μ1 FuGene liposomal transfection reagent(Roche Biochemicals,Indianapolis,IN)於 lml lx 無jk清 (serum-free)RPM 1640培養液中而準備轉染預先劑 (transfection pre-mix)。如實施例一與二所述之具有與不具有 anti-五GFP先驅微核醣核酸介子之办皿办及GF尸載體(20 μδ) 與上述轉染預先劑混合並置於冰上30分鐘後直接導入斑馬魚 〇 幼魚之容器中以進行轉染。所有三個劑量(全部6〇ug)經12小 時間隔島入,並待第一次轉染60小時後收集樣本並觀察。 實施例七細胞湳式儀分折(Flow Cytometry Assay) 細胞經胰蛋白酶作用後、離心收集並用1 ml PBS(預冷的 70%甲醇)重新混勻,並置於_2〇°cl小時。之後細胞經離心收集 並以1 ml PBS洗一次。細胞再一次經離心收集並以1 mi的 PBS(lmg/ml 漢度的破化丙咬(pr0pidium iodide)及 0.5 mg/ml 75 201009073 核酸水解酶)重新混勻並置於3TC,3G分鐘。約有15,〇〇〇個 細胞經BD FACSCalibur (San J0se,CA)分析。細胞偶具現象 (Cell doublet)經由暫止區寬度與暫止域相對值②丨⑽丨呢叫⑹ width versus pulse area)並以單一細胞設定閘門口徑。收集的資 料經 Flowjo 軟體及 Watson Pragmatic 演算法(alg〇rithm)分析 之。 魅例八-圭氧核醣核醆曱棊化試驗DNA Metlwlatimi ❹Mir-302 family precursor microribonucleic acid clusters can be mir_3〇2a_positive strands and mir-302a-anti-hybrid, mir-302b-positive strands and mir-302b-converse hybrids, mir-302c-positive The stock is formed by hybridization with mir-302c-anti-hybrid and mir-302d-positive strands and mir-302d-antisense. Then, mir_302a, mir_3〇2b, and mir-302c were respectively cut by pvui/XhoI, Xhol/Nhel, Nhel/Xbal reverse-restriction enzyme and extracted by gd extraction filter column (Qiagen, CA). ) Extracted in 35 μl of autoclaved ddHe. Immediately thereafter, the collected hybrids are joined to each other by T4 DNA-binding (Roche, 20U) to form a mir-302 family of microribonuclear meson clusters, and these hybrid ribonucleic acids can be further regulated by PVW//MM/etc. The cleavage is incorporated into the expression vector. The recombinant gene comprising the mir_302 family of microribonucleic acid mesoplexes is incorporated into a retroviral vector having a surface antigen which is useful for transgenic infection of hpESC and PC3 cells. In order to form an artificially redesigned mir-302 precursor microribonucleic acid meson, the present invention hybridizes two synthetic sequences of 201009073 (SEQ.ID.NO.27) and (SEQJD.NO.28), and then Pvw//Mw/etc. The restriction enzyme was cleaved and the hybrid sequence was ligated to the expression vector with T4 DNA ligase (20 U). This recombinant gene contains a redesigned mir-302 pioneer microRNA that is available for recombinant DNA recombination of Colo cells. Successfully transfected cells can be isolated and collected for subculture 24 hours later and collected using a single antibody against RGFP and a cell flow meter (Clontech, Palo Alto, CA). The mir-302 precursor microribonucleic acid clustering and mir-302 expression vector can be mass-produced in the plastid vector at the 5.co/z·DH5aLB (50 μg/ml povidine) as described above. 〇〇μg/ml of ampicillin was subjected to extensive replication of the 〆M:Z2 reverse transcription vector. The large number of replicated expression vectors were isolated and purified by mini-prep or maxi-prep plasmid extraction kit (Qiagen, CA). The detailed procedure is described in the instructions. For retroviral vectors, the present invention utilizes a packaging cell line GP2-293 (Qiagen, CA) for the manufacture of a virus that is infectious but not replicable. Infected GP2-293 cells in lxDMEM (carbon-adsorbed 10% fetal bovine serum (FBS), 4 mM L-face valeric acid, 1 mM sodium pyruvate, 100 μg/ml sulphate, 50 μg/ The milliliter neomycin (sigma Chemical, MO) medium was cultured at 37 ° C and 5% carbon dioxide. The amount of virus produced by GP2-293 cells was determined to be at least 1 〇 6 cfil/ml prior to transfection. 71 201009073 Example 3 沅V 〇 〇 〇 忖 忖 对 以 以 以 以 以 以 以 以 以 反 反 反 反 反 反 反 反 反 反 hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp hp The ribonucleic acid mesons were divided into (4) and (7) ϊρ. /?ΖΛ02 reverse transcription expression vectors were co-transfected with pVSV_G Gp2 293 cells (Clontech, CA). After culturing at 37 ° C, 5% carbon dioxide for 36 hours, the broth of GP2-293 cells (per 1 ml) was filtered and directly transferred to hpESC and PC3 cell culture medium by filtration (0.25 μm pore size). . Since the culture medium contains a high dose of the retroviral vector, all of the test cells are transfected with the vector and start to exhibit intron meson and RGFP within 24 hours. In order to transfer the redesigned artificial mir_3〇2 precursor microRNA into Colo cells, the present invention first mixes the prepared pre-prepared cake and the cadaver transfer gene (60 micrograms (pg) per cell culture dish). In 1 ml, the transgenic gene comprises the pre-designed mir-302 precursor microribonucleic acid meson of Example 2, mixed with FuGene reagent (Roche, IN) and operated according to the manual. Next, the mixture was used for Colo cell culture for 24 hours. Because the transgenic gene also contains a transposon-like sequence, which is homologous to a specific human genome region that does not have a codon, and then successfully transfected through a cell flow meter and anti-RGFP monoclonal antibody (Clontech, CA). Dyed cells for subculture. Example 4 Northern Blot Analysis RNA (20pg of total RNA or 2ug of poly[A+]RNA) was separated by electrophoresis using 1% Methyl-72 201009073 (Fonnaidehyde-agarose gels) RNA was adsorbed onto a nylon membrane (Schleicher & Schuell, Keene, NH). A synthetic probe that is complementary to a 75 bp junction sequence between the ligated 5-terminal exon and the previously designed precursor micro-ribonucleotide pre-miRNA insert is subjected to a Prime-It II kit ( Stratagene, La Jolla, CA) Labeled ' and by [jom primer extension] technique, using [32P]-dATP (>3000 Ci/mM, Amersham International, ❹ Arlington Heights, IL) And the purified i〇bp-cutoff Micro Bio-Spin chromatography columns (Bio-Rad, Hercules, CA) to calibrate the