A wave of nascent transcription on activated human genes

Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18357-61. doi: 10.1073/pnas.0902573106. Epub 2009 Oct 13.


Genome-wide studies reveal that transcription by RNA polymerase II (Pol II) is dynamically regulated. To obtain a comprehensive view of a single transcription cycle, we switched on transcription of five long human genes (>100 kbp) with tumor necrosis factor-alpha (TNFalpha) and monitored (using microarrays, RNA fluorescence in situ hybridization, and chromatin immunoprecipitation) the appearance of nascent RNA, changes in binding of Pol II and two insulators (the cohesin subunit RAD21 and the CCCTC-binding factor CTCF), and modifications of histone H3. Activation triggers a wave of transcription that sweeps along the genes at approximately 3.1 kbp/min; splicing occurs cotranscriptionally, a major checkpoint acts several kilobases downstream of the transcription start site to regulate polymerase transit, and Pol II tends to stall at cohesin/CTCF binding sites.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • CCCTC-Binding Factor
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Cells, Cultured
  • Chromatin Immunoprecipitation
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • DNA-Binding Proteins
  • Humans
  • In Situ Hybridization
  • Introns
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Phosphoproteins / genetics
  • Phosphoproteins / metabolism
  • RNA Polymerase II / metabolism
  • RNA Splicing
  • RNA, Messenger / biosynthesis
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism
  • Transcription, Genetic*
  • Transcriptional Activation
  • Tumor Necrosis Factor-alpha / genetics


  • CCCTC-Binding Factor
  • CTCF protein, human
  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • Nuclear Proteins
  • Phosphoproteins
  • RAD21 protein, human
  • RNA, Messenger
  • Repressor Proteins
  • Tumor Necrosis Factor-alpha
  • cohesins
  • RNA Polymerase II

Associated data

  • GEO/GPL5828
  • GEO/GSE15157
  • GEO/GSE9036
  • GEO/GSE9055