JP4371812B2 - マイクロrna分子 - Google Patents
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Description
(a)第1表、第2表、第3表又は第4表に示されているようなヌクレオチド配列、
(b)(a)の補体であるヌクレオチド配列、
(c)(a)又は(b)の配列に対して少なくとも80%、有利には少なくとも90%及びより有利には少なくとも99%のアイデンティティを有するヌクレオチド配列及び/又は
(d)ストリンジェント条件下に、(a)、(b)及び/又は(c)の配列にハイブリダイズするヌクレオチド配列
を有する単離された核酸分子に関する。
I=n:L
[ここで、Iはアイデンティティ(%)であり、nは所定の配列と第1表、第2表、第3表又は第4表に示されているような比較配列との間の同じヌクレオチドの数であり、Lは比較配列の長さである]。第1、2、3及び4表に描かれているようなヌクレオチドA、C、G及びUは、リボヌクレオチド、デオキシリボヌクレオチド及び/又は他のヌクレオチド類似体、即ち合成の非天然由来のヌクレオチド類似体を意味することができる。更に、ヌクレオ塩基は、相補的核酸配列への類似H−結合を形成することのできる相応するヌクレオ塩基により置換されることができ、例えば、UはTで置換されていてよい。
図1A.キイロショウジョウバエ(D.melanogaster)miRNAの発現。キイロショウジョウバエの段階集団から単離された全てのRNAのノーザンブロットを、指示miRNAのプローブとした。このブロット上に76−nt val−tRNAの位置も指示されている。5SrRNAは、ローデイングコントロールとしての役目をする。Eは胚;Lは幼虫段階;Pは蛹;Aは成虫;S2はシュナイダー−2細胞。S2細胞はポリクローナルであり、胚組織の未知のサブセットから誘導されており、培養液中に保持されている間のオリジンのそれらの組織の失われたいくつかの特徴も有しうることが指摘されるべきである。miR−3〜miR−6RNAは、S2細胞中に検出不可能であった(データが示されていない)。miR−14はノーザンブロッティングで検出されず、おそらく非常に弱く発現されており、これはそのクローニング頻度と一致した。類似のmiRNA配列は、プローブの潜在的クロス−ハイブリダイゼーシヨンの故に、ノーザンブロッティングで区別するのが困難である。
本発明者は、以前に、キイロショウジョウバエ(Drosophila melanogaster)胚リゼート中での長いdsRNAのプロセッシングの後のsiRNAを単離するために、方向性クローニング法を開発した(8)。簡単にいえば、5’及び3’アダプター分子をサイズ−分別されたRNA集団の末端にライゲートさせ、引き続き、逆転写、PCR増幅、コンカテマー化、クローニング及びシークエンシングを行った。元来siRNAを単離するために意図されたこの方法は、14の新規20−〜23−ntの短かいRNA(これらはキイロショウジョウバエゲノムでコードされ、かつ0〜2h胚中に発現されている)の同時同定をもたらした(第1表)。この方法は、HeLa細胞全RNAからの類似サイズ範囲内のクローンRNAに適応され、これは19の新規ヒトstRNAの同定をもたらし(第2表)、従って、更に、潜在的調節役割を有する小さいRNAの大クラスの存在の証拠を提供していた。それらの小さいサイズに従って、これらの新規RNAをマイクロRNA又はmiRNAと称する。これらのmiRNAは、miR−1〜miR−33と略記され、この遺伝子をコードしているmiRNAは、mir−1〜mir−33と名付けられている。高い相同性のmiRNAが、小文字の付加、引き続くダッシュ及びmir遺伝子のマルチプルゲノミックコピーを指名する番号により分類されている。
哺乳動物中のmiRNAの分布及び機能へのより詳細な洞察を得るために、成熟マウスでのmiRNAの組織−特異的分布を調査した。通常はノーザンブロット分析で検出されない低量miRNAはクローン的に同定されるので、特異組織からのmiRNAのクローニングを、全体の生物−ベースクローニングに渡って実施した。21−ntRNAを検出するためのin situ ハイブリダイゼーシヨン法は、未だ開発されてもいない。従って、18.5週齢BL6マウスから単離された全RNAから19−〜25−ヌクレオチドRNAをクローニングし、かつシークエンシングした。miRNAのクローニングを次のように実施した:全RNAの0.2〜1mgを15%変性ポリアクリルアミドゲル上で分離し、19−〜25−ntサイズのRNAを回収した。