Cohesin mediates DNA loop extrusion by a “swing and clamp” mechanism

Abstract

Structural maintenance of chromosomes (SMC) complexes organize genome topology in all kingdoms of life and have been proposed to perform this function by DNA loop extrusion. How this process works is unknown. Here, we have analyzed how loop extrusion is mediated by human cohesin-NIPBL complexes, which enable chromatin folding in interphase cells. We have identified DNA binding sites and large-scale conformational changes that are required for loop extrusion and have determined how these are coordinated. Our results suggest that DNA is translocated by a spontaneous 50 nm-swing of cohesin's hinge, which hands DNA over to the ATPase head of SMC3, where upon binding of ATP, DNA is clamped by NIPBL. During this process, NIPBL ''jumps ship'' from the hinge toward the SMC3 head and might thereby couple the spontaneous hinge swing to ATP-dependent DNA clamping. These results reveal mechanistic principles of how cohesin-NIPBL and possibly other SMC complexes mediate loop extrusion. ll

Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events

“…By contrast, our result that ATP binding is the step-generating process is in good agreement with cryo-EM results on cohesin ( 20 , 21 , 55 , 56 ) and with AFM data on condensin that showed a transition from an extended state to a hinge-engaged state upon ATP binding ( 18 ). In addition, our results are also consistent with recent AFM and single-molecule FRET study on human cohesin that showed that ATP-binding promotes head domain engagement that provides DNA binding sites via hinge-head interaction ( 57 ). Importantly, our finding further agrees with results found in vivo , which reported that the hinge domain of cohesin engages with the globular domain to form a B shape ( 58 ).…”

“…Our data are also in good agreement with a DNA scrunching model that we recently hypothesized based on these AFM data ( 18 ), where condensin anchors itself to DNA using the safety belt of the Ycg1-Brn1 domains (Figure 4I , i ) ( 11 , 59 ), whereupon the hinge domain binds to a proximate region of the DNA, and ATP binding induces a transition from an extended O shape to a collapsed hinge-engaged B shape, thereby pulling the hinge-bound DNA to the globular domain (Figure 4I , ii), which establishes a step in the loop extrusion process. In support of this concept, previous studies showed that ATP binding induces the dimerization of the head domains, forming a positively charged cavity that is able to bind DNA ( 21 , 24 , 57 , 60 , 61 ). The low stalling force that we observed is consistent with a type of a motor mechanism that involves a Brownian ratchet motion of the flexible SMC arms that underlies the hinge to globular domain step ( 62 ).…”

Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events

“…By contrast, our result that ATP binding is the step-generating process is in good agreement with cryo-EM results on cohesin (20,21,55,56) and with AFM data on condensin that showed a transition from an extended state to a hinge-engaged state upon ATP binding (18). In addition, our results are also consistent with recent AFM and single-molecule FRET study on human cohesin that showed that ATP-binding promotes head domain engagement that provides DNA binding sites via hingehead interaction (57). Importantly, our finding further agrees with results found in vivo, which reported that the hinge domain of cohesin engages with the globular domain to form a B shape (58).…”

Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains

“…WPL1 deletion increased Smc3 levels in smc3-K112,113R cells ( Figure 9C and D ), but to a lesser extent than in the eco1-aa background ( Figure 3A ). Although the reasons for this are unclear, the finding that these residues are involved in binding DNA ( Shi et al, 2020 ; Bauer et al, 2021 ) suggests that the amino acid substitutions may themselves perturb cohesin loading or translocation, in addition to preventing acetylation by Eco1. Nevertheless, although introduction of the smc3-K112,113R mutation into wpl1Δ cells only slightly reduced Smc3 levels at centromeres, it greatly reduced Smc3 levels at pericentromeric borders and arm sites ( Figure 9C and D , compare wpl1Δ and smc3-K112,113R wpl1Δ ).…”