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BMC Genomics

, 15:545

Human and rodent genomics

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 subfamilies 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.

KeywordsHuman piRNA piRNA cluster Protein coding gene Mobile element High-throughput sequencing AbbreviationsMEsMobile elements

lncRNALong non-coding RNA

PO treatmentThe periodate oxidation and β-elimination treatment

UUridine

RPKMReads per kilobase per million mapped piRNA reads

GOGene ontology

MbpMillion base pair

TSSTranscription start site

SPSSense ping-pong signature

ASPSAnti-sense ping-pong signature

HERV-KHuman endogenous retrovirus family K

RINRNA integrity number

SRAShort read archive

ntNucleotides.

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

Hongseok Ha, Jimin Song contributed equally to this work.

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Autor: Hongseok Ha - Jimin Song - Shuoguo Wang - Aurélie Kapusta - Cédric Feschotte - Kevin C Chen - Jinchuan Xing

Fuente: https://link.springer.com/



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