An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

• Published in: Molecular cell 2021-04, Vol.81 (7), p.1484-1498.e6
• Main Authors: Garcia, David A., Johnson, Thomas A., Presman, Diego M., Fettweis, Gregory, Wagh, Kaustubh, Rinaldi, Lorenzo, Stavreva, Diana A., Paakinaho, Ville, Jensen, Rikke A.M., Mandrup, Susanne, Upadhyaya, Arpita, Hager, Gordon L.
• Format: Article
• Language: English
• Subjects: Animals; bi-exponential; Biochemistry, biophysics & molecular biology; Biochimie, biophysique & biologie moléculaire; Cell Biology; chromatin binding; confinement; Female; glucocorticoid receptor; GRdim; GRmon; Intrinsically Disordered Proteins; Intrinsically Disordered Proteins - chemistry; Intrinsically Disordered Proteins - genetics; Intrinsically Disordered Proteins - metabolism; intrinsically disordered regions; Life sciences; Mice; Molecular Biology; power-law; PPAR; Rats; Receptors, Glucocorticoid; Receptors, Glucocorticoid - chemistry; Receptors, Glucocorticoid - genetics; Receptors, Glucocorticoid - metabolism; Sciences du vivant; single-molecule; transcription dynamics; Transcription Factors; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2021.01.013

Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs within the local chromatin context. The mechanisms by which TFs navigate the nuclear environment as they search for binding sites remain unclear. Here, we used single-molecule tracking and machine-learning-based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic low-mobility populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), implicated in liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Together, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites. [Display omitted] •TF dynamics were analyzed by combining SMT and a machine-learning-based approach•GR exhibits two states with limited mobility: chromatin bound and confinement•Dwell times of both states are distinguishable and follow a power-law distribution•Confinement is mediated by IDRs and might amplify transcriptional output Garcia et al. use a systems-level approach to analyze single-molecule tracks of the glucocorticoid receptor. In addition to the known chromatin-bound state, the authors characterized an IDR-mediated, long-lived confined state consistent with liquid condensates that can amplify transcriptional output by increasing the local concentration of TFs at enhancer sites.