Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing

Mol Cell. 2024 Apr 4;84(7):1243-1256.e5. doi: 10.1016/j.molcel.2024.01.023. Epub 2024 Feb 23.

Abstract

Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that NELF prevents Pol II elongation. Here, we report cryoelectron microscopy structures of Pol II-DSIF-NELF complexes with NELF in two distinct conformations corresponding to paused and poised states. The paused NELF state supports Pol II stalling, whereas the poised NELF state enables transcription elongation as it does not support a tilted RNA-DNA hybrid. Further, the poised NELF state can accommodate TFIIS binding to Pol II, allowing for Pol II reactivation at paused or backtracking sites. Finally, we observe that the NELF-A tentacle interacts with the RPB2 protrusion and is necessary for pausing. Our results define how NELF can support pausing, reactivation, and elongation by Pol II.

Keywords: DSIF; NELF; RNA polymerase II; TFIIS; promoter proximal pausing; transcription.

MeSH terms

  • Animals
  • Cryoelectron Microscopy
  • Nuclear Proteins* / metabolism
  • RNA Polymerase II* / genetics
  • RNA Polymerase II* / metabolism
  • Transcription Factors / metabolism
  • Transcription, Genetic

Substances

  • negative elongation factor
  • RNA Polymerase II
  • Nuclear Proteins
  • Transcription Factors