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

Abstract

Although numerous live-cell measurements have shown that transcription factors 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 p53 and of the glucocorticoid receptor (GR) is transient. We also find residence times roughly comparable to that of endogenous GR REs 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.