Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

Davide Normanno (), Lydia Boudarène, Claire Dugast-Darzacq, Jiji Chen, Christian Richter, Florence Proux, Olivier Bénichou, Raphaël Voituriez, Xavier Darzacq () and Maxime Dahan ()
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Davide Normanno: Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie
Lydia Boudarène: Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie
Claire Dugast-Darzacq: Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l’ENS, IBENS
Jiji Chen: Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute
Christian Richter: Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie
Florence Proux: Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l’ENS, IBENS
Olivier Bénichou: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie
Raphaël Voituriez: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie
Xavier Darzacq: Functional Imaging of Transcription, CNRS UMR 8197, École normale supérieure, Institut de Biologie de l’ENS, IBENS
Maxime Dahan: Laboratoire Kastler Brossel, CNRS UMR 8552, École normale supérieure, Université Pierre et Marie Curie

Nature Communications, 2015, vol. 6, issue 1, 1-10

Abstract: Abstract Many cellular functions rely on DNA-binding proteins finding and associating to specific sites in the genome. Yet the mechanisms underlying the target search remain poorly understood, especially in the case of the highly organized mammalian cell nucleus. Using as a model Tet repressors (TetRs) searching for a multi-array locus, we quantitatively analyse the search process in human cells with single-molecule tracking and single-cell protein–DNA association measurements. We find that TetRs explore the nucleus and reach their target by 3D diffusion interspersed with transient interactions with non-cognate sites, consistent with the facilitated diffusion model. Remarkably, nonspecific binding times are broadly distributed, underlining a lack of clear delimitation between specific and nonspecific interactions. However, the search kinetics is not determined by diffusive transport but by the low association rate to nonspecific sites. Altogether, our results provide a comprehensive view of the recruitment dynamics of proteins at specific loci in mammalian cells.

Date: 2015
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DOI: 10.1038/ncomms8357

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