Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Mol Cell. 2015 Nov 5;60(3):460-74. doi: 10.1016/j.molcel.2015.09.018. Epub 2015 Oct 22.


Upon recruitment to active enhancers and promoters, RNA polymerase II (Pol II) generates short non-coding transcripts of unclear function. The mechanisms that control the length and the amount of ncRNAs generated by cis-regulatory elements are largely unknown. Here, we show that the adaptor protein WDR82 and its associated complexes actively limit such non-coding transcription. WDR82 targets the SET1 H3K4 methyltransferases and the nuclear protein phosphatase 1 (PP1) complexes to the initiating Pol II. WDR82 and PP1 also interact with components of the transcriptional termination and RNA processing machineries. Depletion of WDR82, SET1, or the PP1 subunit required for its nuclear import caused distinct but overlapping transcription termination defects at highly expressed genes and active enhancers and promoters, thus enabling the increased synthesis of unusually long ncRNAs. These data indicate that transcription initiated from cis-regulatory elements is tightly coordinated with termination mechanisms that impose the synthesis of short RNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Active Transport, Cell Nucleus / physiology
  • Animals
  • Cell Nucleus / genetics
  • Cell Nucleus / metabolism*
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • Enhancer Elements, Genetic / physiology*
  • Histone-Lysine N-Methyltransferase / genetics
  • Histone-Lysine N-Methyltransferase / metabolism
  • Mice
  • Phosphoprotein Phosphatases / genetics
  • Phosphoprotein Phosphatases / metabolism
  • Promoter Regions, Genetic / physiology*
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism*
  • RNA, Untranslated / biosynthesis*
  • RNA, Untranslated / genetics
  • Transcription Termination, Genetic / physiology*


  • Chromosomal Proteins, Non-Histone
  • RNA, Untranslated
  • Wdr82 protein, mouse
  • Histone-Lysine N-Methyltransferase
  • RNA Polymerase II
  • Phosphoprotein Phosphatases

Associated data

  • GEO/GSE66955