The Energetics and Physiological Impact of Cohesin Extrusion

Abstract

Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural "stripes," where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.

Differential contribution of steady‐state RNA and active transcription in chromatin organization

“…Interestingly, the weakening of TAD boundaries was independent of CTCF binding (Fig E), suggesting supporting roles for transcription and CTCF in the formation of TADs and regulation of inter‐TAD interactions. This finding is consistent with previous reports that transcriptional inhibition as well as transcriptional elongation can displace cohesin from CTCF sites and disrupt chromatin interactions , correlating with weakening of TAD boundaries.…”

“…ª 2019 The Authors EMBO reports 20: e48068 | 2019 their fine-tuning (i.e., regulation of specific enhancer-promoter interactions or inter-TAD interactions) may be regulated by an interplay between loop extrusion and the act of transcription, in addition to the selective binding of transcription factors and chromatin modifiers at TAD boundaries [1,[55][56][57]. However, it is worth noting that Vian and colleagues have demonstrated that TADs can disappear upon cohesin degradation and reappear after rescue, even in the absence of transcription [32]. Similarly, previous reports suggested that the act of transcription can influence the 3D structure of the nucleus [27,[58][59][60].…”

“…More recently, active transcription has also been postulated as a major driving force in shaping genome architecture [26][27][28][29]. Not only was it shown that transcriptional elongation can remodel 3D genome structure [30,31], but transcription can also affect TAD interactions [26,32]. However, whether it is structural roles involving pre-existing nuclear RNA content-or the processes tied to active transcription-that more strongly impact higher-order nuclear architecture on a genome-wide scale, as detected by Hi-C, has not been previously determined.…”

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection

“…After removal of the insoluble debris, the lysate was incubated with specific antibodies against CTCF (07-729; Millipore), RAD21 (ab992; Abcam), or NIPBL (A301-779A; Bethyl Laboratories) and purified by protein A-agarose beads Millipore). NIPBL and CTCF ChIP-seq for the Igh locus were recently published [58]. ChIP DNA was extracted and prepared for high-throughput sequencing using a DNA library preparation kit for Illumina (NEB).…”

DNA entry, exit and second DNA capture by cohesin: insights from biochemical experiments

“…Cohesin often establishes chromatin loops between enhancers and promoters [8]. Recent high resolution Hi-C studies have also found that cohesin makes contributions to interactions between enhancers and along gene bodies [78,79]. Substantial DNA helices can be opened during gene transcription, which would be potential targets for second DNA capture by cohesin (Figure 2(d)) [80].…”