Integrator is recruited to promoter-proximally paused RNA Pol II to generate Caenorhabditis elegans piRNA precursors

EMBO J. 2021 Mar 1;40(5):e105564. doi: 10.15252/embj.2020105564. Epub 2020 Dec 19.


Piwi-interacting RNAs (piRNAs) play key roles in germline development and genome defence in metazoans. In C. elegans, piRNAs are transcribed from > 15,000 discrete genomic loci by RNA polymerase II (Pol II), resulting in 28 nt short-capped piRNA precursors. Here, we investigate transcription termination at piRNA loci. We show that the Integrator complex, which terminates snRNA transcription, is recruited to piRNA loci. Moreover, we demonstrate that the catalytic activity of Integrator cleaves nascent capped piRNA precursors associated with promoter-proximal Pol II, resulting in termination of transcription. Loss of Integrator activity, however, does not result in transcriptional readthrough at the majority of piRNA loci. Taken together, our results draw new parallels between snRNA and piRNA biogenesis in nematodes and provide evidence of a role for the Integrator complex as a terminator of promoter-proximal RNA polymerase II during piRNA biogenesis.

Keywords: Piwi-interacting RNAs (piRNAs); integrator complex; non-coding RNA; transcription termination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Caenorhabditis elegans / genetics
  • Caenorhabditis elegans / metabolism*
  • Caenorhabditis elegans Proteins / genetics
  • Caenorhabditis elegans Proteins / metabolism*
  • Germ Cells
  • Promoter Regions, Genetic*
  • RNA Caps
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism*
  • RNA Precursors / genetics
  • RNA Precursors / metabolism*
  • RNA Processing, Post-Transcriptional*
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism*
  • Transcription, Genetic


  • Caenorhabditis elegans Proteins
  • RNA Caps
  • RNA Precursors
  • RNA, Small Interfering
  • RNA Polymerase II