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

Hongseok Ha, Jimin Song, Shuoguo Wang, Aurélie Kapusta, Cédric Feschotte, Kevin Chen, Jinchuan Xing

Research output: Contribution to journalArticle

64 Citations (Scopus)

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.

Original languageEnglish (US)
Article number545
JournalBMC genomics
Volume15
Issue number1
DOIs
StatePublished - Jul 1 2014

Fingerprint

Small Interfering RNA
Testis
Genes
Long Noncoding RNA
Interspersed Repetitive Sequences
Endogenous Retroviruses
Biological Phenomena
Small Untranslated RNA
Consensus Sequence
3' Untranslated Regions
Proteins

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Keywords

  • High-throughput sequencing
  • Human piRNA
  • Mobile element
  • PiRNA cluster
  • Protein coding gene

Cite this

Ha, Hongseok ; Song, Jimin ; Wang, Shuoguo ; Kapusta, Aurélie ; Feschotte, Cédric ; Chen, Kevin ; Xing, Jinchuan. / A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. In: BMC genomics. 2014 ; Vol. 15, No. 1.
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A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. / Ha, Hongseok; Song, Jimin; Wang, Shuoguo; Kapusta, Aurélie; Feschotte, Cédric; Chen, Kevin; Xing, Jinchuan.

In: BMC genomics, Vol. 15, No. 1, 545, 01.07.2014.

Research output: Contribution to journalArticle

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T1 - A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements

AU - Ha, Hongseok

AU - Song, Jimin

AU - Wang, Shuoguo

AU - Kapusta, Aurélie

AU - Feschotte, Cédric

AU - Chen, Kevin

AU - Xing, Jinchuan

PY - 2014/7/1

Y1 - 2014/7/1

N2 - 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.

AB - 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.

KW - High-throughput sequencing

KW - Human piRNA

KW - Mobile element

KW - PiRNA cluster

KW - Protein coding gene

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