Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus

Elife. 2014 Jun 12:3:e02230. doi: 10.7554/eLife.02230.


Gene regulation relies on transcription factors (TFs) exploring the nucleus searching their targets. So far, most studies have focused on how fast TFs diffuse, underestimating the role of nuclear architecture. We implemented a single-molecule tracking assay to determine TFs dynamics. We found that c-Myc is a global explorer of the nucleus. In contrast, the positive transcription elongation factor P-TEFb is a local explorer that oversamples its environment. Consequently, each c-Myc molecule is equally available for all nuclear sites while P-TEFb reaches its targets in a position-dependent manner. Our observations are consistent with a model in which the exploration geometry of TFs is restrained by their interactions with nuclear structures and not by exclusion. The geometry-controlled kinetics of TFs target-search illustrates the influence of nuclear architecture on gene regulation, and has strong implications on how proteins react in the nucleus and how their function can be regulated in space and time.

Keywords: biophysics; cell biology; human; nuclear organization; single-molecule tracking; structural biology; target search; transcription regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Cell Nucleus / metabolism*
  • Green Fluorescent Proteins / metabolism
  • Histones / metabolism
  • Humans
  • Luminescent Proteins / metabolism
  • Positive Transcriptional Elongation Factor B / metabolism*
  • Proto-Oncogene Proteins c-myc / metabolism*
  • Transcription Factors / metabolism*


  • Dendra2 protein, Dendronephthya
  • Histones
  • Luminescent Proteins
  • Proto-Oncogene Proteins c-myc
  • Transcription Factors
  • Green Fluorescent Proteins
  • Positive Transcriptional Elongation Factor B

Grants and funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.