SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape

Mol Cell. 2021 Nov 4;81(21):4425-4439.e6. doi: 10.1016/j.molcel.2021.08.029. Epub 2021 Sep 16.


Transcription progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Here we utilize a rapid degradation system and reveal crucial functions of SPT5 in maintaining cellular and chromatin RNA polymerase II (Pol II) levels. Rapid SPT5 depletion causes a pronounced reduction of paused Pol II at promoters and enhancers, distinct from negative elongation factor (NELF) degradation resulting in short-distance paused Pol II redistribution. Most genes exhibit downregulation, but not upregulation, accompanied by greatly impaired transcription activation, altered chromatin landscape at enhancers, and severe Pol II processivity defects at gene bodies. Phosphorylation of an SPT5 linker at serine 666 potentiates pause release and is antagonized by Integrator-PP2A (INTAC) targeting SPT5 and Pol II, while phosphorylation of the SPT5 C-terminal region links to 3' end termination. Our findings position SPT5 as an essential positive regulator of global transcription.

Keywords: INTAC; Integrator; PP2A; Pol II stability; RNA polymerase II; SPT5; elongation; enhancer; pausing; transcription.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens, Differentiation, B-Lymphocyte
  • Chromatin / chemistry
  • Chromatin / metabolism
  • Chromosomal Proteins, Non-Histone / metabolism*
  • Enhancer Elements, Genetic*
  • Fibroblasts / metabolism
  • Genome
  • HEK293 Cells
  • Histocompatibility Antigens Class II
  • Humans
  • Mice
  • Mutation
  • Nuclear Proteins / metabolism*
  • Phosphorylation
  • Promoter Regions, Genetic
  • RNA Polymerase II / metabolism*
  • RNA-Seq
  • Regulatory Sequences, Nucleic Acid
  • Transcription, Genetic*
  • Transcriptional Activation
  • Transcriptional Elongation Factors / metabolism*


  • Antigens, Differentiation, B-Lymphocyte
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • Histocompatibility Antigens Class II
  • Nuclear Proteins
  • SUPT5H protein, human
  • Transcriptional Elongation Factors
  • invariant chain
  • SPT5 transcriptional elongation factor
  • RNA Polymerase II