SPT5 stabilization of promoter-proximal RNA polymerase II

Mol Cell. 2021 Nov 4;81(21):4413-4424.e5. doi: 10.1016/j.molcel.2021.08.006. Epub 2021 Sep 3.

Abstract

Based on in vitro studies, it has been demonstrated that the DSIF complex, composed of SPT4 and SPT5, regulates the elongation stage of transcription catalyzed by RNA polymerase II (RNA Pol II). The precise cellular function of SPT5 is not clear, because conventional gene depletion strategies for SPT5 result in loss of cellular viability. Using an acute inducible protein depletion strategy to circumvent this issue, we report that SPT5 loss triggers the ubiquitination and proteasomal degradation of the core RNA Pol II subunit RPB1, a process that we show to be evolutionarily conserved from yeast to human cells. RPB1 degradation requires the E3 ligase Cullin 3, the unfoldase VCP/p97, and a novel form of CDK9 kinase complex. Our study demonstrates that SPT5 stabilizes RNA Pol II specifically at promoter-proximal regions, permitting RNA Pol II release from promoters into gene bodies and providing mechanistic insight into the cellular function of SPT5 in safeguarding accurate gene expression.

Keywords: CDK9; Cullin 3; NELF; RNA polymerase II; SPT5; VCP; auxin-inducible degron; degradation; elongation; transcription.

Publication types

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

MeSH terms

  • Animals
  • Cell Survival
  • Chromosomal Proteins, Non-Histone / metabolism
  • Cullin Proteins / chemistry
  • Cullin Proteins / metabolism*
  • Fibroblasts / metabolism
  • Humans
  • Indoleacetic Acids / chemistry
  • Mice
  • Nedd4 Ubiquitin Protein Ligases / chemistry
  • Nuclear Proteins / metabolism*
  • Promoter Regions, Genetic
  • Proteasome Endopeptidase Complex / chemistry
  • Proteome
  • Proteomics / methods
  • RNA Polymerase II / chemistry*
  • RNA Polymerase II / metabolism*
  • Transcriptional Elongation Factors / metabolism*
  • Ubiquitin-Protein Ligases / chemistry
  • Valosin Containing Protein / chemistry
  • Valosin Containing Protein / metabolism

Substances

  • CUL3 protein, human
  • Chromosomal Proteins, Non-Histone
  • Cul3 protein, mouse
  • Cullin Proteins
  • Indoleacetic Acids
  • Nuclear Proteins
  • Proteome
  • SUPT5H protein, human
  • Transcriptional Elongation Factors
  • SPT5 transcriptional elongation factor
  • Nedd4 Ubiquitin Protein Ligases
  • Nedd4 protein, human
  • Ubiquitin-Protein Ligases
  • RNA Polymerase II
  • Proteasome Endopeptidase Complex
  • VCP protein, human
  • Valosin Containing Protein
  • Vcp protein, mouse