5’−リン酸化された3’−アダプターオリゴヌクレオチド(5’−pUUUaaccgcgaattccagx:大文字はRNA;小文字はDNA;pはホスフェート;xは3’−アミノ−モディファイアーC−7、ChemGenes,Ashland,Ma,USA,Cat.No.NSS−1004;SEQ ID NO:54)及び5’−アダプターオリゴヌクレオチド(5’−acggaattcctcactAAA:大文字はRNA;小文字はDNA;SEQ ID NO:55)を短かいRNAにライゲートさせた。RT/PCRを、3’−プライマー(5’−GACTAGCTGGAATTCGCGGTTAAA;SEQ ID NO:56)及び5’−プライマー(5’−CAGCCAACGGAATTCCTCACTAAA;SEQ ID NO:57)を用いて実施した。BanI制限部位を導入するために、プライマー対5’−CAGCCAACAGGCACCGAATTCCTCACTAAA(SEQ ID NO:57)及び5’−GACTAGCTTGGTGCCGAATTCGCGGTTAAA(SEQ ID NO:56)を用いて第2PCRを実施し、引き続きBan I消化の後のコンカテマー化及びT4DNAライゲーションを行った。400〜600塩基対のコンカテマーを、1.5%アガロースゲルから切出し、バイオトラップ(Schleicher & Schuell)電気溶出(1×TAEバッファ)及びエタノール沈殿により回収した。引き続き、このコンカテマーの3’末端を、72℃で、Taqポリメラーゼと一緒の15分間インキュベーシヨンにより、充填した。この溶液を水で3倍に希釈し、直接、pCR2.1 TOPOベクター中へのライゲーションのために使用した。クローンをPCRでの挿入のためにスクリーニングし、30〜50試料をシークエンシングに供した。RNAが数匹のマウスの結合組織から製造されたので、多クローン中で複数回検出された微量配列変異は、RT/PCR突然変異よりもむしろ多型を反映しているらしい。約21−ntのRNAをコードするゲノム配列の同定のためにパブリックデータベースサ−チングを使用した。隣接上流又は下流フランキング配列を包含する20〜30塩基対フォールド−バック構造の発生が、miRNAを指定するために用いられた[36−38]。
キイロショウジョウバエmiRNA。与えられている配列は、クローニングにより同定された最も豊富で、かつ典型的な最長のmiRNA配列を表し;miRNAは、屡々その3’末端で1又は2個のヌクレオチドの長さで変動する。シークエンシングされた222の短かいRNAのうち、69(31%)はmiRNAに、103(46%)は既にキャラクテライズされた機能的RNA(rRNA、7SLRNA、tRNA)に、30(14%)はトランスポゾンRNAフラグメントに、かつ20(10%)はデータベース登録のない配列に相当した。全ての同定されたmiRNAに関連している特別なmiRNAをクローニングの頻度(freq)が、パーセントで示されている。キイロショウジョウバエの段階集団から単離された全RNAのノーザンブロッティングの結果がまとめられている。Eは胚;Lは幼虫段階;Pは蛹;Aは成虫:S2はSchneider−2細胞。各ブロットのシグナルの強さは、最強(+++)〜非検出(−)で表されている。対照としてlet−7stRNAを検査した。他の種中でのデータベースサーチングにより同定された遺伝子バンクアクセッシヨン番号及びmiRNAの相同体が補助的マテリアルとして提供されている。
ヒトmiRNA。シークエンシングされた220の短かいRNAのうち、100(45%)はmiRNAに、53(24%)は既にキャラクテライズされた機能的RNA(rRNA、snRNA、tRNA)に、かつ67(30%)はデータベース登録のない配列に相当した。異なる脊椎動物種及びS2から単離された全RNAのノーザンブロッティングの結果が示されている。説明に関しては第1表を参照。
マウスmiRNA。指示されている配列は、クローニングにより同定された最長のmiRNA配列を表す。miRNAの3’−末端は、屡々1又は2個のヌクレオチドで先端切断されている。85%(即ち、21ヌクレオチドの18を占める)より多くが配列において同じであるか又は1−又は2−ヌクレオチド内部欠失を有するmiRNAは、同じ遺伝子番号、引き続く小文字で記載されている。関連miRNAの間の微量配列変異は、一般にmiRNA配列の末端近くに見出され、ターゲットRNA認識を害しないと考えられている。微量配列変異は、ターゲット認識の間にG−Uゆらぎ塩基対として適応されるAからGへ及びCからUへの変化をも表すことができる。末尾の−s又は−asを有するmiRNAは、miRNA前駆体の5’−ハーフ又は3’−ハーフのいずれかから誘導されたRNAを示している。マウス脳を中脳mb、皮質cx、小脳cb中まで解剖した。分析された組織は、心臓ht;肝臓lv;小腸si;結腸co;皮質ct;小脳cb;中脳mbであった。
