title: A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements.
abstract: BACKGROUND
  Piwi-interacting RNAs (piRNAs) are a recently discovered class of small non-coding RNAs whose best-understood function is to repress mobile element (ME) activity in animal germline. To date, nearly all piRNA studies have been conducted in model organisms and little is known about piRNA diversity, target specificity and biological function in human.
  
  
  RESULTS
  Here we performed high-throughput sequencing of piRNAs from three human adult testis samples. We found that more than 81% of the ~17 million putative piRNAs mapped to ~6,000 piRNA-producing genomic clusters using a relaxed definition of clusters. A set of human protein-coding genes produces a relatively large amount of putative piRNAs from their 3'UTRs, and are significantly enriched for certain biological processes, suggestive of non-random sampling by the piRNA biogenesis machinery. Up to 16% of putative piRNAs mapped to a few hundred annotated long non-coding RNA (lncRNA) genes, suggesting that some lncRNA genes can act as piRNA precursors. Among major ME families, young families of LTR and endogenous retroviruses have a greater association with putative piRNAs than other MEs. In addition, piRNAs preferentially mapped to specific regions in the consensus sequences of several ME (sub)families and some piRNA mapping peaks showed patterns consistent with the "ping-pong" cycle of piRNA targeting and amplification.
  
  
  CONCLUSIONS
  Overall our data provide a comprehensive analysis and improved annotation of human piRNAs in adult human testes and shed new light into the relationship of piRNAs with protein-coding genes, lncRNAs, and mobile genetic elements in human.
authors: Hongseok
authors: H
authors: Ha
authors: Jimin
authors: J
authors: Song
authors: Shuoguo
authors: S
authors: Wang
authors: Aurélie
authors: A
authors: Kapusta
authors: Cédric
authors: C
authors: Feschotte
authors: Kevin C
authors: KC
authors: Chen
authors: Department of Genetics, The State University of New Jersey, Piscataway, NJ 08854, USA. xing@biology.rutgers.edu.
authors: Jinchuan
authors: J
authors: Xing
mesh_terms: D020413:3' Untranslated Regions; D000328:Adult; D001483:Base Sequence; D002874:Chromosome Mapping; D016384:Consensus Sequence; D063990:Gene Ontology; D006801:Humans; D008297:Male; D005810:Multigene Family; D034622:RNA Interference; D062085:RNA, Long Noncoding; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism*; D018626:Retroelements; D017423:Sequence Analysis, RNA; D013737:Testis / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D062085:RNA, Long Noncoding; D034741:RNA, Small Interfering; D018626:Retroelements