Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Abstract

The CCCTC-binding factor (CTCF) works together with the cohesin complex to drives the formation of chromatin loops and topologically associating domains, but its role in gene regulation has not been fully defined. Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionally affect genes that are bound by CTCF at promoter and dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which are restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with transcription of over 2,000 genes, across a diverse set of adult tissues. Taken together, our study shows that CTCF binding to promoters may promote long-distance-enhancer dependent transcription at specific genes in diverse cell types.

Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF

“…On the other hand, we see a link between CTCF binding at promoters and downregulation of the expression, suggesting another role of CTCF protein different from insulation. In fact, it has been shown that promoterproximal CTCF can promote long-range enhancer-promoter contacts and facilitate gene activation (Kubo et al, 2021). It is noteworthy that is the case of genes downregulated in mutants, we see enrichment of CTCF bound at introns together with promoters, suggestive of a more complex mechanisms than transcriptional activation by binding to promoter regions.…”

“…Equally, the relationship between for chromatin structure and the regulation of gene expression, although subject to debate, is also clear (Ibrahim and Mundlos, 2020). It is therefore surprising the limited transcriptional effect of CTCF deletion, as observed for example in ES cells (Nora et al, 2017;Kubo et al, 2021). This could be the results of CTCF being necessary for the initial establishment of regulatory interactions along chromatin, but not for the posterior maintenance of these contacts.…”

“…In somatic cells, conditional knockouts showed additional important roles for CTCF in cell-cycle progression, apoptosis, and differentiation (Heath et al, 2008;Soshnikova et al, 2010;Li et al 2007;Arzate-Mejia et al, 2018). However, global depletion of CTCF in cell cultures leads to subtle and context-specific changes in gene expression (Zuin et al, 2014;Nora et al, 2017;Hyle et al, 2019;Kubo et al, 2021) although chromatin structure is affected with a reduction of TAD insulation and intra-TAD loop formation. However, we are still missing a clear understanding of the role of CTCF in the initial establishment of chromatin structure, and its impact on regulated gene expression.…”

PDS5A and PDS5B in Cohesin Function and Human Disease

“…In mammalian genomes, approximately 90% of cohesin is localized to the binding sites for CTCF in chromosome arms [ 140 , 141 ]. It has been hypothesized that cohesin functions as a loop extruder factor, which partners with the CTCF that defines the directional boundaries of chromatin to generate chromatin loops [ 142 , 143 ], and accumulating evidence supports this loop-extruding hypothesis [ 88 , 128 , 136 , 144 , 145 ].…”

Super-Enhancers and CTCF in Early Embryonic Cell Fate Decisions

“…The orientation of the CTCF binding site positions the N-terminus to interact with cohesin, providing a molecular explanation of the necessity of convergent CTCF sites to create a chromatin loop. The necessity of cohesin and CTCF binding for chromatin looping, however, is currently being questioned, as two recent students have shown that depletion of CTCF and cohesin does not affect a majority of enhancer:promoter interactions (Thiecke et al, 2020;Kubo et al, 2021).…”