SMC complexes can traverse physical roadblocks bigger than their ring size

Pradhan, Biswajit; Barth, Roman; Kim, Eugene; Davidson, Iain F.; Bauer, Benedikt; Laar, Theo van; Yang, Wayne; Ryu, Ji Won; Torre, Jaco van der; Peters, Jan‐Michael; Dekker, Cees

doi:10.1016/j.celrep.2022.111491

Cited by 89 publications

(92 citation statements)

References 40 publications

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“…The ability of cohesin to bypass RNAP is consistent with experiments indicating that cohesin does not topologically enclose DNA while it extrudes loops (3, 69). However, our model’s bypassing time is 10-fold longer than predicted for bacterial condensins bypassing RNAPs (50) and measured for SMC complexes bypassing obstacles on DNA in vitro (69). This discrepancy suggests differences between loop extrusion on nucleosomal fibers versus DNA or that cohesin may have some affinity for RNAP.…”

Section: Discussionsupporting

confidence: 84%

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Transcription shapes 3D chromatin organization by interacting with loop extrusion

Banigan

Tang

Berg

et al. 2022

Preprint

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Cohesin organizes mammalian interphase chromosomes by reeling chromatin fibers into dynamic loops (Banigan and Mirny, 2020; Davidson et al., 2019; Kim et al., 2019; Yatskevich et al., 2019). "Loop extrusion" is obstructed when cohesin encounters a properly oriented CTCF protein (Busslinger et al., 2017; de Wit et al., 2015; Fudenberg et al., 2016; Nora et al., 2017; Sanborn et al., 2015; Wutz et al., 2017), and recent work indicates that other factors, such as the replicative helicase MCM (Dequeker et al., 2020), can also act as barriers to loop extrusion. It has been proposed that transcription relocalizes (Busslinger et al., 2017; Glynn et al., 2004; Lengronne et al., 2004) or interferes with cohesin (Heinz et al., 2018; Jeppsson et al., 2020; Valton et al., 2021; S. Zhang et al., 2021), and that active transcription start sites function as cohesin loading sites (Busslinger et al., 2017; Kagey et al., 2010; Zhu et al., 2021; Zuin et al., 2014), but how these effects, and transcription in general, shape chromatin is unknown. To determine whether transcription can modulate loop extrusion, we studied cells in which the primary extrusion barriers could be removed by CTCF depletion and cohesin's residence time and abundance on chromatin could be increased by Wapl knockout. We found evidence that transcription directly interacts with loop extrusion through a novel "moving barrier" mechanism, but not by loading cohesin at active promoters. Hi-C experiments showed intricate, cohesin-dependent genomic contact patterns near actively transcribed genes, and in CTCF-Wapl double knockout (DKO) cells (Busslinger et al., 2017), genomic contacts were enriched between sites of transcription-driven cohesin localization ("cohesin islands"). Similar patterns also emerged in polymer simulations in which transcribing RNA polymerases (RNAPs) acted as "moving barriers" by impeding, slowing, or pushing loop-extruding cohesins. The model predicts that cohesin does not load preferentially at promoters and instead accumulates at TSSs due to the barrier function of RNAPs. We tested this prediction by new ChIP-seq experiments, which revealed that the "cohesin loader" Nipbl (Ciosk et al., 2000) co-localizes with cohesin, but, unlike in previous reports (Busslinger et al., 2017; Kagey et al., 2010; Zhu et al., 2021; Zuin et al., 2014), Nipbl did not accumulate at active promoters. We propose that RNAP acts as a new type of barrier to loop extrusion that, unlike CTCF, is not stationary in its precise genomic position, but is itself dynamically translocating and relocalizes cohesin along DNA. In this way, loop extrusion could enable translocating RNAPs to maintain contacts with distal regulatory elements, allowing transcriptional activity to shape genomic functional organization.