sequence. The hybridization of the sequence is by mixing 50% deionized formamide (pH) 7.0, 5x Denhardfs solution, 0.5% SDS, 4 x SSPE and 250 mg/mL denatured salmon sperm DNA fragments (18 hr, 42 ° C)). Nylon membrane at 2x SSC, 0.1% SDS (15 min, 25°) After washing twice under conditions of C) and washing the strip once with 0.2 x SSC, 0.1% SDS (45 min, 37 ° C), (automatic) radiography (Example). Sodium citrate polyacrylamide colloidal electrophoresis (SDS-PAGE) and Western special point method (West Ern Blot Analysis) Immunoblotting of specific proteins, after removal of the cultured cells, the cells are lysed by ice-saturated phosphate buffered saline (PBS) and dissolved in CelLytic-M cells. Extractant (lysis/extraction. reagent) (Sigma, MO) and supplemented with protein 73 201009073 Protease inhibitors such as Leupeptin, TLCK, TAME and PMSF according to the instructions. The cells are then shaken at room temperature. After shaking for 15 minutes, the cells were scraped into a test tube, and the cells were sacrificed by centrifugation at a speed of 12000 x g for 5 minutes, and the cell extract containing the protein was collected and stored at _7 〇〇 c for use. The protein was quantified using an SOFmax software package on an E-max microplate reader (Molecular Devices, Sunny vale, CA). Each 30 pg of cell extract was added to SDS_PAGE sample buffer (with or without reducing 50 mM DTT) and the sample was boiled for 3 minutes before injecting the sample into 8% polyacrylamide gels. A 2~3 μΐ protein marker (Bio-Rad) was injected into it. SDS-polyacrylamide gel electrophoresis was performed according to a standard procedure (Molecular Cloning, 3rdED). After protein chromatography, the protein was adsorbed on a nitrocellulose membrane by electroblotting, and treated with Odyssey blocking reagent (Li-C〇r Biosciences, Lincoln, NB) at room temperature for 1 to 2 hours. The present invention utilizes a primary antibody to directly target a specific protein (EGFP (1: 5,000; JL-8, BD), RGFP (1: 10,000; BD), Oct3/4 (1:500; Santa Crutz), SSEA-3 (1:500; Santa Crutz), SSEA-4 (1:500; Santa Crutz), Sox2 (l:1000; Santa Crutz), Klf4 (l:200; Santa Crutz)), calibrated at 4 ° C all night , for evaluation of protein expression. Then, it was washed three times with TBS-T buffer, and then the nitrocellulose membrane (goat anti-mouse IgG conjugate with Alexa Fluor 680 reactive dye 201009073 (1:2,000; Molecular Probes)) was applied as a secondary antibody. After an hour, the cells were washed three times with TBS-Τ buffer and imaged and images were recorded with Li-Cor Odyssey Infrared Imager and Odyssey Softearev.10 (Li-Cor). Example 6 Intronic RNA-mediated Gene Silencing of the zebrafish In this Τ§(ύ^/«-ΟΑ]ϋ4:υΑ8$φ) zebrafish juvenile 〇mi ❹ 0·2χ serum-free (semm-jfree) RPMI 1640 medium in a container for transfection. A transfection pre-mix was prepared by lightly dissolving 60 μl of FuGene liposomal transfection reagent (Roche Biochemicals, Indianapolis, IN) in lml lx serum-free RPM 1640 medium. As described in Examples 1 and 2, with and without the anti-five GFP precursor microribonucleic acid meson, the GF cadaver and the GF cadaver (20 μδ) were mixed with the above-mentioned transfection pre-agent and placed on ice for 30 minutes and then directly introduced. The zebrafish juvenile fish is containerd for transfection. All three doses (all 6 ug) were injected over a 12 hour interval and samples were collected and observed after 60 hours of the first transfection. Example 7 Flow Cytometry Assay Cells were trypsinized, collected by centrifugation and re-mixed with 1 ml of PBS (pre-cooled 70% methanol) and placed at _2 °C for 15 hours. The cells were then collected by centrifugation and washed once with 1 ml of PBS. The cells were again collected by centrifugation and re-mixed with 1 mi of PBS (1 mg/ml of pr0pidium iodide and 0.5 mg/ml 75 201009073 nuclease) and placed at 3TC for 3G minutes. Approximately 15 cells were analyzed by BD FACSCalibur (San J0se, CA). The cell doublet (Cell doublet) sets the gate diameter by a single cell by the relative value of the pause zone width and the pause domain 2 (10) width versus pulse area. The collected data was analyzed by Flowjo software and the Watson Pragmatic algorithm (alg〇rithm).魅例八-圭oxyribose nuclear deuteration test DNA Metlwlatimi ❹
Assay 本發明首先經DNA isolation kit(R〇che,IN)分離細胞的基因 體。基因體DNA樣本經培養試驗細胞於1〇 jjjjw Tris_HC1Assay The present invention first isolates the genome of a cell by a DNA isolation kit (R〇che, IN). The genomic DNA sample was cultured in test cells at 1〇 jjjjw Tris_HC1
8.0),10 mM EDTA,and 0.2 mg/ml 蛋白酶 K(proteinase K) 55°C 3小時後經乙醇沉澱而準備。之後分離的基因體經由(^(^(^切 位之限制酶Hpall(lOU)個別地於37°C作用4小時。之後最終 的DNA片段經由1%之洋菜膠電泳所分離。為了決定❹ 啟動子區域的曱基化區域,本發明用重亞硫酸鹽(CpGenome DNA modification kit,Chemicon,CA)處理分離的基因體 DNA。接著經 PCR 技術(long template PCR extension kit, Roche, IN)與兩條向前引子(forward primer) 5’-GAGGAGTTGA GGGTACTGTG-3,(SEQ.ID.N0.47)及 5,-GAGGAGCTGA GGGCACTGTG-3’(SEQ.ID.N0.48)與一相反引子(reverse primer)5’-GTAGAAGTGC CTCTGCCTTC C-3,(SEQ.ID.NO. 76 201009073 49)來分離OdW五端上游啟動子區域。細胞基因體(loo奈克 (ng))首先經引子(全部150 pmole)混合於lx PCR緩衝液,並加 熱至94°C 4分鐘後直接置於冰上。之後進行25個循環的PCR ' 反應,反應條件如下92。(: 1分鐘;55。(: 1分鐘;以及70°C 5 分鐘。最終的 PCR 產物經由 PCR purification kit (Qiagen, CA) 所收集並以等量的ACGT切位之限制酶(5U each)混合進行反 應,限制酶包含 jc// (AACGTT),(CACGTC),尸m/J φ (CACGTG),—5/ (TACGTA)及物C厦Γ (ACGT)。最終 DNA片段經由3%洋菜膠電泳分離之。 實施例九微核骑核酸生物晶片分析(MicroRNA Microarray Analysis、 人類PC3及Colo細胞株經美國型態培養收集機構 (American Type Culture Collection (ATCC,Rockville, MD))獲得 ❹ 且hpESC細胞經由胰蛋白酶從發明人的手臂由皮膚分離而 得。在70%相關性(confluenCy)之下,小核醣核酸經 miRNA isolation kit (Ambion,Inc” Austin, TX)從每株細胞株 中分離,如其使用者說明進行實驗。