Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions

Abstract

Abstract The cohesin complex structures the interphase genome of human cells by extruding loops and organizing topologically associating domains (TADs), yet how chromatin state regulates cohesin-chromatin interactions remains unclear. Here, we show that histone hyperacetylation induced by trichostatin A (TSA) selectively disrupts short-range intra-TAD interactions while largely preserving CTCF-anchored loops. These distinct responses define two functional cohesin populations: a TSA-sensitive pool associated with dynamic loop extrusion, and a TSA-resistant pool at CTCF sites maintained by topological entrapment. Using a semi-in vitro system with TEV-cleavable RAD21, we demonstrate that hyperacetylation increases the sensitivity of CTCF-anchored loops to cohesin ring cleavage, supporting a topological basis for their stability. We further identify a TSA-sensitive cohesin fraction at CTCF sites, suggesting transient, non-encircling intermediates. Together, our results reveal that cohesin exists in distinct biochemical states that differentially regulate chromatin loop stability and responsiveness to epigenomic perturbation.