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Section: Discussionsupporting

confidence: 84%

“…However, it is now known that cohesin can translocate by actively extruding DNA loops (3–5). Cohesin can do so without topologically encircling DNA (3), and furthermore, it can bypass large obstacles on DNA (69). The mechanism introduced here can reconcile these new developments with older observations of the effects of RNAP on cohesin.…”

Section: Discussionmentioning

confidence: 99%

Transcription shapes 3D chromatin organization by interacting with loop extrusion

Banigan

Tang

Berg

et al. 2022

Preprint

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“…While the notion of DNA entrapment was challenged again recently by single-molecule imaging that apparently showed the bypass of very large obstacles on DNA by translocating cohesin and condensin 5 , we argue based on our new findings and previous reports that DNA entrapment must not be discounted. Earlier studies measuring saltstable DNA binding are in support of DNA entrapment by cohesin, condensin and Smc5/6, but they did go short of revealing the mode architecture of the hexameric Smc5/6 coreof DNA entrapment or the DNA-containing compartment 16,20,56–58 .…”

Section: Discussionsupporting

confidence: 46%

“…We reveal the DNA entry gate and characterize the trajectory of DNA into the Smc5/6 ring showing that DNA loading involves a looped DNA substrate and eventually leads to the capture of a DNA segment by Smc5/6. While the notion of DNA entrapment was challenged again recently by single-molecule imaging that apparently showed the bypass of very large obstacles on DNA by translocating cohesin and condensin 5 , we argue based on our new findings and previous reports that DNA entrapment must not be discounted. Earlier studies measuring saltstable DNA binding are in support of DNA entrapment by cohesin, condensin and Smc5/6, but they did go short of revealing the mode of DNA entrapment or the DNA-containing compartment 16,20,[56][57][58] .…”

Section: Dna Entrapment By Smc Complexessupporting

confidence: 46%

“…However, the requirement of DNA entrapment and the exact nature of the DNA interaction remain contested with all possibilities being considered in the recent literature ( Fig 1A ): topological DNA entrapment, DNA loop entrapment (also denoted as pseudo-topological entrapment), and exclusively external DNA association. The latter scenario was bolstered by the perceived bypass of very large obstacles by purified cohesin and condensin in single molecule imaging experiments 5 . Cryo-electron microscopy studies have not yet been able to adequately address this question and particularly little is known about how Smc5/6 associates with DNA.…”

Section: Introductionmentioning

confidence: 99%

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DNA segment capture by Smc5/6 holo-complexes

Täschner

Gruber

2022

Preprint

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Three distinct SMC complexes facilitate chromosome folding and segregation in eukaryotes, presumably by DNA translocation and loop extrusion. How SMCs interact with DNA is however not well understood. Among the SMC complexes, Smc5/6 has dedicated roles in DNA repair and in preventing a lethal buildup of aberrant DNA junctions. Here, we describe the reconstitution of ATP-dependent topological DNA loading by Smc5/6 rings. By inserting cysteine residues at selected protein interfaces, we obtained covalently closed compartments upon chemical cross-linking. We show that two SMC sub-compartments and the kleisin compartment topologically entrap a plasmid molecule, but not the full SMC compartment. This is explained by a looped DNA segment inserting into the SMC compartment with the kleisin neck gate locking the loop in place when passing between the two DNA flanks and closing. This DNA segment capture strictly requires the Nse5/6 loader, which opens the neck gate prior to DNA passage. Similar segment capture events without gate opening may provide the power stroke for DNA translocation/loop extrusion in subsequent ATP hydrolysis cycles. Our biochemical experiments thus offer a unifying principle for SMC ATPase function in loading and translocation/extrusion, which is likely relevant to other members of the family of SMC proteins too.

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The dynamic role of cohesin in maintaining human genome architecture

Agarwal,

Korsak,

Choudhury

et al. 2023

BioEssays

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Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher‐order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC‐binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin‐DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin‐centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling.

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SMC complexes can traverse physical roadblocks bigger than their ring size

Cited by 89 publications

References 40 publications

Transcription shapes 3D chromatin organization by interacting with loop extrusion

Transcription shapes 3D chromatin organization by interacting with loop extrusion

DNA segment capture by Smc5/6 holo-complexes

The dynamic role of cohesin in maintaining human genome architecture

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