Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5' Pause Release, Termination, and Transcription Elongation Rate

Mol Cell. 2019 Jan 3;73(1):107-118.e4. doi: 10.1016/j.molcel.2018.10.031. Epub 2018 Nov 29.


In addition to phosphodiester bond formation, RNA polymerase II has an RNA endonuclease activity, stimulated by TFIIS, which rescues complexes that have arrested and backtracked. How TFIIS affects transcription under normal conditions is poorly understood. We identified backtracking sites in human cells using a dominant-negative TFIIS (TFIISDN) that inhibits RNA cleavage and stabilizes backtracked complexes. Backtracking is most frequent within 2 kb of start sites, consistent with slow elongation early in transcription, and in 3' flanking regions where termination is enhanced by TFIISDN, suggesting that backtracked pol II is a favorable substrate for termination. Rescue from backtracking by RNA cleavage also promotes escape from 5' pause sites, prevents premature termination of long transcripts, and enhances activation of stress-inducible genes. TFIISDN slowed elongation rates genome-wide by half, suggesting that rescue of backtracked pol II by TFIIS is a major stimulus of elongation under normal conditions.

Keywords: RNA polymerase pausing; TFIIS; hypoxia response; transcription elongation; transcription termination; transcriptional backtracking.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Flanking Region
  • Animals
  • Gene Expression Regulation
  • HEK293 Cells
  • Humans
  • Kinetics
  • Mice
  • Mutation
  • RNA / genetics
  • RNA / metabolism*
  • RNA Cleavage*
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism*
  • Transcription Elongation, Genetic*
  • Transcription Termination, Genetic*
  • Transcriptional Activation*
  • Transcriptional Elongation Factors / genetics
  • Transcriptional Elongation Factors / metabolism


  • Transcriptional Elongation Factors
  • transcription factor S-II
  • RNA
  • RNA Polymerase II