title: Computational identification of piRNA targets on mouse mRNAs.
abstract: 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.
  
  
  
  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.
  
  
  
  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
  
  
  
  crs@sun5.ibp.ac.cn or heshunmin@gmail.com
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Yuan
authors.affiliation: Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.affiliation: CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Ya
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and.
authors.forename: Jiajia
authors.initials: J
authors.lastname: Wang
authors.affiliation: CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.affiliation: Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and.
authors.forename: Da-Wei
authors.initials: DW
authors.lastname: Huang
authors.affiliation: CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.affiliation: Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and.
authors.forename: Shunmin
authors.initials: S
authors.lastname: He
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements; D051379:Mice; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D060388:Support Vector Machine
chemical_list: D004251:DNA Transposable Elements; D012333:RNA, Messenger; D034741:RNA, Small Interfering