piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals

PLoS One. 2015 May 7;10(5):e0124860. doi: 10.1371/journal.pone.0124860. eCollection 2015.

Abstract

Piwi-interacting (pi-) RNAs guide germline-expressed Piwi proteins in order to suppress the activity of transposable elements (TEs). But notably, the majority of pachytene piRNAs in mammalian testes is not related to TEs. This raises the question of whether the Piwi/piRNA pathway exerts functions beyond TE silencing. Although gene-derived piRNAs were described many times, a possible gene-regulatory function was doubted due to the absence of antisense piRNAs. Here we sequenced and analyzed piRNAs expressed in the adult testis of the pig, as this taxon possesses the full set of mammalian Piwi paralogs while their spermatozoa are marked by an extreme fitness due to selective breeding. We provide an exhaustive characterization of porcine piRNAs and genomic piRNA clusters. Moreover, we reveal that both sense and antisense piRNAs derive from protein-coding genes, while exhibiting features that clearly show that they originate from the Piwi/piRNA-mediated post-transcriptional silencing pathway, commonly referred to as ping-pong cycle. We further show that the majority of identified piRNA clusters in the porcine genome spans exonic sequences of protein-coding genes or pseudogenes, which reveals a mechanism by which primary antisense piRNAs directed against mRNA can be generated. Our data provide evidence that spliced mRNAs, derived from such loci, are not only targeted by piRNAs but are also subject to ping-pong cycle processing. Finally, we demonstrate that homologous genes are targeted and processed by piRNAs in pig, mouse and human. Altogether, this strongly suggests a conserved role for the mammalian Piwi/piRNA pathway in post-transcriptional regulation of protein-coding genes, which did not receive much attention so far.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Argonaute Proteins / genetics*
  • Argonaute Proteins / metabolism
  • Conserved Sequence
  • Humans
  • Male
  • Mice
  • Multigene Family
  • RNA Interference*
  • RNA, Small Interfering / genetics*
  • RNA, Small Interfering / metabolism*
  • Sequence Analysis, RNA
  • Signal Transduction
  • Sus scrofa
  • Testis / metabolism*

Substances

  • Argonaute Proteins
  • RNA, Small Interfering

Grant support

DR was supported by the research funding program MAIFOR (University Medical Center of the Johannes Gutenberg-University Mainz, Germany). DG holds a stipend from the International PhD Programme on the “Dynamics of Gene Regulation, Epigenetics and DNA Damage Response” from the Institute of Molecular Biology gGmbH, (Mainz, Germany) funded by the Boehringer Ingelheim Foundation. This work was also supported by the Deutsche Forschungsgemeinschaft DFG (Großgeräteantrag GZ Inst. 247-594-1 FUGG Genome sequencer, Illumina) and is part of the research focus GeneRED (Gene Regulation in Evolution and Development). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.