Single-molecule imaging of the transcription factor SRF reveals prolonged chromatin-binding kinetics upon cell stimulation

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  • Lisa Hipp
    Institute of Physiological Chemistry, Ulm University, 89081 Ulm, Germany;
  • Judith Beer
    Institute of Physiological Chemistry, Ulm University, 89081 Ulm, Germany;
  • Oliver Kuchler
    Institute of Physiological Chemistry, Ulm University, 89081 Ulm, Germany;
  • Matthias Reisser
    Institute of Biophysics, Ulm University, 89081 Ulm, Germany
  • Daniela Sinske
    Institute of Physiological Chemistry, Ulm University, 89081 Ulm, Germany;
  • Jens Michaelis
    Institute of Biophysics, Ulm University, 89081 Ulm, Germany
  • J. Christof M. Gebhardt
    Institute of Biophysics, Ulm University, 89081 Ulm, Germany
  • Bernd Knöll
    Institute of Physiological Chemistry, Ulm University, 89081 Ulm, Germany;

Abstract

<jats:title>Significance</jats:title> <jats:p>How transcription factors (TFs) activate transcription is a long-standing but still unsolved question. We analyzed serum response factor (SRF), a stimulus-responsive TF mediating immediate early gene (IEG) and cytoskeletal gene expression at single-molecule resolution. Cell stimulation enhanced SRF activity by increasing the number of long chromatin-associated SRF molecules in an oscillating pattern. Further, stimulation enhanced the SRF chromatin residence time, and SRF binding events segregated into three distinct residence time regimes (short, intermediate, and long bound). In summary, our single-molecule imaging study reveals highly dynamic and diverse SRF interactions with DNA. Thus, cell stimulation regulates TF activity by several interconnected mechanisms including nucleus−cytoplasm shuttling, TF phosphorylation, cofactor recruitment, and extension of chromatin residence time and enhancing chromatin-bound TF numbers.</jats:p>

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