The topology of DNA entrapment by cohesin rings

Chapard, Christophe; Jones, R. E.; T, van Oepen; Jc, Scheinost; Nasmyth, K

doi:10.1101/495762

Cited by 3 publications

(4 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The reaction cycle begins and ends with the enzyme in its apo state ‘0’ (Figure 4A, leftmost and rightmost states). A DNA segment is encircled by the lower compartment in bsSMC and yeast cohesin in the apo state (25,26), either sterically held, or possibly bound non-covalently to a DNA binding site as observed in eukaryotic SMC complexes (27–30). The configuration of state 0 can be imagined to be the result of the type of ‘loading’ reaction associated with initiation of SMC complex activity.…”

Section: Methodsmentioning

confidence: 99%

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Marko

Rios

Barducci

et al. 2019

Nucleic Acids Research

105

125

View full text Add to dashboard Cite

Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs into series of loops. Experimental data suggest that SMC complexes are able to translocate on DNA, as well as pull out lengths of DNA via a ‘loop extrusion’ process. We describe a Brownian loop-capture-ratchet model for translocation and loop extrusion based on known structural, catalytic, and DNA-binding properties of the Bacillus subtilis SMC complex. Our model provides an example of a new class of molecular motor where large conformational fluctuations of the motor ‘track’—in this case DNA—are involved in the basic translocation process. Quantitative analysis of our model leads to a series of predictions for the motor properties of SMC complexes, most strikingly a strong dependence of SMC translocation velocity and step size on tension in the DNA track that it is moving along, with ‘stalling’ occuring at subpiconewton tensions. We discuss how the same mechanism might be used by structurally related SMC complexes (Escherichia coli MukBEF and eukaryote condensin, cohesin and SMC5/6) to organize genomic DNA.

show abstract

Section: Methodsmentioning

confidence: 99%

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Marko

Rios

Barducci

et al. 2019

Nucleic Acids Research

105

125

View full text Add to dashboard Cite

show abstract

“…4a, leftmost and rightmost states). A DNA segment is encircled by the lower compartment in bsSMC and yeast cohesin in the apo state [25,26], either sterically held, or possibly bound noncovalently to a DNA binding site as observed in eukaryotic SMC complexes [27][28][29][30]. The configuration of state 0 can be imagined to be the result of the type of 'loading' reaction associated with initiation of SMC complex activity.…”

Section: Reaction Cycle For Translocation Of Smc Along Dnamentioning

confidence: 99%

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Marko¹,

Rios

Barducci

et al. 2018

Preprint

View full text Add to dashboard Cite

Cells possess remarkable control of the folding and entanglement topology of very long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs into series of loops.Recent experimental data suggest that SMC complexes are able to translocate on DNA, as well as pull out lengths of DNA via a 'loop extrusion' process. We describe a Brownian loop-captureratchet model for translocation and loop extrusion based on known structural, catalytic, and DNA-binding properties of the Bacillus subtilis SMC complex. Our model provides an example of a new class of molecular motor where large conformational fluctuations of the motor 'track' -in this case DNA -are involved in the basic translocation process. Quantitative analysis of our model leads to a series of predictions for the motor properties of SMC complexes, most strikingly a strong dependence of SMC translocation velocity on tension in the DNA track that it is moving along.

show abstract

“…2A) (Huang et al, 2005;Zhang et al, 2008). More recent structural and spectroscopic studies provide strong support that tethering involves a single copy of the cohesin complex with two distinct chromatinbinding sites (model 2) (Chapard et al, 2019;Liu et al, 2020;Xu and Yanagida, 2019). However, evidence pointing to cohesin dimerization (Eng et al, 2014(Eng et al, , 2015 needs to be reconciled with this model.…”

Section: The Dual Role Of Cohesin In Sister Chromatid Cohesion and Interphase Chromatin Organizationmentioning

confidence: 99%

“…chromatid is locked between the kleisin and the HEAT-repeats subunits (Fig. 2A) (Chapard et al, 2019;Xu and Yanagida, 2019); and (3) a model that is based on the entrapment of a single chromatid in the central lumen of cohesin, while cohesion is achieved through the dimerization of cohesins (Fig. 2A) (Huang et al, 2005;Zhang et al, 2008).…”

Section: The Dual Role Of Cohesin In Sister Chromatid Cohesion and Interphase Chromatin Organizationmentioning

confidence: 99%

Hit the brakes – a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes

Matityahu

Onn

2021

Journal of Cell Science

View full text Add to dashboard Cite

The three-dimensional structure of chromatin is determined by the action of protein complexes of the structural maintenance of chromosome (SMC) family. Eukaryotic cells contain three SMC complexes, cohesin, condensin, and a complex of Smc5 and Smc6. Initially, cohesin was linked to sister chromatid cohesion, the process that ensures the fidelity of chromosome segregation in mitosis. In recent years, a second function in the organization of interphase chromatin into topologically associated domains has been determined, and loop extrusion has emerged as the leading mechanism of this process. Interestingly, fundamental mechanistic differences exist between mitotic tethering and loop extrusion. As distinct molecular switches that aim to suppress loop extrusion in different biological contexts have been identified, we hypothesize here that loop extrusion is the default biochemical activity of cohesin and that its suppression shifts cohesin into a tethering mode. With this model, we aim to provide an explanation for how loop extrusion and tethering can coexist in a single cohesin complex and also apply it to the other eukaryotic SMC complexes, describing both similarities and differences between them. Finally, we present model-derived molecular predictions that can be tested experimentally, thus offering a new perspective on the mechanisms by which SMC complexes shape the higher-order structure of chromatin.

show abstract

The topology of DNA entrapment by cohesin rings

Cited by 3 publications

References 46 publications

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Hit the brakes – a new perspective on the loop extrusion mechanism of cohesin and other SMC complexes

Contact Info

Product

Resources

About