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

Abstract

BackgroundPiwi-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.ResultsHere 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.ConclusionsOverall 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-545) contains supplementary material, which is available to authorized users.

Genetic effects on gene expression across human tissues

“…PiRNAs are strongly expressed in testis and may regulate gene expression and play a role in protection against transposable elements in germ line cells 32 . We tested for enrichment of trans -eVariants in piRNA clusters identified in testis 33 . We found that 38.6% of testis trans -eVariants, corresponding to 12 independent loci ( R 2 ≤ 0.2), directly overlapped piRNA clusters, a significant enrichment compared to the 2.5% of the genome covered by these regions (permutation test, P ≤ 1.0 × 10 −4 ).…”

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

“…Gene-derived piRNAs were studied in Drosophila, Xenopus, mice, pig and primates including human. [56][57][58][59] However, these studies identify protein-coding genes as piRNA targets computationally with little or without any experimental validation. In contrast, with the analysis of our degradome library we provide the first direct biochemical observation of the actual slicing of protein-coding gene transcripts and TEs mediated by piRNAs in a non-bilaterian animal.…”

Two modes of targeting transposable elements by piRNA pathway in human testis

“…Though earlier work established that piRNA pathway features are conserved between humans and other mammals (Aravin et al 2006;Girard et al 2006;Yang et al 2013;Ha et al 2014;Roovers et al 2015;Rosenkranz et al 2015a;Rounge et al 2015;Williams et al 2015), due to ethical and technical limitations, research progress in humans has been slower. Specifically, while all postnatal human piRNAs were previously mapped to piRNA clusters (Ha et al 2014;Roovers et al 2015;Rosenkranz et al 2015a;Williams et al 2015), these clusters were ill-defined in the genome.…”

“…Specifically, while all postnatal human piRNAs were previously mapped to piRNA clusters (Ha et al 2014;Roovers et al 2015;Rosenkranz et al 2015a;Williams et al 2015), these clusters were ill-defined in the genome. Also, no prior study has performed a thorough analysis of TE targeting by the piRNA pathway at different stages of spermatogenesis (i.e., prenatal and postnatal).…”