Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

Abstract

In addition to mediating sister chromatid cohesion during the cell cycle, the cohesin complex associates with CTCF and with active gene regulatory elements to form long-range interactions between its binding sites. Genome-wide chromosome conformation capture had shown that cohesin's main role in interphase genome organization is in mediating interactions within architectural chromosome compartments, rather than specifying compartments per se. However, it remains unclear how cohesin-mediated interactions contribute to the regulation of gene expression. We have found that the binding of CTCF and cohesin is highly enriched at enhancers and in particular at enhancer arrays or "super-enhancers" in mouse thymocytes. Using local and global chromosome conformation capture, we demonstrate that enhancer elements associate not just in linear sequence, but also in 3D, and that spatial enhancer clustering is facilitated by cohesin. The conditional deletion of cohesin from noncycling thymocytes preserved enhancer position, H3K27ac, H4K4me1, and enhancer transcription, but weakened interactions between enhancers. Interestingly, ∼50% of deregulated genes reside in the vicinity of enhancer elements, suggesting that cohesin regulates gene expression through spatial clustering of enhancer elements. We propose a model for cohesin-dependent gene regulation in which spatial clustering of enhancer elements acts as a unified mechanism for both enhancer-promoter "connections" and "insulation."

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

“…In contrast, only one TF (JUND) showed significantly greater enrichment in Enh5. Notably, SMC3 and RAD21 are constituents of the cohesin complex, which has been shown to link active enhancers to promoters (Ing-Simmons et al 2015), and CTCF frequently associates with such cohesin complexes (Sanyal et al 2012). Similarly, in IMR90 cells, enhancers acetylated only on H2BK20 (Ienh4) showed greater enrichment for cohesin and CTCF binding than enhancers marked by H3K27ac as well as H2BK20ac (Ienh5) (Supplemental Fig.…”

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

“…At finer scales, physical interactions between promoter-distal sites appear to be widespread (Fullwood et al 2009;Sahlén et al 2015;Ghavi-Helm et al 2014;Phillips-Cremins et al 2013) and might function to provide specificity and robustness to enhancer-promoter interactions within cis-regulatory units (Ing-Simmons et al 2015;Markenscoff-Papadimitriou et al 2014). Previous work suggests that enhancer elements tend to cluster in the nuclear space in a cohesin-dependent manner (IngSimmons et al 2015), but how enhancer-enhancer interactions are modulated by extracellular signaling remains largely unknown.…”

“…Transcriptional enhancers not only interact with each other through long-range interactions but also within dense enhancer hotspots known as super-enhancers (SEs) or stretch-enhancers (Whyte et al 2013;Parker et al 2013;Ing-Simmons et al 2015), which have been implicated in the transcriptional control of cell identity genes . Intriguingly, a recent study revealed that SE-associated genes are enriched for functional categories relevant to cytokine biology in mouse T lymphocytes (Vahedi et al 2015).…”

“…Secondly, studies analyzing this relation on developmental timescales lack the temporal resolution necessary to capture the early chromatin changes induced by signaling events. Thirdly, physical interactions other than promoter-enhancer loops, such as enhancer-enhancer interactions, received comparatively little attention, albeit they likely represent an important layer of gene regulation in the three-dimensional nuclear space (Ing-Simmons et al 2015).…”

The long range regulation of breast cancer associated genes

“…This clustering of enhancer elements is mediated by cohesin, a complex of proteins that form a ring shaped structure around DNA to link sister chromatids or interacting enhancer-promoter segments [98]. Knockout experiments reveal a decrease in interactions between enhancer interactions when cohesion is not present [99]. It is suggested that synergy between multiple enhancers provides robustness in gene expression throughout evolution and may compensate for any inherent failure rate of an individual enhancer [76].…”