CN102485904A - A method for predicting mammalian microRNA genes - Google Patents
A method for predicting mammalian microRNA genes Download PDFInfo
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- CN102485904A CN102485904A CN2010105720528A CN201010572052A CN102485904A CN 102485904 A CN102485904 A CN 102485904A CN 2010105720528 A CN2010105720528 A CN 2010105720528A CN 201010572052 A CN201010572052 A CN 201010572052A CN 102485904 A CN102485904 A CN 102485904A
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- 108700011259 MicroRNAs Proteins 0.000 title claims abstract description 58
- 239000002679 microRNA Substances 0.000 title claims abstract description 56
- 108090000623 proteins and genes Proteins 0.000 title claims abstract description 22
- 238000000034 method Methods 0.000 title abstract description 11
- 239000002243 precursor Substances 0.000 claims abstract description 21
- 229920002477 rna polymer Polymers 0.000 claims abstract 4
- 108091007426 microRNA precursor Proteins 0.000 claims abstract 3
- 238000003766 bioinformatics method Methods 0.000 claims description 3
- 238000003757 reverse transcription PCR Methods 0.000 claims 2
- 125000003367 polycyclic group Chemical group 0.000 claims 1
- 241000124008 Mammalia Species 0.000 abstract description 6
- 241000894007 species Species 0.000 abstract description 4
- 238000002474 experimental method Methods 0.000 abstract description 3
- 238000012216 screening Methods 0.000 abstract description 3
- 238000010200 validation analysis Methods 0.000 abstract 1
- 238000012795 verification Methods 0.000 abstract 1
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- 108020004999 messenger RNA Proteins 0.000 description 5
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- 108091070501 miRNA Proteins 0.000 description 2
- 238000003752 polymerase chain reaction Methods 0.000 description 2
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- 230000035897 transcription Effects 0.000 description 2
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- 240000004808 Saccharomyces cerevisiae Species 0.000 description 1
- 230000006907 apoptotic process Effects 0.000 description 1
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- 230000030279 gene silencing Effects 0.000 description 1
- 108091053410 let-7 family Proteins 0.000 description 1
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Abstract
本发明根据哺乳动物微小核糖核酸(microRNA)前体序列具有高度跨物种保守性的特点，从已知的微小核糖核酸序列出发，找到了一种可行的基于同源预测的微小核糖核酸基因鉴定的生物信息学方法，可直接针对微小核糖核酸基因进行锁定，以便于进一步的生物学实验验证。本发明主要包括如下流程：步骤1：获取已知哺乳动物的微小核糖核酸前体发卡环序列；步骤2：获得未知物种的基因组序列；步骤3：利用局部比对，从基因组内寻找微小核糖核酸的同源序列；步骤4：根据一定的标准筛选潜在的前体序列；步骤5：利用核糖核酸(RNA)二级结构折叠软件生成二级结构；步骤6：计算二级结构自由能，筛选合格微小核糖核酸前体；步骤7：预测微小核糖核酸成熟体。最终，对于感兴趣的微小核糖核酸，可以直接进行实验验证。
According to the characteristic that the precursor sequence of mammalian microRNA (microRNA) has high cross-species conservation, starting from the known microRNA sequence, the present invention finds a feasible identification method of microRNA gene based on homology prediction The method of bioinformatics can directly target microRNA genes to facilitate further biological experiment verification. The present invention mainly includes the following process: Step 1: Obtain the hairpin loop sequence of the microRNA precursor of a known mammal; Step 2: Obtain the genome sequence of an unknown species; Step 3: Use local alignment to search for microRNA from the genome homologous sequence; step 4: screen potential precursor sequences according to certain criteria; step 5: use ribonucleic acid (RNA) secondary structure folding software to generate secondary structure; step 6: calculate secondary structure free energy, and pass the screening MicroRNA precursor; Step 7: Predict mature microRNA. Ultimately, experimental validation can be directly performed for microRNAs of interest.
Description
Technical field
The invention belongs to biological technical field, relate to miRNA (microRNA) predictive genes aspect.
Background technology
The present invention is a kind of Mammals miRNA method for forecasting gene.Be applicable to the biomedical research or the fundamental biological knowledge research of miRNA.
MiRNA originates from the endogenous expression transcript, is the singlestranded RNA that is about 21～24 Nucleotide, and its characteristic feature is that precursor has hairpin structure.The miRNA approach starts from the initial transcript of a miRNA gene.The hair fastener ring of these 70～100 Nucleotide is finally become precursor by the rnase processing treatment in nuclear.Gone into kytoplasm by nuclear output protein transport afterwards, then in kytoplasm, be processed as the ripe body miRNA of 21～24 Nucleotide by second rnase.The miRNA in this stage can combine silencing complex.It can suppress the translation of its messenger RNA(mRNA) (mRNA) through combining with target gene 3 ' end non-translational region identification, or degraded target messenger RNA(mRNA).MiRNA plays important regulation in the expression of post-transcriptional level regulatory gene and in processes such as the propagation of cell, differentiation, apoptosis.
