Computational identification of piRNA targets on mouse mRNAs

• Published in: Bioinformatics Vol. 32; no. 8; pp. 1170 - 1177
• Main Authors: Yuan, Jiao, Zhang, Peng, Cui, Ya, Wang, Jiajia, Skogerbø, Geir, Huang, Da-Wei, Chen, Runsheng, He, Shunmin
• Format: Journal Article
• Language: English
• Published: England 15.04.2016
• Subjects: Animals; Bioinformatics; Computational Biology - methods; Computer programs; DNA Transposable Elements; Gene expression; Genes; Genomes; Integrity; Mice; Ribonucleic acids; RNA, Messenger; RNA, Small Interfering; Software; Support Vector Machine
• ISSN: 1367-4803; 1367-4811; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btv729

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.