CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II-transcribed genes

Nat Struct Mol Biol. 2015 May;22(5):396-403. doi: 10.1038/nsmb.3000. Epub 2015 Apr 6.


Transcription through early-elongation checkpoints requires phosphorylation of negative transcription elongation factors (NTEFs) by the cyclin-dependent kinase (CDK) 9. Using CDK9 inhibitors and global run-on sequencing (GRO-seq), we have mapped CDK9 inhibitor-sensitive checkpoints genome wide in human cells. Our data indicate that early-elongation checkpoints are a general feature of RNA polymerase (pol) II-transcribed human genes and occur independently of polymerase stalling. Pol II that has negotiated the early-elongation checkpoint can elongate in the presence of inhibitors but, remarkably, terminates transcription prematurely close to the terminal polyadenylation (poly(A)) site. Our analysis has revealed an unexpected poly(A)-associated elongation checkpoint, which has major implications for the regulation of gene expression. Interestingly, the pattern of modification of the C-terminal domain of pol II terminated at this new checkpoint largely mirrors the pattern normally found downstream of the poly(A) site, thus suggesting common mechanisms of termination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cell Line, Tumor
  • Cyclin-Dependent Kinase 9 / antagonists & inhibitors*
  • Cyclin-Dependent Kinase 9 / genetics
  • Cyclin-Dependent Kinase 9 / metabolism
  • Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) / biosynthesis*
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Peptide Chain Elongation, Translational / drug effects*
  • Peptide Chain Elongation, Translational / genetics
  • Promoter Regions, Genetic / genetics
  • RNA Interference
  • RNA Polymerase II
  • RNA, Small Interfering
  • Sequence Analysis, DNA
  • Transcription, Genetic / drug effects*


  • RNA, Small Interfering
  • Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)
  • CDK9 protein, human
  • Cyclin-Dependent Kinase 9
  • RNA Polymerase II