A Role for Chromatin Remodeling in Cohesin Loading onto Chromosomes

Abstract

Summary Cohesin is a conserved, ring-shaped protein complex that topologically embraces DNA. Its central role in genome organization includes functions in sister chromatid cohesion, DNA repair, and transcriptional regulation. Cohesin loading onto chromosomes requires the Scc2-Scc4 cohesin loader, whose presence on chromatin in budding yeast depends on the RSC chromatin remodeling complex. Here we reveal a dual role of RSC in cohesin loading. RSC acts as a chromatin receptor that recruits Scc2-Scc4 by a direct protein interaction independent of chromatin remodeling. In addition, chromatin remodeling is required to generate a nucleosome-free region that is the substrate for cohesin loading. An engineered cohesin loading module can be created by fusing the Scc2 C terminus to RSC or to other chromatin remodelers, but not to unrelated DNA binding proteins. These observations demonstrate the importance of nucleosome-free DNA for cohesin loading and provide insight into how cohesin accesses DNA during its varied chromosomal activities.

Loops and the activity of loop extrusion factors constrain chromatin dynamics

“…On top of this backdrop, further elaborations likely play important roles, including factors that recognize specific DNA sequences and/or bridge two genomic regions, such as CTCF. This picture is consistent with numerous prior observations including the prevalence of cohesin at TSSs [14][15][16][17][18] that is enhanced in response to transcriptional inhibition 38 and the accumulation of cohesin at sites of transcription termination, particularly at convergent genes in yeast 21 . Our model suggests that CTCF likely reinforces rather than originates TADs, consistent with the variability in the predictive nature of CTCF binding sites to TAD boundaries in some contexts 33 , the observation that depletion of cohesin has a much stronger effect on TAD architecture than CTCF depletion 38,39 , and the full maintenance of insulation at 20% of CTCF-positive boundaries upon CTCF depletion 40 .…”

“…3 and 4 ). Importantly, our model is consistent with the observed ability of cohesin to extrude and compact DNA with a low level of incorporated nucleosomes (about 1 per 8 kb of DNA) 12 , which would be permissive to cohesin loading 17 and loop extrusion between nucleosomes, achieving substantial DNA compaction. Our work also underscores that factors underlying chromatin looping are intimately linked to chromatin dynamics.…”

“…DNA 29 and that nucleosome removal is required for efficient loop extrusion in Xenopus egg 3 extracts 13 . Moreover, numerous studies suggest that cohesin loading on chromosomes occurs at nucleosome-depleted regions (often associated with transcription start sites (TSSs)) and requires ATP-dependent nucleosome remodeling activities [14][15][16][17][18] . In addition, it has been suggested that cohesin translocation requires transcription-coupled nucleosome remodeling [19][20][21][22][23] .…”

“…As expected based on the strong correlation between CTCF binding and TAD boundaries, these models recapitulate experimentally determined TAD patterns 6,9,10 . However, if chromatin restricts where LEFs can be loaded to TSSs [14][15][16][17][18]31 and has to be remodeled to allow loop extrusion, then the organization of transcriptional units (position, size, and direction) necessarily affects the size and location of loops and therefore the TAD pattern. We therefore hypothesized that in vivo translocating LEFs require both an SMC complex and a nucleosome remodeling complex, effectively being composite objects ( Fig.…”

“…We show that the activity of the INO80 nucleosome remodeler enhances chromatin mobility, while cohesin and condensin restrain chromatin mobility. Motivated by these findings and the observations that cohesin is loaded preferentially at nucleosome-depleted transcriptional start sites [14][15][16][17][18] and its efficient translocation requires nucleosome remodeling [19][20][21][22][23] Chromatin organization is inextricably linked to its dynamics. The LEF model posits that multiple dynamic DNA loops appear and disappear in a stochastic fashion, leading to a statistical pattern of increased intra-domain interactions (i.e.…”