Computational identification of piRNA targets on mouse mRNAs

J Yuan, P Zhang, Y Cui, J Wang, G Skogerbø… - …, 2016 - academic.oup.com
J Yuan, P Zhang, Y Cui, J Wang, G Skogerbø, DW Huang, R Chen, S He
Bioinformatics, 2016academic.oup.com
Abstract Motivation: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs
that are highly abundant in the germline. One important role of piRNAs is to defend genome
integrity by guiding PIWI proteins to silence transposable elements (TEs), which have a high
potential to cause deleterious effects on their host. The mechanism of piRNA-mediated post-
transcriptional silencing was also observed to affect mRNAs, suggesting that piRNAs might
play a broad role in gene expression regulation. However, there has been no systematic …
Abstract
Motivation: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly abundant in the germline. One important role of piRNAs is to defend genome integrity by guiding PIWI proteins to silence transposable elements (TEs), which have a high potential to cause deleterious effects on their host. The mechanism of piRNA-mediated post-transcriptional silencing was also observed to affect mRNAs, suggesting that piRNAs might play a broad role in gene expression regulation. However, there has been no systematic report with regard to how many protein-coding genes might be targeted and regulated by piRNAs.
Results: We trained a support vector machine classifier based on a combination of Miwi CLIP-Seq-derived features and position-derived features to predict the potential targets of piRNAs on mRNAs in the mouse. Reanalysis of a published microarray dataset suggested that the expression level of the 2587 protein-coding genes predicted as piRNA targets showed significant upregulation as a whole after abolishing the slicer activity of Miwi, supporting the conclusion that they are subject to piRNA-mediated regulation.
Availability and implementation: A web version of the method called pirnaPre as well as our results for browse is available at http://www.regulatoryrna.org/software/piRNA/piRNA_target_mRNA/index.php.
Contact:  crs@sun5.ibp.ac.cn or heshunmin@gmail.com
Supplementary information:  Supplementary data are available at Bioinformatics online.
Oxford University Press
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