Single-molecule analysis of transcription factor binding at transcription sites in live cells

Nat Commun. 2014 Jul 18;5:4456. doi: 10.1038/ncomms5456.


Although numerous live-cell measurements have shown that transcription factors (TFs) bind chromatin transiently, no measurements of transient binding have been reported at the endogenous response elements (REs) where transcription is normally induced. Here we show that at endogenous REs the transcriptionally productive specific binding of two TFs, p53 and the glucocorticoid receptor (GR), is transient. We also find that the transient residence times of GR at endogenous REs are roughly comparable to those at an artificial, multi-copy array of gene regulatory sites, supporting the use of multi-copy arrays for live-cell analysis of transcription. Finally, we find that at any moment only a small fraction of TF molecules are engaged in transcriptionally productive binding at endogenous REs. The small fraction of bound factors provides one explanation for gene bursting and it also indicates that REs may often be unoccupied, resulting in partial responses to transcriptional signals.

Publication types

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

MeSH terms

  • Binding Sites
  • Chromatin / metabolism
  • Humans
  • Protein Structure, Tertiary
  • Receptors, Glucocorticoid / genetics
  • Receptors, Glucocorticoid / metabolism*
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Response Elements
  • Transcription Factors / analysis*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcription Initiation Site
  • Tumor Suppressor Protein p53 / genetics
  • Tumor Suppressor Protein p53 / metabolism*


  • Chromatin
  • Receptors, Glucocorticoid
  • Recombinant Fusion Proteins
  • Transcription Factors
  • Tumor Suppressor Protein p53