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Open Access Highly Accessed Research article

A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements

Hongseok Ha12, Jimin Song13, Shuoguo Wang12, Aurélie Kapusta4, Cédric Feschotte4, Kevin C Chen13 and Jinchuan Xing12*

Author Affiliations

1 Department of Genetics, The State University of New Jersey, Piscataway, NJ 08854, USA

2 Department of Genetics, Human Genetic Institute of New Jersey, The State University of New Jersey, Piscataway, NJ 08854, USA

3 BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA

4 Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA

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BMC Genomics 2014, 15:545  doi:10.1186/1471-2164-15-545

Published: 1 July 2014

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.

Keywords:
Human piRNA; piRNA cluster; Protein coding gene; Mobile element; High-throughput sequencing