Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism

Abstract

SUMMARY Transcriptional dysregulation of the MYC oncogene is among the most frequent events in aggressive tumor cells, and this is generally accomplished by acquisition of a super-enhancer somewhere within the 2.8 Mb TAD where MYC resides. We find that these diverse cancer-specific super-enhancers, differing in size and location, interact with the MYC gene through a common and conserved CTCF binding site located 2 kb upstream of the MYC promoter. Genetic perturbation of this enhancer-docking site in tumor cells reduces CTCF binding, super-enhancer interaction, MYC gene expression, and cell proliferation. CTCF binding is highly sensitive to DNA methylation, and this enhancer-docking site, which is hypomethylated in diverse cancers, can be inactivated through epigenetic editing with dCas9-DNMT. Similar enhancer-docking sites occur at other genes, including genes with prominent roles in multiple cancers, suggesting a mechanism by which tumor cell oncogenes can generally hijack enhancers. These results provide insights into mechanisms that allow a single target gene to be regulated by diverse enhancer elements in different cell types.

BET inhibition disrupts transcription but retains enhancer-promoter contact

“…Depletion of cohesin or its loader NIPBL disrupts interactions between promoters and distal enhancers 21,72,73 , although this may be an indirect effect through loss of TAD boundaries rather than physical contact with enhancers. As has been reported 23 , in our analysis we observed an enrichment for CTCF/RAD21 binding at promoter-interacting loci, consistent with a direct role for loop extrusion in mediating enhancer-promoter interactions. Indeed, loss of Rad21 results in decreased enhancer-promoter contacts and transcriptional downregulation at Sik1 and Elf3 in mESCs 72 .…”

“…This long-distance interaction has also been observed and characterized in several other cell types 22,23,45,46 . Reciprocal Capture-C from the more proximal of the two enhancer regions demonstrated contact exclusively with the MYC promoter, avoiding intervening regions, as well as a relatively weak interaction with the more distal enhancer domain (Fig 1c).…”

“…Indeed, loss of Rad21 results in decreased enhancer-promoter contacts and transcriptional downregulation at Sik1 and Elf3 in mESCs 72 . Similarly, enhancer-promoter interactions at MYC are dependent on CTCF 22,23 . However, it is possible that this gene is unusual, as long distance enhancer-promoter interactions over 1 Mb are not common.…”

“…Whilst loop extrusion mediated by CTCF and cohesin is the most common explanation for controlling large scale chromatin structure, less is known about what stabilizes more localized enhancer-promoter loops. Possible models include CTCF/cohesin-stabilized enhancer-promoter interactions [21][22][23] and protein/RNA complexes bound to both the enhancer and promoter that interact with one another [24][25][26] . Binding of these complexes is likely initiated by key sequencespecific TFs.…”

“…Indeed, the promoter CTCF sites have previously been shown to play a role in interaction with distinct enhancer regions in different cancer cell lines 23 . At the MYC enhancer, the proximal domain is bounded by a pair of CTCF/RAD21 binding sites, and the major peak of the distal region is marked by two peaks (Fig 5a).…”