Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

Abstract

The mammalian genome has been segmented into thousands of topologically associated domains (TADs) based on chromosome conformation capture studies, such as Hi-C.TADs have been proposed to act as insulated neighborhoods, spatially sequestering and insulating the enclosed genes and regulatory elements through self-association and chromatin looping. Recent results indicate that inter-TAD interactions can also occur. However, the nature, extent, and function of these inter-TAD interactions remains unclear. Here, we combine Hi-C data with Oligopaint technology to precisely visualize neighboring TADs and quantify their interaction frequency in human cells. We find that intra-TAD interactions are indeed more enriched than inter-TAD interactions. However, we also observe extensive intermingling between neighboring domains in the majority of cells. Moreover, we find that cohesin depletion, which is known to abolish TADs at the population-average level, does not induce ectopic interactions but instead reduces interactions between neighboring domains. We find that cohesin loss preferentially alters locus topology and transcriptional bursting frequencies at genes close to domain boundaries, potentially explaining the gene expression changes observed in the cohesinopathy Cornelia de Lange syndrome. Together, our results challenge the notion that cohesin forms spatially insulated domains to regulate gene expression. Instead, we propose that cohesin normally antagonizes domain insulation by frequently bypassing boundaries to promote proper gene regulation at a subset of boundary-proximal genes.We would like to thank Leah Rosin, Melike Lakadamyali, and members of the Joyce lab for helpful discussions and critical reading of the manuscript. Additionally, we thank Masato Kanemaki for the HCT-116-RAD21-AID cell line and Suhas Rao and Erez Lieberman-Aiden for sharing critical primary datasets. We also thank Andrea Stout at the Penn Cell and Developmental Biology Microscopy core and Carl Eberling from Bruker for assistance with super-resolution imaging and analysis.

Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers

“…Notably, most of these interactions are retained throughout interphase, and a subset are also observed in mitosis, in contrast to the largely transient interactions between cis-regulatory regions observed in early G1 that may reflect the A/B compartment signal . This finding is consistent with observations that cohesin depletion abrogates TADs but not all chromosomal interactions (El Khattabi et al, 2019;Gassler et al, 2017;Rao et al, 2017;Schwarzer et al, 2017;Wutz et al, 2017)is also in line with evidence of cohesin-independent fine-scale chromosomal topology obtained in recent microscopy studies (Bintu et al, 2018;Luppino et al, 2019). These cohesin-independent contacts are presumably separate in nature from the well-characterised A/B compartment structure that is also independent of architectural proteins (Nora et al, 2017;Nuebler et al, 2018;Rao et al, 2017;Wutz et al, 2017).…”

Visualizing the genome in high resolution challenges our textbook understanding

“…However, super-resolution imaging and chromatin tracing revealed a more complex picture of TAD architecture in single cells with highly variable boundaries that persisted after cohesin depletion 48 . More recent studies also revealed a similar picture in which neighboring TADs intermingled with each other extensively 76 . Even more surprisingly, depletion of cohesin lead to a reduction in the intermingling between neighboring TADs rather than inducing ectopic interactions as would be expected from the global loss of TADs observed in Hi-C 76 .…”

“…More recent studies also revealed a similar picture in which neighboring TADs intermingled with each other extensively 76 . Even more surprisingly, depletion of cohesin lead to a reduction in the intermingling between neighboring TADs rather than inducing ectopic interactions as would be expected from the global loss of TADs observed in Hi-C 76 . Overall, architectural proteins like cohesin and CTCF do seem to play an important role in genome organization, however the precise principles of how these proteins cooperate to organize the genome are still being uncovered.…”

“…Indeed, Hi-C showed that short term repeats that become expanded in diseases like Fragile X Syndrome are found at domain boundaries of TADs and these boundaries are severely disrupted in disease states, uncovering correlation between chromatin architecture and repeat expansion diseases 86 . Oligopaint imaging showed that reduced intermixing of TADs upon cohesin loss affects the transcriptional bursting of genes near domain boundaries, which can potentially explain gene expression changes observed in the cohesinopathy Cornelia de Lange syndrome 76 .…”