CN102321735A - Method for searching target gene of reverse miRNA - Google Patents
Method for searching target gene of reverse miRNA Download PDFInfo
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- CN102321735A CN102321735A CN201010561628A CN201010561628A CN102321735A CN 102321735 A CN102321735 A CN 102321735A CN 201010561628 A CN201010561628 A CN 201010561628A CN 201010561628 A CN201010561628 A CN 201010561628A CN 102321735 A CN102321735 A CN 102321735A
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Abstract
The invention designs a method for searching the target gene of reverse miRNA, which obtains the target gene of the given miRNA by analyzing the miRNA. The method mainly includes the following steps: step 1, data information analysis; step 2, 3'-UTR sequence obtainment; step 3, miRNA sequence extraction; and step 4, target gene prediction.
Description
Technical field
The invention belongs to biological technical field, the target gene that relates to reverse miRNA is searched the aspect.
Background technology
MiRNA or be called MicroRNA, promptly miRNA is non-coding single stranded RNA (Yeast Nucleic Acid) molecule that one type of length by the native gene coding is about 22 Nucleotide, wide expression in animal and plant.The size of miRNA is about 21-23 base; The miRNA that has been differentiated is generated through Dicer (rnase iii a kind of) enzyme processing back by the single stranded RNA precursor of about 70-90 base size with hairpin structure; 5 ' phosphate and 3 ' hydroxyl are arranged; Be positioned the 3 ' end or the 5 ' end of RNA precursor, extensively be present in the higher organism cell.The function that therefore has the transcription product that destroys the target specific gene or induce translation to suppress, miRNA is considered in the regulation and control growth course, play an important role
The mechanism of action of miRNA is different from general mRNA (messenger RNA(mRNA)) degradation mechanism.Sophisticated miRNA is directed in the silencing complex (RISC), and the miRNA of strand not exclusively complementary mode is attached on the mRNA binding site that target gene transcribes, through the complementary pairing of base, and the translation of arrestin matter, thereby regulate target gene expression.The miRNA binding site of this mechanism is usually in 3 ' the end non-coding region section of mRNA, promptly 3 '-the UTR section.
MiRNA is as a kind of molecule of participating in regulate gene expression; Extensively act in Eukaryotic physiology, the biochemical action process, these miRNAs are attached to the transcription product of target gene usually through the mode with base complementrity---on the particular section of mRNA; Inhibition or promotion mRNA translate into peptide chain; Thereby influence the accurate translation of target gene, realize regulating the growth of cell, the effect of vital processes such as tissue differentiation.Thereby; The research of miRNA target gene is very important, and at present, investigators have developed various miRNA target gene analysis software based on the information biology method of calculation; Through importing specific miRNA and the gene database of having confirmed the species scopes, find out the target gene of this miRNA more accurately.
The present invention has designed a kind of analytical procedure, with the miRNA sequence that miRNA converts reverse complemental to, in the mRNA of genetic transcription arrangement set, carries out the comparison of miRNA target gene and searches, to dope the target gene of this miRNA.
Summary of the invention
A kind of method of searching reverse miRNA target gene of the present invention's design through given miRNA is analyzed, draws the target gene of this miRNA, and it comprises following several steps:
Step 1, data message analysis.
Step 2, obtain 3 '-the UTR sequence.
Step 3, extraction miRNA sequence.
Step 3, prediction target gene.
Present method can be set interested direction or scope to the prediction of miRNA target gene, therefrom dopes useful miRNA target gene result.
Description of drawings
Fig. 1, a kind of implementing procedure figure that searches the method for reverse miRNA target gene of the present invention.
Embodiment
The concrete mode of below implementing for present method:
Step 1, the preparatory information analysis of data.Before analyzing,, confirm to search the scope that the miRNA of target gene and miRNA target gene that institute needs are searched according to the required purpose that reaches of practical study.