小核醣核酸的純度及品質 經由1%曱醛洋菜膠電泳及光譜分析儀(Bio-Rad,Hercules,CA) 來評估’之後送至LC Sciences (San Diego, CA)以供微核醣核 酸生物晶片分析。每一生物晶片經由一標定Cy3或Cy5之單 一樣本或個別標定Cy3或Cy5的樣本方式雜合。消除背景並 77 201009073 標準化(normalization)。對於雙樣本分析(dual sample assay), 尸-value計算後’顯現出表現差異超過3倍之轉錄分子。 實施例十基因生物晶Μ合析 為了準備經標定之探針(probe)以用來與生物晶片上的基因 雜合’將萃取出來之全部核醣核酸(2jig)轉變成雙股CDNA,並 使用 Superscript Choice system kit(Gibco/BRL,Gaithersburg, MD)及修飾後之oligh(dT)24_T7啟動子引子(promoter primer)如 ❿ 5'-GGCCAGTGAA TTGTAATACG ACTCACTATA GGGAGGCGG-(dT)24_3'(SEQJD.NO.50),接續步驟如同其使用 者說明步驟。將雙股cDNAs用酚/氣仿(phenol/chloroform)萃取 出.來後,利用乙醇將之沉澱並再回溶至0.5 μδ/μ1焦碳酸二乙 酯(diethyl pyrocarbonate (DEPC))-treated ddH20。而 Phase-Lock8.0), 10 mM EDTA, and 0.2 mg/ml Protease K (proteinase K) Prepared by ethanol precipitation at 55 ° C for 3 hours. The isolated gene body was then allowed to act individually at 37 ° C for 4 hours via (^(^(^) restriction enzyme Hpall (lOU). The final DNA fragment was then separated by 1% acacia gel electrophoresis. The thiolated region of the promoter region, the present invention treats the isolated genomic DNA with a bisulfite (CpGenome DNA modification kit, Chemicon, CA), followed by PCR (long template PCR extension kit, Roche, IN) and two Forward primer 5'-GAGGAGTTGA GGGTACTGTG-3, (SEQ.ID.N0.47) and 5,-GAGGAGCTGA GGGCACTGTG-3' (SEQ.ID.N0.48) and a reverse primer (reverse primer) 5'-GTAGAAGTGC CTCTGCCTTC C-3, (SEQ. ID. NO. 76 201009073 49) to isolate the OdW five-terminal upstream promoter region. The cell genome (loo Nike (ng)) was first introduced (all 150 pmole) Mix in lx PCR buffer and heat to 94 ° C for 4 minutes and then directly on ice. Then carry out 25 cycles of PCR 'reaction, the reaction conditions are as follows 92 (: 1 minute; 55. (: 1 minute; 5 minutes at 70 ° C. The final PCR product was collected via PCR purification kit (Qiagen, CA) and equal ACGT cleavage restriction enzymes (5U each) were mixed and reacted. The restriction enzymes contained jc// (AACGTT), (CACGTC), cadaver m/J φ (CACGTG), -5/ (TACGTA) and substance C Γ (ACGT) The final DNA fragment was separated by 3% acacia gel electrophoresis. Example 9 Micronucleus riding nucleic acid biochip analysis (MicroRNA Microarray Analysis, human PC3 and Colo cell strains by American Type Culture Collection (ATCC) , Rockville, MD)) obtained ❹ and hpESC cells were isolated from the skin of the inventor via trypsin. Under 70% correlation (confluenCy), small RNA was passed through the miRNA isolation kit (Ambion, Inc" Austin, TX) was isolated from each cell line and tested as described by the user. The purity and quality of the small RNA was assessed by 1% furfural gel electrophoresis and spectrometer (Bio-Rad, Hercules, CA). Sent to LC Sciences (San Diego, CA) for microRNA biochip analysis. Each biochip is hybridized via a single sample that calibrates Cy3 or Cy5 or individually calibrates a sample of Cy3 or Cy5. Eliminate the background and 77 201009073 normalization. For the dual sample assay, the cadaver-value calculation showed a transcriptional molecule with a difference of more than 3 fold. Example 10 Gene Biocrystallization Synthetic Analysis In order to prepare a calibrated probe for hybridization with a gene on a biochip, the entire extracted ribonucleic acid (2jig) was converted into a double-stranded DNA, and Superscript was used. Choice system kit (Gibco/BRL, Gaithersburg, MD) and modified oligh(dT)24_T7 promoter primer such as ❿ 5'-GGCCAGTGAA TTGTAATACG ACTCACTATA GGGAGGCGG-(dT)24_3' (SEQJD.NO.50) The subsequent steps are as described by their user. The double-stranded cDNAs were extracted with phenol/chloroform, and then precipitated with ethanol and re-dissolved to 0.5 μδ/μ1 diethyl pyrocarbonate (DEPC)-treated ddH20. Phase-Lock
Gel(5Trime->3'Prime,Inc.,Boulder,CO)可被用來增加萃取 率。而轉錄可用T7核醣核酸聚合酶與1 0f CDNA, ©Gel (5 Trime-> 3' Prime, Inc., Boulder, CO) can be used to increase the extraction rate. While transcription can be used with T7 RNA polymerase with 10f CDNA, ©
7.5 mM unlabeled ATP and GTP,5 mM unlabeled UTP 和 CTP 及 2 mM biotin-labeled CTP 及 UTP (biotin-11-CTP, biotin-16-UTP,Enzo Diagnostics)共同於 37°C反應 4 小時產生 cRNA,接著 cRNA 利用 RNeasy spin columns(Qiagen, CA)純 化。樣品經1%之洋菜膠來證實其尺寸大小,接著於4〇應 Tris_acetate, pH 8.0,100 mM KOAc/30 mM MgOAc 緩衝液中藉 加熱到94°C35分鐘而使cRNA隨機分裂成約50個核苷酸的大 78 201009073 利用四個核苷酸一組之生物晶片(GeneChip U133A&B arrays,Affymetrix,Santa Clara^ CA)及 U133 plus 2 人類基因體 之生物晶片(Affymetrix,Santa Clara,CA),其中總共包含32668 個基因可供進行雜合’雜合反應係於2〇〇μ1之AFFY緩衝液 (Affymetrix)於40°C中16小時連續攪動下完成。在雜合反應完 成後,生物晶片用200 μΐ之6x SSPE-T緩衝液(lx 0.25 Μ氯化 ❹ 鈉/15 mM 磷酸鈉,pH 7.6/1 mM EDTA/0.005% Triton)潤拭 3 次並接著用200 μΐ之6x SSPE-T緩衝液於5(TC洗一小時。接 著用0.5X SSPE-T潤拭兩次及〇.5x SSPE-T於50。(:沖洗15分 鐘。之後用 2 pg/ml streptavidin-phycoerytiirin (Molecular Probes) 及 1 mg/ml acetylated BSA (Sigma)於 6x SSPE-T (pH 7.6)緩衝 液中進行染色後,將生物晶片置入confocal scanner (Molecular Dynamics)以 7.5μιη 進行判讀並以 Afifymetrix Microarray Suite ❹ version 4.0軟體進行分析。藉由完美配對(perfectly matched)探 針與非配對(mismatched)探針之全部的平均差將樣本標準化 (normalize)後,收集訊號差異大於兩倍之訊號。 實施例細胞分化測試(Cell Differentiation Assay) 本發明所有的細胞株皆培養於無盼紅(phenol red-free)之 DMEM培養液(10%炭吸附的胎牛血清(1〇% charcoal_stripped fetal bovine semm(FBS))) ’ 在 70%相關性(confluency)之下,不 79 201009073 同的贺爾蒙(hormones)及生長因子被各別地添加入細胞培養 液中,如 50 ng/ml DHT、100 ng/ml TGF-βΙ 及/或 100 ng/ml BMP4。經過6到12個小時培養,經處理後的細胞在胰蛋白 酶作用下以4份(aliquot)的200 μΐ lx PBS溶液收集後,立刻瘦 入6周大無胸腺免疫喪失之SCID米黃色小鼠之頸部皮膚、尾 部靜脈、子宮及肝臟中體内。 實施例十二統計分姘 生物晶片結果係被呈現為平均值土SE。這些樣本資料之統計分 析藉由one-way ANOVA方式計算。當具有統計上顯著差異 時’ D_ett’s post-hoc test被用來辨認與標準具有差異之樣本 組。為了在兩組之間_行比對,SU(jent (test係被使 用。為了比對超過兩組,ANOVA比對後再由post_h〇c multiple range test來進行比對。或然率值p<〇.〇5被認定為具有統計上 的意義’所有p值是藉由two-tailed test來決定。 【圖式簡單說明】 本發明或申請案槽案包含至少—圖式為彩色。本發明或專 利申叫案與純圖式崎求而提交給相關單位錄交相關規 費。圖1顯示細胞_含子之微核軸酸㈣―mirc_A, miRNA)生賴制。