Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

Abstract

Mammalian genomes are folded into topologically associating domains (TADs), consisting of chromatin loops anchored by CTCF and cohesin. Some loops are cell-type specific. Here we asked whether CTCF loops are established by a universal or locus-specific mechanism. Investigating the molecular determinants of CTCF clustering, we found that CTCF self-association in vitro is RNase sensitive and that an internal RNA-binding region (RBR_i) mediates CTCF clustering and RNA interaction in vivo. Strikingly, deleting the RBR_i impairs about half of all chromatin loops in mESCs and causes deregulation of gene expression. Disrupted loop formation correlates with diminished clustering and chromatin binding of RBR_i mutant CTCF, which in turn results in a failure to halt cohesin-mediated extrusion. Thus, CTCF loops fall into at least two classes: RBR_i-independent and RBR_i-dependent loops. We speculate that evidence for RBR_i-dependent loops may provide a molecular mechanism for establishing cell-specific CTCF loops, potentially regulated by RNA(s) or other RBR_i-interacting partners.

Keywords: CTCF; Micro-C; RNA; TAD; cohesin; genome organization; loop; loop extrusion; super-resolution imaging.