マウス及びヒトmiRNA。指示されている配列は、クローニングにより同定された最長のmiRNA配列を表している。miRNAの3’末端は、屡々1又は2個のヌクレオチドで先端切断されている。85%(即ち21ヌクレオチドの18を占める)より多くが配列において同じであるか、又は1−又は2−ヌクレオチド内部欠失を有するmiRNAが、同じ遺伝子番号、引き続く小文字で記載されている。関連miRNAの間の微量配列変異は、一般にmiRNA配列の末端近くに見出され、ターゲットRNA認識を害しないと考えられている。微量配列変異は、ターゲット認識の間のG−Uゆらぎ塩基対として適応されるAからG及びCからUへの変化をも表すこともできる。マウス脳を中脳mb;皮質cx;小脳cb中まで解剖した。分析された組織は、肺ln;肝臓lv;脾臓sp;腎臓kd;皮膚sk;精巣ts;卵巣ov;胸腺thy;眼ey;皮質ct;小脳cb;中脳mbであった。ヒト骨肉腫細胞SAOS−2細胞は、誘導可能なp53遺伝子(p53−は誘導されていないp53;p53+は誘導されたp53)を含有し、誘導された及び誘導されていないSAOS細胞から同定されたmiRNA中の差異は、統計的に有意ではなかった。
キイロショウジョウバエmiRNA配列及びゲノム位置。挙げられている配列は、クローニングにより同定された最も豊富でかつ典型的な最長のmiRNA配列を表している。miRNAsは、それらの3’−末端で1又は2個のヌクレオチドの長さで変動することが屡々観察された。シークエンシングされた222の短かいRNAのうち、69(31%)はmiRNAに、103(14%)は既にキャラクテライズされた機能的RNA(rRNA、7SLRNA、tRNA)に、30(14%)はトランスポゾンRNAフラグメントに、かつ20(10%)はデータベース登録のない配列に相当していた。5’−グアノシンを有するRNA配列は、クローニング操作の故に、おそらく他より少ない(8)。他の種中に見出されたmiRNA相同体が指示されている。染色体位置(chr)及び遺伝子バンクアクセッシヨン番号(acc.nb.)が示されている。データベースサーチングによってESTマッチングmiR−1〜miR−4は検出不能であった。
ヒトmiRNA配列及びゲノム位置。シークエンシングされた220の短かいRNAのうち、100(45%)はmiRNAsに、53(24%)は既にキャラクテライズされた機能的RNA(rRNA、snRNA、tRNA)に、かつ67(39%)はデータベース登録のない配列に相当した。
Claims (11)
- (a)配列番号145、配列番号146または147から成るヌクレオチド配列、
(b)(a)の相補体であるヌクレオチド配列、又は
(c)(a)又は(b)の配列に対して少なくとも90%のアイデンティティを有する、肝臓細胞又は組織を特定するマーカーとして使用される、ヌクレオチド配列
を有する単離された核酸分子。 - 配列(c)のアイデンティティが少なくとも95%である、請求項1に記載の核酸分子。
- 18〜25ヌクレオチドの長さを有するmiRNA分子である、請求項1又は2に記載の核酸分子。
- 60〜80ヌクレオチドの長さを有するmiRNA前駆体分子又はそれをコードするDNA分子である、請求項1又は2に記載の核酸分子を含む核酸分子。
- 一本鎖である、請求項1から4までのいずれか1項に記載の核酸分子。
- 少なくとも部分的に二本鎖である、請求項1から4までのいずれか1項に記載の核酸分子。
- RNA、DNA又は核酸類似体分子から選択されている、請求項1から6までのいずれか1項に記載の核酸分子。
- 少なくとも1個の修飾ヌクレオチド類似体を含有する分子である、請求項7に記載の核酸分子。
- 組み換え発現ベクターである、請求項7に記載の核酸分子。
- (a)配列番号145、配列番号146または147から成るヌクレオチド配列、又は
(b)(a)の相補体であるヌクレオチド配列、
を有し、少なくとも1個の修飾ヌクレオチド類似体を含有する、単離された核酸分子。 - サイズ−分別されたRNA集団の末端への5’−及び3’−アダプター分子のライゲーション、このライゲーションにより得られたアダプター含有RNA集団の逆転写及びこの逆転写産生物のキャラクテライゼーションからなる、請求項1から10までのいずれか1項に記載の核酸分子を同定する方法。
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