上助含子錢嫌滅與先驅訊息核醋 核酸共_錄並經RNAsplieing_,⑽齡顯子而連接為 訊息核醋猶,以供生合成蛋㈣。雜接後_含子之微核 201009073 聽核S夂被it步處理成為成熟之微核軸酸,以供產生馳^ . 相縣賺紐應。目此’我們mt-人勒含子包含至少- 先驅微驗核酸結構(或稱办細),以供模擬細胞本身内含 子之微核醣核酸之生合成過程(圖3A及圖3B)。你細^經併 入細胞或纽基目中,經第二型聚合酶啟動子或病毒啟動子調 控’而由第—型聚合酶系統表現。在細助轉錄生成後,經 RNA splidng處理後轉咖先設計之时子之娜核酸分 ❹ +。在其它實_中,聽料之时仅獅減分子可為 反意核醣核酸結構,上述反意結構可供基因剔除作用。在其它 實施例中’預先設計之内含子之核醣核酸分子可包含部分反意 及正股核醣核酸片段以供形成雙股的siRNA並產生j^Ai機 制。在其它實施例中,預先設計之内含子之核醣核酸分子可為 類小夾核醣核酸結構’以供產生RNAi相關基因靜默效應。 圖1顯示細胞内内含子之微核醣核酸(化如咖mirc〇RNA, ⑩ miRNA)生成機制。 圖2顯示siRNA、外顯子之微核酷核酸(exonie(intergenic) microRNA)及内含子之微核醣核酸(intronic microRNA)路徑 機制。 圖3A到3D顯示本發明較佳實施例之φ臟重組 基因結構化合物(圖3A)(SEQ.ID.N0.32)及其原理(圖3Β)以產 生一模仿内含子之微核醣核酸(intronic miRNA)之人造微核醣 核酸。办表現載體於細胞内之測試顯示,直接於 81 201009073 斑馬魚中抑制綠色螢光蛋白有超過85%基因抑制(kn〇ckd〇wn) 效應,並由西方墨點法證實,如圖3C。而具有能靜默綠色螢 光蛋白之内含子之微核醣核酸(iconic miRNA)及其煎接先驅 物能經由l%f〇rmaldhyde瓊膠電泳並於北方墨點法後被觀察 到(圖3D)。 圖4A到4C顯示本發明之办及G/rp結構之不同設計 的内含子之核酷核酸介子(intronic insert)的效用評價。有 效率的miRNA生合成,及於兩周大之斑馬魚幼魚中有效率地 @ 產生綠色螢光蛋白靜默效應,證實了核醣核酸誘導靜默複合 體在 5’-miRNA*-stemloop-miRNA-3,[l]與 5,-miRNA-stemloop-miRNA*-3’ [2]兩種小夾核醣核酸之間,有不對稱之 偏好傾向(圖4A)。綠色螢光蛋白之基因靜默只在轉染先驅微 核醣核酸結構[2]中發現,而不是在轉染結構[1:|中被發現,而 證實其偏好。因綠色螢光蛋白與紅色螢光蛋白的顏色重疊後 會呈現紅色大於綠色如圖所顯現之深橘色,因此綠色螢光蛋 ❹ 白的量是遠低於紅色螢光蛋白於先驅微核醣核酸結構[2]轉染 組,此時載體之指標紅色螢光蛋白則是平均表現地(圖 4B)(SEQ.ID.N0.33-35)。用西方墨點法分析綠色螢光蛋白之 量,證實在轉染先驅微核醣核酸結構組[2]中具有明顯的基因 靜默效應(圖4C)。在其他實驗組例如脂質體組(Lip〇s〇me only(Lipo))、無任何介子之空載體組(Vctr)以及siRNA(siR)組 皆無基因靜默效應出現。 82 201009073 圖5A到5C顯示在mir-302-like核醣核酸分子經過轉染表 現於人類上皮細胞(hpESC)、人類前列腺癌細胞株(PC3)及人 類初始黑色素瘤細胞株(Colo),導致細胞型態及細胞增生的改 變。在mir-302轉染後,表現mir-302的細胞個別稱為 hpESC+mir-302、PC3+ mir-302 及 C0I0+ mir-302,在 mir-g^ 轉染後(mir-gfp為靜默綠色螢光蛋白的序列),表現的7.5 mM unlabeled ATP and GTP, 5 mM unlabeled UTP and CTP and 2 mM biotin-labeled CTP and UTP (biotin-11-CTP, biotin-16-UTP, Enzo Diagnostics) were reacted at 37 ° C for 4 hours to generate cRNA, followed by cRNA was purified using RNeasy spin columns (Qiagen, CA). The sample was confirmed by 1% acacia gum, and then cRNA was randomly divided into about 50 nuclei by heating to 94 ° C for 35 minutes in Tris_acetate, pH 8.0, 100 mM KOAc/30 mM MgOAc buffer. Large 78 of the nucleotides 201009073 Biochips of four nucleotide sets (GeneChip U133A & B arrays, Affymetrix, Santa Clara ^ CA) and U133 plus 2 human genome biofilm (Affymetrix, Santa Clara, CA), A total of 32668 genes were included for hybridization. The heterozygous reaction was carried out in 2 μl of AFFY buffer (Affymetrix) at 40 ° C for 16 hours with continuous agitation. After the hybridization reaction was completed, the biochip was rinsed 3 times with 200 μL of 6x SSPE-T buffer (lx 0.25 ❹ sodium citrate/15 mM sodium phosphate, pH 7.6/1 mM EDTA/0.005% Triton) and then Wash with 200 μL of 6x SSPE-T buffer at 5 (TC for one hour. Then wipe with 0.5X SSPE-T twice and 〇.5x SSPE-T at 50. (: rinse for 15 minutes. Then use 2 pg/ Molstreptavidin-phycoerytiirin (Molecular Probes) and 1 mg/ml acetylated BSA (Sigma) were stained in 6x SSPE-T (pH 7.6) buffer, and the biochip was placed in a confocal scanner (Molecular Dynamics) for interpretation at 7.5 μηη. The analysis was performed with Afifymetrix Microarray Suite ❹ version 4.0 software. After the samples were normalized by the average difference between the perfectly matched probe and the mismatched probe, the difference in the collected signal was more than twice. Signals. Cell Differentiation Assay All cell lines of the present invention were cultured in phenol red-free DMEM medium (10% charcoal-adsorbed fetal bovine serum (1% charcoal_stripped fetal bovine) Semm(FBS))) Under 70% confluency, no 79 201009073 hormones and growth factors were added separately to the cell culture medium, such as 50 ng/ml DHT, 100 ng/ml TGF-βΙ And / or 100 ng / ml BMP4. After 6 to 12 hours of culture, the treated cells were collected by trypsin in 4 parts (aliquot) of 200 μΐ lx PBS solution, and then immediately diluted into 6 weeks of athymic gland. Immunodeficient SCID beige mice in the neck skin, tail vein, uterus and liver. Example 12 Statistical tiller biochip results are presented as mean soil SE. Statistical analysis of these sample data by One-way ANOVA method calculation. When there is a statistically significant difference, 'D_ett's post-hoc test is used to identify the sample group that differs from the standard. In order to compare _ rows between the two groups, SU(jent (test system is use. For comparison, the ANOVA was compared and then compared by post_h〇c multiple range test. The probability value p < 〇.〇5 is considered to be statistically significant. 'All p values are determined by a two-tailed test. BRIEF DESCRIPTION OF THE DRAWINGS The present invention or application slot contains at least the drawings in color. The invention or the patent application and the pure drawing are submitted to the relevant unit to record the relevant fees. Figure 1 shows the cell-containing micronucleic acid (IV)-mirc_A, miRNA). The helper contains the money and the precursor message, and the nucleic acid is shared with RNAsplieing_, (10)-aged and connected to the message nucleus to produce synthetic eggs (4). After the miscellaneous _ _ sub-nuclear 201009073 nucleus S 夂 is treated by it step into a mature micro-nucleic acid, for the production of Chi ^. Thus, our mt-human inclusions contain at least a precursor micro-nucleic acid structure (or fine) for the synthesis of microRNAs that mimic the introns of the cells themselves (Fig. 3A and Fig. 3B). You are introduced into the cell or New Zealand by a second type polymerase promoter or viral promoter and are expressed by a first-type polymerase system. After the fine transcription-promoting production, after the RNA splidng treatment, the nucleic acid of the time is designed to be ❹+. In other real cases, only the lion-reducing molecule can be an anti-intentional ribonucleic acid structure, and the above-mentioned anti-intentional structure can be used for gene knocking. In other embodiments, the 'predesigned intron ribonucleic acid molecule can comprise a partial antisense and a positive ribonucleic acid fragment for use in forming a double stranded siRNA and generating a J^Ai mechanism. In other embodiments, the pre-designed intron ribonucleic acid molecule can be a small ribonucleic acid structure' for generating an RNAi-related gene silencing effect. Figure 1 shows the mechanism of micronucleic acid (in vivo, such as coffee mirc〇RNA, 10 miRNA) in the intracellular intron. Figure 2 shows the siRNA, the exonie (intergenic microRNA) of the exon and the intronic microRNA pathway mechanism of the intron. 