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.
Highlights
Piwi-interacting RNAs are a recently discovered class of small non-coding RNAs whose best-understood function is to repress mobile element (ME) activity in animal germline
Different populations of Piwi-interacting RNAs (piRNAs) are expressed at different stages of sperm development. piRNAs produced during the pre-pachytene stage of spermatogenesis often map to MEs and a fraction of pre-pachytene piRNAs participate in the ping-pong cycle [9]
Our preliminary analysis showed that the PO treatment is very effective in eliminating the non-piRNA component of the small RNA population (Additional file 1: Figure S1)
Summary
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. The best understood role of piRNAs, which is based primarily on work in Drosophila and mouse, is to act as an adaptive immune system for repressing mobile elements (MEs) in the germline through a combination of post-transcriptional cleavage and DNA methylation (reviewed in [3]). This defense mechanism is thought to have deep evolutionary roots as both the piRNA machinery and ME-derived piRNAs have been identified in a wide range of metazoans, including basal lineages [6]. PiRNAs produced during and after the pachytene stage are strongly depleted in ME sequences and are likely to have biological functions largely independent of ME silencing
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