Rapid depletion of CTCF and cohesin proteins reveals dynamic features of chromosome architecture.

Abstract

The interphase genome is mainly shaped by cohesin-mediated loop extrusion and cohesin-independent compartmentalization. Extrusion is a dynamic process of cohesin loading, loop extension and release. Cohesin release is mediated by WAPL. Loss of WAPL leads to the formation of longer loops and counters compartmentalization. The dynamics of these changes in chromosome organization have been unclear. We have used acute depletion of WAPL to show that within six hours cohesin accumulates at CTCF-bound loop anchors and extended loops are formed. When we deplete WAPL and CTCF simultaneously, new loops are formed between active genes. Surprisingly, active gene clustering is independent of cohesin. Stabilization of cohesin on chromatin leads to a decrease in compartmentalization, which is rapidly restored by depletion of cohesin. Our analyses show that loop extrusion counters compartmentalization and plays a central role in many aspects of chromosome organization. HIGHLIGHTSO_LICohesin accumulates at CTCF-mediated chromatin loop anchors following WAPL depletion. C_LIO_LIActively transcribed genes form long-range gene clusters independent of the cohesin complex. C_LIO_LIPlumes are a novel architectural feature of juxtaposed DNA formed by cohesin at open chromatin islands. C_LIO_LIChromosome compartmentalization can be uncoupled from nuclear lamina interactions. C_LI