3A to 3D show a φ-turbine recombinant gene structural compound (Fig. 3A) (SEQ. ID. N0.32) and its principle (Fig. 3A) of a preferred embodiment of the present invention to produce a microRNA which mimics an intron (Fig. 3A). Artificial microRNA of intronic miRNA). Tests of intracellular expression of the expression vector showed that the inhibition of green fluorescent protein in zebrafish was more than 85% of the gene inhibition (kn〇ckd〇wn) effect directly in 81 201009073 and was confirmed by Western blotting, as shown in Fig. 3C. The iconic miRNA with the intron of the green fluorescent protein and its fried precursor can be electrophoresed by l%f〇rmaldhyde agar and observed after the northern dot method (Fig. 3D). . Figures 4A through 4C show the evaluation of the utility of the intronic insert of the intron of the different designs of the G/rp structure of the present invention. Efficient miRNA biosynthesis and efficient generation of green fluorescent protein silencing in two-week zebrafish juveniles confirms that the ribonuclease-induced silent complex is in 5'-miRNA*-stemloop-miRNA-3, [l There is a tendency to asymmetry between the two small ribonucleic acids with 5,-miRNA-stemloop-miRNA*-3' [2] (Fig. 4A). The gene silencing of green fluorescent protein was only found in the transfection of the precursor microRNA structure [2], but not in the transfected structure [1:|, but confirmed its preference. Because the color of green fluorescent protein and red fluorescent protein overlap, the red color is larger than the dark orange color as shown in the figure. Therefore, the amount of green fluorescent egg white is much lower than that of red fluorescent protein in the pioneer microRNA. Structure [2] transfection group, at this time the indicator of the vector red fluorescent protein is the average performance (Fig. 4B) (SEQ. ID. N0.33-35). Analysis of the amount of green fluorescent protein by Western blotting confirmed a significant gene silencing effect in the transfected precursor microRNA structural group [2] (Fig. 4C). No gene silencing effect occurred in other experimental groups such as the liposome group (Lip〇s〇me only (Lipo)), the empty vector group without any meson (Vctr), and the siRNA (siR) group. 82 201009073 Figures 5A to 5C show that mir-302-like ribonucleic acid molecules are transfected in human epithelial cells (hpESC), human prostate cancer cell line (PC3) and human primary melanoma cell line (Colo), resulting in cell type State and changes in cell proliferation. After mir-302 transfection, the cells expressing mir-302 were individually called hpESC+mir-302, PC3+ mir-302 and C0I0+ mir-302, after mir-g^ transfection (mir-gfp is silent green fluorescence) Sequence of protein)
細胞個別稱為 hpESC+mir-g^)、PC3+mir-gj53 及 Colo+mir-g^D。 圖6A到6E顯示Colo及PC3細胞株轉染mir-302之胚胎 幹細胞特性。這些特性包含形成胚樣體(embry〇id b〇dy),如 圖6A所示。〇ct3/4、SSEA-3及SSEA-4等蛋白之西方墨點 法分析’如圖6B。基因體的去曱基化分析,如圖6C。CpG 去甲基化分析,如圖6D。及細胞位移,如圖6E。 圖7A到7B顯示微核醣核酸生物晶片分析,證實mir_3〇2 家族全部高度表現於Colo+ mir_3〇2細胞中。 圖8A到8B顯示在c〇I〇+ mir-3〇2細胞中基因晶片的分析 結果(Affymetrix human GeneChip U133A&B,CA),結果顯 示’與人類胚胎幹細胞HuEC8及H9細胞的基因表現狀態相 比,有許多胚胎幹細胞的標諸(marker)基因有顯著地上升,而 癌症及發育基因的表現則有顯著地下降。 〜圖9A到9C顯示具有紅色榮光蛋白之c〇i〇+ ^观細胞The cells are individually referred to as hpESC+mir-g^), PC3+mir-gj53 and Colo+mir-g^D. Figures 6A to 6E show the characteristics of embryonic stem cells transfected with mir-302 by Colo and PC3 cell lines. These characteristics include the formation of embryoid bodies (embry〇id b〇dy) as shown in Figure 6A. Western blot analysis of proteins such as 〇ct3/4, SSEA-3 and SSEA-4 is shown in Fig. 6B. De-mercaptolysis analysis of the gene body, as shown in Figure 6C. CpG demethylation analysis, as shown in Figure 6D. And cell displacement, as shown in Figure 6E. Figures 7A through 7B show microRNA biochip analysis confirming that the mir_3〇2 family is all highly expressed in Colo+ mir_3〇2 cells. Figures 8A to 8B show the results of analysis of gene chips in c〇I〇+ mir-3〇2 cells (Affymetrix human GeneChip U133A & B, CA), and the results show that 'the gene expression status of human embryonic stem cells HuEC8 and H9 cells In contrast, there are many embryonic stem cell marker genes that have risen significantly, while cancer and developmental genes have decreased significantly. ~ Figures 9A to 9C show c〇i〇+ ^ viewing cells with red glory protein
