The Cohesin Ring Uses Its Hinge to Organize DNA Using Non-topological as well as Topological Mechanisms

Abstract

As predicted by the notion that sister chromatid cohesion is mediated by entrapment of sister DNAs inside cohesin rings, there is perfect correlation between co-entrapment of circular minichromosomes and sister chromatid cohesion. In most cells where cohesin loads without conferring cohesion, it does so by entrapment of individual DNAs. However, cohesin with a hinge domain whose positively charged lumen is neutralized loads and moves along chromatin despite failing to entrap DNAs. Thus, cohesin engages chromatin in non-topological, as well as topological, manners. Since hinge mutations, but not Smc-kleisin fusions, abolish entrapment, DNAs may enter cohesin rings through hinge opening. Mutation of three highly conserved lysine residues inside the Smc1 moiety of Smc1/3 hinges abolishes all loading without affecting cohesin's recruitment to CEN loading sites or its ability to hydrolyze ATP. We suggest that loading and translocation are mediated by conformational changes in cohesin's hinge driven by cycles of ATP hydrolysis.

Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

“…These results are consistent with earlier observations that showed that in yeast stable chromatin binding by cohesin requires intact DNA (Ciosk et al, 2000). These data can be interpreted in the context of the model where cohesin rings encircle DNA (pseudo-) topologically (Srinivasan et al, 2018). This model of binding predicts that when DNA is fragmented, the cohesin ring can slide off nearby free ends.…”

“…As a result, CTCF-CTCF loops form, and interactions between loci located between convergent CTCF sites are generally increased (TADs). The mechanisms of loop extrusion are not known in detail yet, but may involve the cohesin ring encircling strands of DNA at the bases of loops in a topological or pseudo-topological manner Haering et al, 2008;Ivanov and Nasmyth, 2005;Kagey et al, 2010;Srinivasan et al, 2018).…”

Tandem Directional CTCF Sites Balance Protocadherin Promoter Usage

“…To understand this puzzling phenomenon, we simulated chromosome-conformation dynamics of the Pcdh cluster by a "double clamp" Cohesin dimer extrusion mechanism on a coarse-grained chromatin fragment ( Figure S7E) [18][19][20], based on the location and relative orientation of the Pcdh CBS elements that are dynamically bound by CTCF proteins (Figure 2A and Figure S8) [9,10,12]. Specifically, we assume that Cohesin topologically slides along the Pcdh chromatin fiber until it encounters an opposite CBS element or another sliding Cohesin ring ( Figure S7E) [18,19,39]. Remarkably, computational simulations revealed that, in addition to proximal Pcdh promoter insulation, Cohesin loop extrusion results in a significant increase of chromatin interactions between the HS5-1 enhancer and the distal Pcdh promoters upon insertions of various CBS insulators ( Figure 2B), consistent with the observed data from the QHR-4C experiments (Figure 1, G and H and Figures S3F, S5B, S6B, and S7B).…”

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

“…Nonetheless, a positively charged cluster at the interface of the hinge domains, which faces the inside of the ring, also contributes to DNA binding [44]. Interestingly, a recent budding yeast study has demonstrated a critical role for positively charged patches at the hinge in initial DNA loading as well as topological DNA binding by cohesin [45]. This also leads to the proposal that the hinge domain functions as the initial DNA contact site for subsequent topological DNA entrapment.…”