Research at present thinks that miRNA has the conservative property (generally having only the difference of 1～2 base) of height in the mammalian genes group.What have conservative property most is let-7 family, and it extensively is present in the monosymmetric organism, and its sequence is conservative property very.The conservative property of miRNA has important biological significance, and prompting is in different biological development processes, and miRNA has identical regulatory mechanism, also for biological early stage evolution homology certain foundation is provided simultaneously.Utilize the characteristics of high conservative property can from the genome of the unknown, dope the miRNA gene.
Summary of the invention
The present invention has the advantages that highly stride the species conservative property according to Mammals miRNA (microRNA) precursor sequence; From known miRNA sequence; Found a kind of bioinformatics method of feasible miRNA gene identification based on the homology prediction; Can directly lock, so that further biological experiment checking to the miRNA gene.Implementation step is following:
Step 1: obtain known mammiferous miRNA precursor hair fastener ring sequence.
Step 2: the genome sequence that obtains species to be predicted.
Step 3: utilize local comparison, seek the homologous sequence of miRNA in the genome.
Step 4: according to certain standard screening potential precursor sequence.Concrete standard: 1) comparison length is greater than 95%, and base unanimity degree is greater than 80%; 2) precursor meets the hair fastener ring structure, and stem's length is greater than 15 bases, and there are not many ring phenomenons in ring portion; 3) there is not mutating alkali yl in ripe body position.
Step 5: utilize the folding software of Yeast Nucleic Acid (RNA) secondary structure to generate secondary structure.
Step 6: calculate the secondary structure free energy, screen qualified miRNA precursor.
Step 7: the ripe body sequence of prediction miRNA.
Step 8: final, for interested miRNA, checking can directly experimentize.
The present invention has the advantages that highly stride the species conservative property according to Mammals miRNA (microRNA) precursor sequence; From known miRNA sequence; Found a kind of bioinformatics method of feasible miRNA gene identification based on the homology prediction; Can directly lock, so that further biological experiment checking to the miRNA gene.
Aspect novelty, it is characterized in that: our method utilizes the miRNA precursor sequence in the conservative characteristics of Mammals camber, utilizes the method prediction miRNA gene of homology comparison.It is more reliable to predict the outcome, and helps in full genome range, excavating the miRNA gene.
Description of drawings
Fig. 1: basic flow sheet of the present invention
Fig. 2: the precursor secondary structure of miRNA and the instance that predicts the outcome of ripe body sequence.
Fig. 3: the result who utilizes RT-PCR (inverse transcription polymerase chain reaction) technology that the miRNA gene of prediction is verified
Embodiment:
Be instance with primate-monkey below, do further explanation.
Step 1: obtain known mammiferous all miRNA precursor hair fastener ring sequences from NCBi (www.ncbi.nlm.nih.gov/) website.
Step 2: the genome sequence that obtains monkey from NCBi (www.ncbi.nlm.nih.gov/) website.
Step 3: utilize local comparison software Blastn (http://blast.ncbi.nlm.nih.gov/), seek the homologous sequence of miRNA in the genome.
Step 4: according to certain standard screening potential precursor sequence.Concrete standard: 1) comparison length is greater than 95%, and base unanimity degree is greater than 80%; 2) precursor meets the hair fastener ring structure, and stem's length is greater than 15 bases, and there are not many ring phenomenons in ring portion; 3) there is not mutating alkali yl in ripe body position.
Step 5: utilize RNAfold (http://www.tbi.univie.ac.at/RNA/) software to carry out preceding folded body, analyze the secondary structure of precursor.
Step 6: utilize RNAeval (http://www.tbi.univie.ac.at/RNA/) to calculate the secondary structure free energy, screen qualified miRNA precursor.
Step 7: the ripe body sequence of prediction miRNA.Figure of description 2 is seen in predicting the outcome of the precursor secondary structure of one of them miRNA and ripe body sequence.
Step 8: final, for interested miRNA, utilize RT-PCR (inverse transcription polymerase chain reaction) technology that the miRNA gene of prediction is verified.The checking result sees accompanying drawing 3, and the result shows that the miRNA gene of the method prediction that utilizes us is accurately and reliably
More than be the description of this invention and non-limiting, based on other embodiment of inventive concept, all among protection scope of the present invention.
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| CN201010572052.8A CN102485904B (en) | 2010-12-03 | 2010-12-03 | Method of mammal micro RNA gene prediction |
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN106460041A (en) * | 2014-03-25 | 2017-02-22 | 亚利桑那州立大学董事会 | Detection of high variability regions between protein sequence sets representing a binary phenotype |
| CN106755378A (en) * | 2016-12-13 | 2017-05-31 | 北京林业大学 | A kind of method in detection miRNA sources |
-
2010
- 2010-12-03 CN CN201010572052.8A patent/CN102485904B/en not_active Expired - Fee Related
Non-Patent Citations (2)
| Title |
|---|
| 张志明等: "用生物信息学挖掘玉米中的microRNAs及其靶基因", 《作物学报》 * |
| 盛熙晖: "应用文库构建法和生物信息学方法鉴定绵羊microRNA", 《中国博士学位论文全文数据库》 * |
Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN106460041A (en) * | 2014-03-25 | 2017-02-22 | 亚利桑那州立大学董事会 | Detection of high variability regions between protein sequence sets representing a binary phenotype |
| CN106755378A (en) * | 2016-12-13 | 2017-05-31 | 北京林业大学 | A kind of method in detection miRNA sources |
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