Step 2, obtain 3 '-the UTR sequence.Confirm after the gene scope all genes to be listed as into table, the corresponding mRNA sequence of inquiry is listed as into table in ncbi database (http://www.ncbi.nlm.nih.gov/).Utilize Perl Programming with Pascal Language handling procedure then, extract 3 of all gene mRNAs '-the UTR sequence is as arrangement set.
Step 3, extraction miRNA sequence.Download interested miRNA sequence from miRBase Release 16:Sept 2010 (http://www.mirbase.org/), extract second sequence,, be used for the comparison inquiry as the kind subsequence of miRNA to the 8th bit base.
Step 4, prediction target gene.Use TargetScan 5.1 (http://www.targetscan.org/) software, with 3 in the step 2 '-UTR sequence sets and step 3 in miRNA kind subsequence as input, the inquiry of comparing.TargetScan can convert miRNA kind subsequence to reverse complementary sequence, with 3 '-the UTR sequence sets in sequence compare, find out the said target mrna sequence of complete matched sequence as kind of subsequence, its corresponding gene is the target gene of this miRNA.
Utilize present method, also can obtain the information such as binding site of miRNA and target gene.
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.
Claims (1)
1. a kind of method of searching reverse miRNA target gene of the present invention, it comprises following a few step principal character:
Step 1, data message analysis.
Step 2, obtain 3 '-the UTR sequence.
Step 3, extraction miRNA sequence.
Step 3, prediction target gene.
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| CN201010561628A CN102321735A (en) | 2010-11-25 | 2010-11-25 | Method for searching target gene of reverse miRNA |
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| CN201010561628A CN102321735A (en) | 2010-11-25 | 2010-11-25 | Method for searching target gene of reverse miRNA |
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Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102643898A (en) * | 2012-02-13 | 2012-08-22 | 内蒙古农业大学 | Method for detecting micro target gene of RNA (Ribose Nucleic Acid) in goat tissue or organ by using seed sequence |
| CN103194441A (en) * | 2013-04-17 | 2013-07-10 | 新疆农垦科学院 | Method for obtaining miRNA (Ribose Nucleic Acid) candidate target gene and special reverse transcription primer for method |
| CN105701365A (en) * | 2016-01-12 | 2016-06-22 | 西安电子科技大学 | Cancer-related genes finding method by using miRNA expression data |
| CN110164505A (en) * | 2018-02-07 | 2019-08-23 | 深圳华大基因科技服务有限公司 | A kind of method of the target gene of quick predict target miRNA |
-
2010
- 2010-11-25 CN CN201010561628A patent/CN102321735A/en active Pending
Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102643898A (en) * | 2012-02-13 | 2012-08-22 | 内蒙古农业大学 | Method for detecting micro target gene of RNA (Ribose Nucleic Acid) in goat tissue or organ by using seed sequence |
| CN102643898B (en) * | 2012-02-13 | 2013-11-06 | 内蒙古农业大学 | Method for detecting micro target gene of RNA (Ribose Nucleic Acid) in goat tissue or organ by using seed sequence |
| CN103194441A (en) * | 2013-04-17 | 2013-07-10 | 新疆农垦科学院 | Method for obtaining miRNA (Ribose Nucleic Acid) candidate target gene and special reverse transcription primer for method |
| CN103194441B (en) * | 2013-04-17 | 2014-08-27 | 新疆农垦科学院 | Method for obtaining miRNA (Ribose Nucleic Acid) candidate target gene and special reverse transcription primer for method |
| CN105701365A (en) * | 2016-01-12 | 2016-06-22 | 西安电子科技大学 | Cancer-related genes finding method by using miRNA expression data |
| CN105701365B (en) * | 2016-01-12 | 2018-09-07 | 西安电子科技大学 | It was found that the method and related system of cancer related gene, process for preparing medicine |
| CN110164505A (en) * | 2018-02-07 | 2019-08-23 | 深圳华大基因科技服务有限公司 | A kind of method of the target gene of quick predict target miRNA |
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Application publication date: 20120118 |