The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation.
MicroRNAs (miRNAs) guide posttranscriptional repression of mRNAs. Hundreds of miRNAs have been identified but the target identification of mammalian mRNAs is still a difficult task due to a poor understanding of the interaction between miRNAs and the miRNA recognizing element (MRE). In recent resear...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2008-03-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18320040/?tool=EBI |
| _version_ | 1818980509843193856 |
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| author | Wenbin Ye Qing Lv Chung-Kwun Amy Wong Sean Hu Chao Fu Zhong Hua Guoping Cai Guoxi Li Burton B Yang Yaou Zhang |
| author_facet | Wenbin Ye Qing Lv Chung-Kwun Amy Wong Sean Hu Chao Fu Zhong Hua Guoping Cai Guoxi Li Burton B Yang Yaou Zhang |
| author_sort | Wenbin Ye |
| collection | DOAJ |
| description | MicroRNAs (miRNAs) guide posttranscriptional repression of mRNAs. Hundreds of miRNAs have been identified but the target identification of mammalian mRNAs is still a difficult task due to a poor understanding of the interaction between miRNAs and the miRNA recognizing element (MRE). In recent research, the importance of the 5' end of the miRNA:MRE duplex has been emphasized and the effect of the tail region addressed, but the role of the central loop has largely remained unexplored. Here we examined the effect of the loop region in miRNA:MRE duplexes and found that the location of the central loop is one of the important factors affecting the efficiency of gene regulation mediated by miRNAs. It was further determined that the addition of a loop score combining both location and size as a new criterion for predicting MREs and their cognate miRNAs significantly decreased the false positive rates and increased the specificity of MRE prediction. |
| first_indexed | 2024-12-20T17:16:34Z |
| format | Article |
| id | doaj.art-8c6348d8a48d43a3b6460cb98488eec0 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T17:16:34Z |
| publishDate | 2008-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-8c6348d8a48d43a3b6460cb98488eec02022-12-21T19:31:59ZengPublic Library of Science (PLoS)PLoS ONE1932-62032008-03-0133e171910.1371/journal.pone.0001719The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation.Wenbin YeQing LvChung-Kwun Amy WongSean HuChao FuZhong HuaGuoping CaiGuoxi LiBurton B YangYaou ZhangMicroRNAs (miRNAs) guide posttranscriptional repression of mRNAs. Hundreds of miRNAs have been identified but the target identification of mammalian mRNAs is still a difficult task due to a poor understanding of the interaction between miRNAs and the miRNA recognizing element (MRE). In recent research, the importance of the 5' end of the miRNA:MRE duplex has been emphasized and the effect of the tail region addressed, but the role of the central loop has largely remained unexplored. Here we examined the effect of the loop region in miRNA:MRE duplexes and found that the location of the central loop is one of the important factors affecting the efficiency of gene regulation mediated by miRNAs. It was further determined that the addition of a loop score combining both location and size as a new criterion for predicting MREs and their cognate miRNAs significantly decreased the false positive rates and increased the specificity of MRE prediction.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18320040/?tool=EBI |
| spellingShingle | Wenbin Ye Qing Lv Chung-Kwun Amy Wong Sean Hu Chao Fu Zhong Hua Guoping Cai Guoxi Li Burton B Yang Yaou Zhang The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. PLoS ONE |
| title | The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. |
| title_full | The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. |
| title_fullStr | The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. |
| title_full_unstemmed | The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. |
| title_short | The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. |
| title_sort | effect of central loops in mirna mre duplexes on the efficiency of mirna mediated gene regulation |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18320040/?tool=EBI |
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