St許多細峨’例如’原始軟骨細胞、纖維母細胞及 在處理過列發育訊號物質(如,不同的Ϊ爾蒙及/ 83 201009073 或生長因子)後’證實其分化乡能性相似於那些胚胎幹細胞。 圖 10 為生物晶片(Affymetrix U133 plus 2 human genome genechips)的資料,其顯示係表現在c〇1〇+ mir_3〇2細 胞,然而Klf4基因則不表現。此外,許多標準人類胚胎幹細 胞標誌細高度表達於Colo+mir-302細胞而非原本的c〇1〇細 胞’例如 ’ 0ct4、Sox2、Nanog、Utfl、Rexl、SALL2 及 SALL4, 此結果呼應圖8B的實驗結果。 ❹ 84 201009073 序列表St many fine 峨 'such as 'primitive chondrocytes, fibroblasts and after treatment of the developmental signaling material (eg, different hormones and / 83 201009073 or growth factors) 'proven that their differentiation is similar to those embryos stem cell. Figure 10 is a data of a biochip (Affymetrix U133 plus 2 human genome gene chips) showing that it is expressed in c〇1〇+mir_3〇2 cells, whereas the Klf4 gene does not. In addition, many standard human embryonic stem cell markers are highly expressed in Colo+mir-302 cells rather than native c〇1〇 cells such as '0ct4, Sox2, Nanog, Utfl, Rexl, SALL2, and SALL4, and this result echoes Figure 8B. Experimental results. ❹ 84 201009073 Sequence Listing
<110> LIN,Shi-Lung,etal.林希龍等人 <120>使用内含子之核St核酸於生成類胚胎幹細胞/Generation of Human Embryonic Stem-Like Cells Using Intronic RNA <130> 5199-0138PUS1 <140> 098114452 <141> 2009-04-30 <160〉 50 ❹<110> LIN, Shi-Lung, et al. Lin Xilong et al. <120> Using an intron nuclear St gene in Generation Embryonic Stem-Like Cells Using Intronic RNA <130> 5199- 0138PUS1 <140> 098114452 <141> 2009-04-30 <160> 50 ❹
< 170> Patentln version 3.5 <210> 1 <211> 12 <212〉DNA <213>人造序列 <220〉 <223>化學合成寡核苷酸 <400> 1 gctaagccag gc 12 <210> 2 <211> 12 <212> DNA <213> 人造序列 <220> <223>化學合成募核苷酸<170> Patentln version 3.5 <210> 1 <211> 12 <212>DNA<213> artificial sequence<220><223> chemical synthesis oligonucleotide<400> 1 gctaagccag gc 12 <210> 2 <211> 12 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotide
<400> 2 gcctggctta gc <210> 3 <211> 17 <212> RNA 85 12 201009073 <213>人造序列 <220> <223>化學合成寡核苷酸 <400> 3 uaagugcuuc cauguuu <210> 4 <211> 8 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 4 gtaagagk <210> 5 <211> 10 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 5 gwkscyrcag <210> 6 <211> 7 <212> DNA <213>人造序列 <220〉 <223>化學合成募核苷酸 <400> 6 tactway 201009073 <210> 7 <211> 17 <212> DNA <213〉人造序列 <220> <223>化學合成寡核苷酸 <400〉 7 tytycttttt tttttts <210> 8 <211> 19<400> 2 gcctggctta gc <210> 3 <211> 17 <212> RNA 85 12 201009073 <213> Artificial sequence <220><223> Chemical synthesis oligonucleotide <400> Uaagugcuuc cauguuu <210> 4 <211> 8 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 4 gtaagagk <210> 5 < 211 > 10 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 5 gwkscyrcag <210> 6 <211> 7 <212> DNA <;213> artificial sequence <220> <223> chemical synthesis nucleotides <400> 6 tactway 201009073 <210> 7 <211> 17 <212> DNA <213>artificial sequence <220>;<223>Chemical Synthesis Oligonucleotide<400> 7 tytycttttt tttttts <210> 8 <211> 19
⑩ <212〉DNA <213>人造序列 <220> <223>化學合成寡核苷酸 <220〉 <221> misc_feature <222〉(15)..(15) <223〉n is a,c,g,ort <400〉 8 tctctctctc tctcnctag ❿ <210> 9 <211> 23 <212> RNA <213>人造序列 <220> <223>化學合成寡核苷酸 <400〉 9 uaagugcuuc cauguuuuag ugu <210> 10 201009073 <211> 23 <212> RNA <213>人造序列 <220> <223>化學合成募核苷酸 <400〉 10 uaagugcuuc cauguuuugg uga 23 2310 <212>DNA<213> artificial sequence <220><223> chemical synthesis oligonucleotide <220>221> misc_feature <222>(15)..(15) <223 〉n is a,c,g,ort <400〉 8 tctctctctc tctcnctag ❿ <210> 9 <211> 23 <212> RNA <213> artificial sequence <220><223> Nucleotide <400> 9 uaagugcuuc cauguuuuag ugu <210> 10 201009073 <211> 23 <212> RNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400 〉 10 uaagugcuuc cauguuuugg uga 23 23
<210> 11 <211> 23 <212> RNA <213>人造序列 <220> <223>化學合成寡核苷酸 <400〉 11 uaagugcuuc cauguuuuag uag <210〉 12 <211> 23 <212> RNA <213>人造序列 <220> <223>化學合成募核苷酸 <400〉 12 uaagugcuuc cauguuucag ugg 23 <210> 13 <211> 23 <212> RNA <213>人造序列 <220> <223>化學合成寡核苷酸 <400〉 13 88 201009073 uaagugcuuc cauguuugag ugu <210> 14 <211> 42 <212> DNA <213>人造序列 <220> <223>化學合成寡核苷酸 <400〉 14 gtaagaggat ccgatcgcag gagcgcacca tcttcttcaa ga Q <210〉 15 <211> 46 <212> DNA <213>人造序列 <220〉 <223>化學合成寡核苷酸 <400> 15 cgcgtcttga agaagatggt gcgctcctgc gatcggatcc tcttac <210> 16 <211> 42<210> 11 <211> 23 <212> RNA <213> artificial sequence <220><223> chemical synthesis oligonucleotide <400> 11 uaagugcuuc cauguuuuag uag <210> 12 < 211 > 23 <212> RNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 12 uaagugcuuc cauguuucag ugg 23 <210> 13 <211> 23 <212> RNA <213> artificial sequence <220><223> chemical synthesis oligonucleotide <400> 13 88 201009073 uaagugcuuc cauguuugag ugu <210> 14 <211> 42 <212> DNA <213> Artificial sequence <220><223> chemical synthesis oligonucleotide <400> 14 gtaagaggat ccgatcgcag gagcgcacca tcttcttcaa ga Q <210> 15 <211> 46 <212> DNA <213> artificial sequence< 220> <223>Chemical Synthesis Oligonucleotide <400> 15 cgcgtcttga agaagatggt gcgctcctgc gatcggatcc tcttac <210> 16 <211>
❹ <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400〉 16 gtaagaggat ccgatcgctt gaagaagatg gtgcgctcct ga <210> 17 <211> 46 <212> DNA <213>人造序列 ❿ 60 70 60 〇 201009073 <220> <223>化學合成募核苷酸 <400> 17 cgcgtcagga gcgcaccatc ttcttcaagc gatcggatcc tcttac 46 <210> 18 <211> 70 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 18 gtaagaggat ccgatcgcag gagcgcacca tcttcttcaa gttaacttga agaagatggt gcgctcctga <210> 19 <211> 74 <212> DNA <213〉人造序列 <220> <223>化學合成募核苷酸 <400〉 19 cgcgtcagga gcgcaccatc ttcttcaagt taacttgaag aagatggtgc gctcctgcga tcggatcctc ttac <210> 20 <211> 47 <212> DNA <213>人造序列 <220> <223>化學合成寡核苷酸 <400> 20 cgcgttacta actggtacct cttctttttt tttttgatat cctgcag 47 90 201009073 <210> 21 <211> 45 <212〉DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 21 gtcctgcagg atatcaaaaa aaaaagaaga ggtaccagtt agtaa 45❹ <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 16 gtaagaggat ccgatcgctt gaagaagatg gtgcgctcct ga <210> 17 <211> 46 <212> DNA <213> artificial sequence ❿ 60 70 60 〇201009073 <220><223> chemical synthesis nucleotides <400> 17 cgcgtcagga gcgcaccatc ttcttcaagc gatcggatcc tcttac 46 <210> 18 <211> 70 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 18 gtaagaggat ccgatcgcag gagcgcacca tcttcttcaa gttaacttga agaagatggt gcgctcctga <210> 19 <211> 74 <212> DNA <213> artificial sequence <220><223> chemical synthetic nucleotide <400> 19 cgcgtcagga gcgcaccatc ttcttcaagt taacttgaag aagatggtgc gctcctgcga tcggatcctc ttac <210> 20 <211> 47 <212> DNA < 213 > artificial sequence <220><223> chemical synthesis oligonucleotide <400> 20 cgcgttacta actggtacct cttctttttt tttttgatat cctgcag 47 90 201009073 <210&g t; 21 <211> 45 <212>DNA<213> artificial sequence <220><223> chemical synthesis nucleotides <400> 21 gtcctgcagg atatcaaaaa aaaaagaaga ggtaccagtt agtaa 45
