Transcriptional interference by RNA polymerase III affects expression of the Polr3e gene

Genes Dev. 2017 Feb 15;31(4):413-421. doi: 10.1101/gad.293324.116. Epub 2017 Mar 13.


Overlapping gene arrangements can potentially contribute to gene expression regulation. A mammalian interspersed repeat (MIR) nested in antisense orientation within the first intron of the Polr3e gene, encoding an RNA polymerase III (Pol III) subunit, is conserved in mammals and highly occupied by Pol III. Using a fluorescence assay, CRISPR/Cas9-mediated deletion of the MIR in mouse embryonic stem cells, and chromatin immunoprecipitation assays, we show that the MIR affects Polr3e expression through transcriptional interference. Our study reveals a mechanism by which a Pol II gene can be regulated at the transcription elongation level by transcription of an embedded antisense Pol III gene.

Keywords: Polr3e gene; RNA polymerase; SINE; antisense transcription; gene expression regulation; transcriptional interference.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Conserved Sequence / genetics
  • DNA, Antisense / genetics
  • Embryonic Stem Cells
  • Gene Expression Regulation / genetics*
  • Interspersed Repetitive Sequences / genetics
  • Introns / genetics
  • Mice
  • RNA Polymerase II / genetics
  • RNA Polymerase III / genetics
  • RNA Polymerase III / metabolism*
  • RNA, Messenger / genetics
  • Sequence Deletion


  • DNA, Antisense
  • RNA, Messenger
  • RNA Polymerase II
  • Polr3e protein, mouse
  • RNA Polymerase III