RNA polymerase is poised for activation across the genome

Nat Genet. 2007 Dec;39(12):1507-11. doi: 10.1038/ng.2007.21. Epub 2007 Nov 11.


Regulation of gene expression is integral to the development and survival of all organisms. Transcription begins with the assembly of a pre-initiation complex at the gene promoter, followed by initiation of RNA synthesis and the transition to productive elongation. In many cases, recruitment of RNA polymerase II (Pol II) to a promoter is necessary and sufficient for activation of genes. However, there are a few notable exceptions to this paradigm, including heat shock genes and several proto-oncogenes, whose expression is attenuated by regulated stalling of polymerase elongation within the promoter-proximal region. To determine the importance of polymerase stalling for transcription regulation, we carried out a genome-wide search for Drosophila melanogaster genes with Pol II stalled within the promoter-proximal region. Our data show that stalling is widespread, occurring at hundreds of genes that respond to stimuli and developmental signals. This finding indicates a role for regulation of polymerase elongation in the transcriptional responses to dynamic environmental and developmental cues.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Animals
  • Chromatin Immunoprecipitation
  • Drosophila melanogaster
  • Gene Expression Regulation*
  • Genome, Insect*
  • RNA Polymerase II / metabolism*
  • Transcription, Genetic*
  • Transcriptional Activation


  • RNA Polymerase II

Associated data

  • GEO/GSE6714