A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks.
MicroRNAs are small non-coding RNAs that can regulate expressions of their target genes at the post-transcriptional level. In this study, we propose a tri-component strategy that combines the conservation of microRNAs, homology of mRNA coding regions, and conserved microRNA binding sites in the 3�...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4108425?pdf=render |
| _version_ | 1828885466546438144 |
|---|---|
| author | Chen-Ching Lin Ramkrishna Mitra Zhongming Zhao |
| author_facet | Chen-Ching Lin Ramkrishna Mitra Zhongming Zhao |
| author_sort | Chen-Ching Lin |
| collection | DOAJ |
| description | MicroRNAs are small non-coding RNAs that can regulate expressions of their target genes at the post-transcriptional level. In this study, we propose a tri-component strategy that combines the conservation of microRNAs, homology of mRNA coding regions, and conserved microRNA binding sites in the 3' untranslated regions to discover conserved microRNA-mRNA interactions. To validate the performance of our conservation strategy, we collected the experimentally validated microRNA-mRNA interactions from three databases as the golden standard. We found that the proposed strategy can improve the performance of existing target prediction algorithms by approximately 2-4 fold. In addition, we demonstrated that the proposed strategy could efficiently retain highly confident interactions from the intersection results of the existing algorithms and filter out the possible false positive predictions in the union one. Furthermore, this strategy can facilitate our ability to trace the homologues in different species that are targeted by the same miRNA family because it combines these three features to identify the conserved miRNA-mRNA interactions during evolution. Through an extensive application of the proposed conservation strategy to a study of the miR-1/206 regulatory network, we demonstrate that the target mRNA recruiting process could be associated with expansion of miRNA family during its evolution. We also uncovered the functional evolution of the miR-1/206 regulatory network. In this network, the early targeted genes tend to participate in more general and development-related functions. In summary, the conservation strategy is capable of helping to highlight the highly confident miRNA-mRNA interactions and can be further applied to reveal the evolutionary features of miRNA regulatory network and functions. |
| first_indexed | 2024-12-13T11:27:05Z |
| format | Article |
| id | doaj.art-9b8089191d094f4891429f682916a2af |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T11:27:05Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-9b8089191d094f4891429f682916a2af2022-12-21T23:48:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0197e10314210.1371/journal.pone.0103142A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks.Chen-Ching LinRamkrishna MitraZhongming ZhaoMicroRNAs are small non-coding RNAs that can regulate expressions of their target genes at the post-transcriptional level. In this study, we propose a tri-component strategy that combines the conservation of microRNAs, homology of mRNA coding regions, and conserved microRNA binding sites in the 3' untranslated regions to discover conserved microRNA-mRNA interactions. To validate the performance of our conservation strategy, we collected the experimentally validated microRNA-mRNA interactions from three databases as the golden standard. We found that the proposed strategy can improve the performance of existing target prediction algorithms by approximately 2-4 fold. In addition, we demonstrated that the proposed strategy could efficiently retain highly confident interactions from the intersection results of the existing algorithms and filter out the possible false positive predictions in the union one. Furthermore, this strategy can facilitate our ability to trace the homologues in different species that are targeted by the same miRNA family because it combines these three features to identify the conserved miRNA-mRNA interactions during evolution. Through an extensive application of the proposed conservation strategy to a study of the miR-1/206 regulatory network, we demonstrate that the target mRNA recruiting process could be associated with expansion of miRNA family during its evolution. We also uncovered the functional evolution of the miR-1/206 regulatory network. In this network, the early targeted genes tend to participate in more general and development-related functions. In summary, the conservation strategy is capable of helping to highlight the highly confident miRNA-mRNA interactions and can be further applied to reveal the evolutionary features of miRNA regulatory network and functions.http://europepmc.org/articles/PMC4108425?pdf=render |
| spellingShingle | Chen-Ching Lin Ramkrishna Mitra Zhongming Zhao A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. PLoS ONE |
| title | A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. |
| title_full | A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. |
| title_fullStr | A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. |
| title_full_unstemmed | A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. |
| title_short | A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. |
| title_sort | tri component conservation strategy reveals highly confident microrna mrna interactions and evolution of microrna regulatory networks |
| url | http://europepmc.org/articles/PMC4108425?pdf=render |
| work_keys_str_mv | AT chenchinglin atricomponentconservationstrategyrevealshighlyconfidentmicrornamrnainteractionsandevolutionofmicrornaregulatorynetworks AT ramkrishnamitra atricomponentconservationstrategyrevealshighlyconfidentmicrornamrnainteractionsandevolutionofmicrornaregulatorynetworks AT zhongmingzhao atricomponentconservationstrategyrevealshighlyconfidentmicrornamrnainteractionsandevolutionofmicrornaregulatorynetworks AT chenchinglin tricomponentconservationstrategyrevealshighlyconfidentmicrornamrnainteractionsandevolutionofmicrornaregulatorynetworks AT ramkrishnamitra tricomponentconservationstrategyrevealshighlyconfidentmicrornamrnainteractionsandevolutionofmicrornaregulatorynetworks AT zhongmingzhao tricomponentconservationstrategyrevealshighlyconfidentmicrornamrnainteractionsandevolutionofmicrornaregulatorynetworks |