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

• Published in: eLife Vol. 3
• Main Authors: Izeddin, Ignacio, Récamier, Vincent, Bosanac, Lana, Cissé, Ibrahim I, Boudarene, Lydia, Dugast-Darzacq, Claire, Proux, Florence, Bénichou, Olivier, Voituriez, Raphaël, Bensaude, Olivier, Dahan, Maxime, Darzacq, Xavier
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 12-06-2014; eLife Sciences Publications, Ltd
• Subjects: Biology; Biophysics and Structural Biology; c-Myc protein; Cell Biology; Cell Line, Tumor; Cell Nucleus - metabolism; Cyclin-dependent kinases; Deoxyribonucleic acid; DNA; Exploration; Fractals; Gene regulation; Genes; Genomes; Geometry; Green Fluorescent Proteins - metabolism; Histones - metabolism; Humans; Kinases; Luminescent Proteins - metabolism; Myc protein; nuclear organization; Nuclei; Positive Transcriptional Elongation Factor B - metabolism; Proto-Oncogene Proteins c-myc - metabolism; Random access memory; RNA polymerase; Simulation; single-molecule tracking; target search; Transcription factors; Transcription Factors - metabolism; transcription regulation; single-molecule tracking; transcription regulation; cell biology; structural biology; nuclear organization; target search; biophysics; human
• ISSN: 2050-084X; 2050-084X
• 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.