| Autor: |
Banigan EJ; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139.; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139., Tang W; Research Institute of Molecular Pathology, Vienna BioCenter 1030 Vienna, Austria., van den Berg AA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139.; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139., Stocsits RR; Research Institute of Molecular Pathology, Vienna BioCenter 1030 Vienna, Austria., Wutz G; Research Institute of Molecular Pathology, Vienna BioCenter 1030 Vienna, Austria., Brandão HB; Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138.; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.; The Broad Institute of MIT and Harvard, Cambridge, MA 02142., Busslinger GA; Research Institute of Molecular Pathology, Vienna BioCenter 1030 Vienna, Austria.; Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria.; Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna 1090, Austria., Peters JM; Research Institute of Molecular Pathology, Vienna BioCenter 1030 Vienna, Austria., Mirny LA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139.; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139. |
| Abstrakt: |
Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. "Loop extrusion" can be impeded by chromatin-bound factors, such as CTCF, which generates characteristic and functional chromatin organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin and that active promoters are cohesin loading sites. However, the effects of transcription on cohesin have not been reconciled with observations of active extrusion by cohesin. To determine how transcription modulates extrusion, we studied mouse cells in which we could alter cohesin abundance, dynamics, and localization by genetic "knockouts" of the cohesin regulators CTCF and Wapl. Through Hi-C experiments, we discovered intricate, cohesin-dependent contact patterns near active genes. Chromatin organization around active genes exhibited hallmarks of interactions between transcribing RNA polymerases (RNAPs) and extruding cohesins. These observations could be reproduced by polymer simulations in which RNAPs were moving barriers to extrusion that obstructed, slowed, and pushed cohesins. The simulations predicted that preferential loading of cohesin at promoters is inconsistent with our experimental data. Additional ChIP-seq experiments showed that the putative cohesin loader Nipbl is not predominantly enriched at promoters. Therefore, we propose that cohesin is not preferentially loaded at promoters and that the barrier function of RNAP accounts for cohesin accumulation at active promoters. Altogether, we find that RNAP is an extrusion barrier that is not stationary, but rather, translocates and relocalizes cohesin. Loop extrusion and transcription might interact to dynamically generate and maintain gene interactions with regulatory elements and shape functional genomic organization. |