<210〉 22 <211> 689 <212〉DNA <213>人造序列 <220〉 <223> 藉由從海葵(i/eiemcri·? crfjpa)衍生來之HcRedl彩色蛋白質基因 (chromoprotein gene)於第69個胺基酸插入天門冬胺酸(aspartate (Asp))而生成之突 變紅色螢光蛋白基因 <400> 22 atggtgagcg gcctgctgaa gg£^agtatg cgcatcaaga tgtacatgga gggcaccgtg 60 aacggccact acttcaagtg cgagggcgag ggcgacggca accccttcgc cggcacccag 120 agcatgagaa tccacgtgac cgagggcgcc cccctgccct tcgccttcga catcctggcc 180 ccctgctgcg agtacggcag caggacgacc ttcgtgcacc acaccgccga gatccccgac 240 ttcttcaagc agagcttccc cgagggcttc acctgggaga gaaccaccac ctacgaggac 300 ggcggcatcc tgaccgccca ccaggacacc agcctggagg gcaactgcct gatctacaag 360 gtgaaggtgc acggcaccaa cttccccgcc gacggccccg tgatgaagaa caagagcggc 420 ggctgggagc ccagcaccga ggtggtgtac cccgagaacg gcgtgctgtg cggccggaac 480 gtgatggccc tgaaggtggg cgaccggcac ctgatctgcc accactacac cagctaccgg 540 agcaagaagg ccgtgcgcgc cctgaccatg cccggcttcc acttcaccga catccggctc 600 cagatgctgc ggaagaagaa ggacgagtac ttcgagctgt acgaggccag cgtggcccgg 660 tacagcgacc tgcccgagaa ggccaactg 689 <210> 23 <211> 27 <212> DNA <213> 人造序列 91 201009073 <220> <223>化學合成募核苷酸 <400〉 23 ctcgagcatg gtgagcggcc tgctgaa 27 <210> 24 <211> 27 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400〉 24 tctagaagtt ggccttctcg ggcaggt G 27 <210> 25 <211> 89 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 25 gtaagtggtc cgatcgtcgc gacgcgtcat tactaactat caatatctta atcctgtccc ttttttttcc acagtaggac cttcgtgca 60 89 ❹ <210> 26 <211> 89 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 26 tgcacgaagg tcctactgtg gaaaaaaaag ggacaggatt aagatattga tagttagtaa 60 tgacgcgtcg cgacgatcgg accacttac 89 92 201009073 <210> 27 <211> 82 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 27 gtccgatcgt cataagtgct tccatgtttt agtgtgctaa gccaggcaca ctaaaacatg gaagcactta tcgacgcgtc at <210> 28 0 <211> 82 <212> DNA <213〉人造序列 <220> <223>化學合成寡核苷酸 <400〉 28 atgacgcgtc gataagtgct tccatgtttt agtgtgcctg gcttagcaca ctaaaacatg gaagcactta tgacgatcgg ac <210> 29 <211> 11<210> 22 <211> 689 <212>DNA<213> artificial sequence <220><223> by HcRedl color protein gene derived from sea anemone (i/eiemcri·? crfjpa) Chromoprotein gene) The mutant red fluorescent protein gene generated by the insertion of aspartate (Asp) in the 69th amino acid <400> 22 atggtgagcg gcctgctgaa gg£^agtatg cgcatcaaga tgtacatgga gggcaccgtg 60 aacggccact acttcaagtg cgagggcgag ggcgacggca accccttcgc cggcacccag 120 agcatgagaa tccacgtgac cgagggcgcc cccctgccct tcgccttcga catcctggcc 180 ccctgctgcg agtacggcag caggacgacc ttcgtgcacc acaccgccga gatccccgac 240 ttcttcaagc agagcttccc cgagggcttc acctgggaga gaaccaccac ctacgaggac 300 ggcggcatcc tgaccgccca ccaggacacc agcctggagg gcaactgcct gatctacaag 360 gtgaaggtgc acggcaccaa cttccccgcc gacggccccg tgatgaagaa caagagcggc 420 ggctgggagc ccagcaccga ggtggtgtac cccgagaacg gcgtgctgtg cggccggaac 480 gtgatggccc tgaaggtggg cgaccggcac ctgatctgcc accactacac cagctaccgg 540 agcaagaagg ccgtgcgcgc cctgaccatg cccggcttcc acttcaccga catccggctc 600 cagatgctgc ggaagaagaa ggacgagtac ttcgagctgt acgaggccag cgtggcccgg 660 tacagcgacc tgcccgagaa ggccaactg 689 <210> 23 <211> 27 <212> DNA <213> Artificial sequence 91 201009073 <220><223>Chemical synthesis of nucleotides <223> 400> 23 ctcgagcatg gtgagcggcc tgctgaa 27 <210> 24 <211> 27 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 24 tctagaagtt ggccttctcg Ggcaggt G 27 <210> 25 <211> 89 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 25 gtaagtggtc cgatcgtcgc gacgcgtcat tactaactat caatatctta atcctgtccc ttttttttcc Acagtaggac cttcgtgca 60 89 ❹ <210> 26 <211> 89 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 26 tgcacgaagg tcctactgtg gaaaaaaaag ggacaggatt aagatattga Tagttagtaa 60 tgacgcgtcg cgacgatcgg accacttac 89 92 201009073 <210> 27 <211> 82 <212> DNA < 213 > artificial sequence <220><223> chemical synthetic nucleotide <400> 27 gtccgatcgt cataagtgct tccatgtttt agtgtgctaa gccaggcaca ctaaaacatg gaagcactta tcgacgcgtc at <210> 28 0 <211> 82 <212> DNA < 213> artificial sequence <220><223> chemical synthesis oligonucleotide <400> 28 atgacgcgtc gataagtgct tccatgtttt agtgtgcctg gcttagcaca ctaaaacatg gaagcactta tgacgatcgg ac <210> 29 <211>
❹ <212> RNA <213>人造序列 <220〉 <223>化學合成募核苷睃 <400〉 29 wuccaagggg g <210> 30 <211> 10 <212> DNA <213〉人造序列 201009073 <220> <223>化學合成募核苷酸 <400> 30 gtaagaggat 10 <210> 31 <211> 12 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 12 60 65❹ <212> RNA <213> artificial sequence <220><223> chemical synthesis nucleoside 睃 <400> 29 wuccaagggg g <210> 30 <211> 10 <212> DNA < 213> artificial sequence 201009073 <220><223> chemical synthesis nucleotides <400> 30 gtaagaggat 10 <210> 31 <211> 12 <212> DNA <213> artificial sequence <220>;<223> chemical synthesis of nucleotides 12 60 65
