Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

Abstract

It remains unclear why acute depletion of CTCF and cohesin only marginally affects expression of most genes despite substantially perturbing 3D genome folding at the level of domains and structural loops. To address this conundrum, we used high-resolution Micro-C and nascent transcript profiling to find that enhancer-promoter (E-P) interactions are largely insensitive to acute (3-hour) depletion of CTCF, cohesin, and WAPL. YY1 has been proposed to be a structural regulator of E-P loops, but acute YY1 depletion also had minimal effects on E-P loops, transcription, and 3D genome folding. Strikingly, live-cell single-molecule imaging revealed that cohesin depletion reduced transcription factor binding to chromatin. Thus, although neither CTCF, cohesin, WAPL, nor YY1 are required for the short-term maintenance of most E-P interactions and gene expression, we propose that cohesin may serve as a "transcription factor binding platform" that facilitates transcription factor binding to chromatin.

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

“…In contrast, interactions between enhancer and promoters are still present in the absence of cohesin. This is consistent with the findings of a recent preprint 39 . However, our data show that enhancer-promoter interactions are reduced upon cohesin depletion, which indicates that cohesin does contribute to the robustness of enhancer-promoter interactions.…”

Transcriptional enhancers and their communication with gene promoters

“…Surprisingly however, deletion or degradation of cohesin or CTCF in differentiated cells has only mild effects on gene expression [344][345][346][347][348][349]. Consistent with this, significant numbers of enhancer-promoter contacts remain unaffected upon rapid degradation of these proteins, and some contacts even appear de novo [349,350]. Mechanisms underlying this phenomenon are still not fully understood, but recent studies suggest that loops that require CTCF might be preferentially long-range (> 100 kb) and situated in loci where enhancers are generally sparse [301,349].…”

“…Meanwhile, ZNF143 binds to promoters globally [367] and was found at the anchors of many lineage-specific enhancer-promoter loops in human and mouse cells [362][363][364]368]. Unlike CTCF and cohesin, long-term depletion of YY1 or ZNF143 in mammalian cells causes a significant reduction of enhancer-promoter loops, coupled with substantial changes in gene expression [295,368,369] (although short-term YY1 depletion has only a modest effect on both [350]).…”

The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication

“…Whereas Drosophila have several known insulator-binding proteins, the only one that has been characterized in mammalian cells is CTCF. Since depletion of CTCF has very mild effects on transcription, both in number of genes affected and in the magnitude of that effect (Hsieh et al 2021), insulators were not a focus here. However, generally speaking, the TAG model accounts for boundary elements in that TAD organization will inform 3D distances, which will then affect the ability of a CRE to influence a promoter; that is, if a topological boundary moves a promoter outside an enhancer's gradient of activity, it should effectively insulate the two elements in a seemingly stepwise fashion.…”