<400〉 31 gatatcctgc ag <210> 32 <211> 65 <212> DNA <213>人造序列 <220〉 <223>化學合成募核苷酸 <400〉 32 aggtaagagt cgatcgacgc gttactaact ggtacctctt cttttttttt tgatatcctg caggc <210> 33 <211> 53 <212> DNA <213>人造序列 <220> <223>化學合成寡核苷酸 <400〉 33 aagaagatgg tgcgctcctg gatcaagaga ttccaggagc gcaccatctt ctt 53 94 201009073 <210> 34 <211> 54 <212> DNA <213> 人造序列 <220> <223>化學合成募核苷酸 <400> 34 caagaagatg gtgcgctcct ggatcaagag attccaggag cgcaccatct tctt 54<400> 31 gatatcctgc ag <210> 32 <211> 65 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 32 aggtaagagt cgatcgacgc gttactaact Ggtacctctt cttttttttt tgatatcctg caggc <210> 33 <211> 53 <212> DNA <213> artificial sequence <220><223> chemical synthesis oligonucleotide <400> 33 aagaagatgg tgcgctcctg gatcaagaga ttccaggagc gcaccatctt ctt 53 94 201009073 <210> 34 <211> 54 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 34 caagaagatg gtgcgctcct ggatcaagag attccaggag cgcaccatct tctt 54
<210> 35 <211> 53 <212> DNA Q <213>人造序列 <220〉 <223>化學合成募核苷酸 <400> 35 aagaagatgg tgcgctcctg gatcaagaga ttccaggagc gcaccatctt ctt 53 <210> 36 <211> 25 <212> DNA <213> 人造序列 〇 <220> <223>化學合成寡核苷酸 <400> 36 gttgttttgt tttggttttg gatat 25 <210> 37 <211> 26 <212> DNA <213>人造序列 <220> <223>化學合成寡核苷酸 95 201009073 <400> 37 attgttttgt tttggttttg gattta <210> 38 <211> 21 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 38 gtagaagtgc ctctgccttc c <210> 39 <211> 91 <212〉DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 39 gtccgatcgt cccaccactt aaacgtggat gtacttgctt tgaaactaaa gaagtaagtg cttccatgtt ttggtgatgg atctcgagct c <210> 40 <211> 91 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 40 gagctcgaga tccatcacca aaacatggaa gcacttactt ctttagtttc aaagcaagta catccacgtt taagtggtgg gacgatcgga c <210> 41 <211> 95 201009073 <212> DNA <213>人造序列 • <220〉 ’ <223>化學合成募核苷酸 ' <400> 41 atctcgagct cgctcccttc aactttaaca tggaagtgct ttctgtgact ttgaaagtaa gtgcttccat gttttagtag gagtcgctag cgcta <210> 42 <211> 95 <212> DNA <213>人造序列 ❹ <220> <223>化學合成寡核苷酸 <400> 42 tagcgctagc gactcctact aaaacatgga agcacttact ttcaaagtca cagaaagcac ttccatgtta aagttgaagg gagcgagctc gagat <210> 43 <211> 89 <212> DNA <213> 人造序列 © <220〉 <223>化學合成募核苷酸 <400> 43 cgctagcgct acctttgctt taacatggag gtacctgctg tgtgaaacag aagtaagtcg ttcatgtttc agtggaggcg tctagacat <210> 44 <211> 89 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 60 82<210> 35 <211> 53 <212> DNA Q < 213 > artificial sequence <220 < 223 > chemical synthetic nucleotides <400> 35 aagaagatgg tgcgctcctg gatcaagaga ttccaggagc gcaccatctt ctt 53 <210> 36 <211> 25 <212> DNA <213> artificial sequence 〇<220><223> chemical synthesis oligonucleotide <400> 36 gttgttttgt tttggttttg gatat 25 <210> 37 < 211 > 26 <212> DNA <213> artificial sequence <220><223> chemical synthesis oligonucleotide 95 201009073 <400> 37 attgttttgt tttggttttg gattta <210> 38 <211> 21 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleotides <400> 38 gtagaagtgc ctctgccttc c <210> 39 <211> 91 <212>DNA <213> Artificial sequence <220><223> chemical synthetic nucleotide <400> 39 gtccgatcgt cccaccactt aaacgtggat gtacttgctt tgaaactaaa gaagtaagtg cttccatgtt ttggtgatgg atctcgagct c <210> 40 <211> 91 <212> DNA <213> Artificial sequence ≪220><223>Chemical Synthetic Nucleotide<400> 40 gagctcgaga tccatcacca aaacatggaa gcacttactt ctttagtttc aaagcaagta catccacgtt taagtggtgg gacgatcgga c <210> 41 <211> 95 201009073 <212> DNA <213> Sequence • <220〉 ' <223>Chemical Synthetic Nucleotide' <400> 41 atctcgagct cgctcccttc aactttaaca tggaagtgct ttctgtgact ttgaaagtaa gtgcttccat gttttagtag gagtcgctag cgcta <210> 42 <211> 95 <212> DNA < 213 > artificial sequence ❹ <220><223> chemical synthesis oligonucleotide <400> 42 tagcgctagc gactcctact aaaacatgga agcacttact ttcaaagtca cagaaagcac ttccatgtta aagttgaagg gagcgagctc gagat <210> 43 <211> 89 <212> DNA <;213> artificial sequence © <220> <223> chemical synthesis nucleotides <400> 43 cgctagcgct acctttgctt taacatggag gtacctgctg tgtgaaacag aagtaagtcg ttcatgtttc agtggaggcg tctagacat <210> 44 <211> 89 <212> DNA <;213>artificialsequence<220><223> chemical combination Raised nucleotides 6082
60 8260 82
201009073 <400> 44 atgtctagac gcctccactg aaacatgaac gacttacttc tgtttcacac agcaggtacc 60 tccatgttaa agcaaaggta gcgctagcg 89 <210> 45 <211> 82 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 45 cgtctagaca taacactcaa acatggaagc acttagctaa gccaggctaa gtgcttccat gtttgagtgt tcgacgcgtc at <210> 46 <211> 82 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <400> 46 atgacgcgtc gaacactcaa acatggaagc acttagcctg gcttagctaa gtgcttccat gtttgagtgt tatgtctaga eg <210> 47 <211> 20 <212> DNA <213>人造序列 <220> <223>化學合成募核苷酸 <4〇〇> 47 gaggagttga gggtactgtg 20 98 201009073 <210> 48 <211> 20 <212> DNA <213> 人造序列 <220> <223>化學合成寡核苷酸 <400> 48 gaggagctga gggcactgtg 20201009073 <400> 44 atgtctagac gcctccactg aaacatgaac gacttacttc tgtttcacac agcaggtacc 60 tccatgttaa agcaaaggta gcgctagcg 89 <210> 45 <211> 82 <212> DNA <213> artificial sequence <220><223> Glycoside <400> 45 cgtctagaca taacactcaa acatggaagc acttagctaa gccaggctaa gtgcttccat gtttgagtgt tcgacgcgtc at <210> 46 <211> 82 <212> DNA <213> artificial sequence <220><223> chemical synthesis nucleoside Acid <400> 46 atgacgcgtc gaacactcaa acatggaagc acttagcctg gcttagctaa gtgcttccat gtttgagtgt tatgtctaga eg <210> 47 <211> 20 <212> DNA <213> artificial sequence <220><223><4〇〇> 47 gaggagttga gggtactgtg 20 98 201009073 <210> 48 <211> 20 <212> DNA <213> Artificial sequence <220><223> Chemical synthesis oligonucleotide <400> 48 gaggagctga gggcactgtg 20
<210> 49 <211> 21 <212〉 DNA <213>人造序列 <220〉 <223>化學合成寡核苷酸 <400> 49 gtagaagtgc ctctgccttc c <210〉 50 <211> 63 <212> DNA <213> 人造序列<210> 49 <211> 21 <212> DNA <213> artificial sequence <220><223> chemical synthesis oligonucleotide <400> 49 gtagaagtgc ctctgccttc c <210> 50 <211> 63 <212> DNA <213> artificial sequence
<220〉 <223>化學合成寡核苷酸 <400〉 50 60 63 ggccagtgaa ttgtaatacg actcactata gggaggcggt tttttttttt tttttttttt ttt 99<220〉 <223>Chemical Synthesis Oligonucleotide <400> 50 60 63 ggccagtgaa ttgtaatacg actcactata gggaggcggt tttttttttt tttttttttt ttt 99
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