scholarly journals A major role for Eco1 in regulating cohesin-mediated mitotic chromosome folding

2019 ◽  
Author(s):  
Lise Dauban ◽  
Rémi Montagne ◽  
Agnès Thierry ◽  
Luciana Lazar-Stefanita ◽  
Olivier Gadal ◽  
...  
Keyword(s):  
Mitotic Chromosome ◽  
Dna Looping ◽  
Loop Formation ◽  
Dna Loops ◽  
Sister Chromatids ◽  
Topologically Associating Domains ◽  
Dna Loop ◽  
Main Barrier ◽  
Structural Maintenance Of Chromosomes ◽  
Mitotic Chromatin

AbstractUnderstanding how chromatin organizes spatially into chromatid and how sister chromatids are maintained together during mitosis is of fundamental importance in chromosome biology. Cohesin, a member of the Structural Maintenance of Chromosomes (SMC) complex family, holds sister chromatids together 1–3 and promotes long-range intra-chromatid DNA looping 4,5. These cohesin-mediated DNA loops are important for both higher-order mitotic chromatin compaction6,7 and, in some organisms, compartmentalization of chromosomes during interphase into topologically associating domains (TADs) 8,9. Our understanding of the mechanism(s) by which cohesin generates large DNA loops remains incomplete. It involves a combination of molecular partners and active expansion/extrusion of DNA loops. Here we dissect the roles on loop formation of three partners of the cohesin complex: Pds5 10, Wpl1 11 and Eco1 acetylase 12, during yeast mitosis. We identify a new function for Eco1 in negatively regulating cohesin translocase activity, which powers loop extrusion. In the absence of negative regulation, the main barrier to DNA loop expansion appears to be the centromere. Those results provide new insights on the mechanisms regulating cohesin dependent DNA looping.

DNA loop extrusion by human cohesin

Science ◽  
2019 ◽  
Vol 366 (6471) ◽  
pp. 1338-1345 ◽  
Author(s):  
Iain F. Davidson ◽  
Benedikt Bauer ◽  
Daniela Goetz ◽  
Wen Tang ◽  
Gordana Wutz ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Atpase Activity ◽  
Chromatin Structure ◽  
Adenosine Triphosphatase ◽  
Gene Recombination ◽  
Loop Formation ◽  
Base Pairs ◽  
Topologically Associating Domains ◽  
Dna Loop ◽  
Eukaryotic Genomes

Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo–base pairs per second. Loop formation and maintenance depend on cohesin’s ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.

scholarly journals Facilitation of DNA loop formation by protein–DNA non-specific interactions

Soft Matter ◽  
2019 ◽  
Vol 15 (26) ◽  
pp. 5255-5263 ◽  
Author(s):  
Jaeoh Shin ◽  
Anatoly B. Kolomeisky
Keyword(s):  
Specific Protein ◽  
Dna Looping ◽  
Specific Interactions ◽  
Loop Formation ◽  
Dna Interactions ◽  
Dna Loop ◽  
Protein Dna Interactions

DNA looping is facilitated by non-specific protein–DNA interactions.

scholarly journals Contribution of hCAP-D2, a Non-SMC Subunit of Condensin I, to Chromosome and Chromosomal Protein Dynamics during Mitosis

2005 ◽  
Vol 25 (2) ◽  
pp. 740-750 ◽  
Author(s):  
Erwan Watrin ◽  
Vincent Legagneux
Keyword(s):  
Rna Interference ◽  
Mitotic Spindle ◽  
Topoisomerase Ii ◽  
Mitotic Chromosome ◽  
Chromosomal Protein ◽  
Structural Components ◽  
Mitotic Chromosomes ◽  
Sister Chromatids ◽  
Chromosome Alignment ◽  
Structural Maintenance Of Chromosomes

ABSTRACT Condensins are heteropentameric complexes that were first identified as structural components of mitotic chromosomes. They are composed of two SMC (structural maintenance of chromosomes) and three non-SMC subunits. Condensins play a role in the resolution and segregation of sister chromatids during mitosis, as well as in some aspects of mitotic chromosome assembly. Two distinct condensin complexes, condensin I and condensin II, which differ only in their non-SMC subunits, exist. Here, we used an RNA interference approach to deplete hCAP-D2, a non-SMC subunit of condensin I, in HeLa cells. We found that the association of hCAP-H, another non-SMC subunit of condensin I, with mitotic chromosomes depends on the presence of hCAP-D2. Moreover, chromatid axes, as defined by topoisomerase II and hCAP-E localization, are disorganized in the absence of hCAP-D2, and the resolution and segregation of sister chromatids are impaired. In addition, hCAP-D2 depletion affects chromosome alignment in metaphase and delays entry into anaphase. This suggests that condensin I is involved in the correct attachment between chromosome kinetochores and microtubules of the mitotic spindle. These results are discussed relative to the effects of depleting both condensin complexes.

scholarly journals Fork pausing allows centromere DNA loop formation and kinetochore assembly

2018 ◽  
Vol 115 (46) ◽  
pp. 11784-11789 ◽  
Author(s):  
Diana M. Cook ◽  
Maggie Bennett ◽  
Brandon Friedman ◽  
Josh Lawrimore ◽  
Elaine Yeh ◽  
...  
Keyword(s):  
Replication Fork ◽  
De Novo ◽  
Directed Assembly ◽  
Thermal Fluctuations ◽  
Dna Looping ◽  
Loop Formation ◽  
Replication Fork Progression ◽  
Kinetochore Assembly ◽  
Dna Loop ◽  
Fork Stalling

De novo kinetochore assembly, but not template-directed assembly, is dependent on COMA, the kinetochore complex engaged in cohesin recruitment. The slowing of replication fork progression by treatment with phleomycin (PHL), hydroxyurea, or deletion of the replication fork protection protein Csm3 can activate de novo kinetochore assembly in COMA mutants. Centromere DNA looping at the site of de novo kinetochore assembly can be detected shortly after exposure to PHL. Using simulations to explore the thermodynamics of DNA loops, we propose that loop formation is disfavored during bidirectional replication fork migration. One function of replication fork stalling upon encounters with DNA damage or other blockades may be to allow time for thermal fluctuations of the DNA chain to explore numerous configurations. Biasing thermodynamics provides a mechanism to facilitate macromolecular assembly, DNA repair, and other nucleic acid transactions at the replication fork. These loop configurations are essential for sister centromere separation and kinetochore assembly in the absence of the COMA complex.

scholarly journals Condensin complexes: understanding loop extrusion one conformational change at a time

2020 ◽  
Vol 48 (5) ◽  
pp. 2089-2100
Author(s):  
Erin E. Cutts ◽  
Alessandro Vannini
Keyword(s):  
Protein Structure ◽  
Recent Work ◽  
Conformational Change ◽  
Mechanistic Model ◽  
Loop Formation ◽  
Dna Loops ◽  
Dna Loop ◽  
Higher Eukaryotes ◽  
Structural Maintenance Of Chromosome

Condensin and cohesin, both members of the structural maintenance of chromosome (SMC) family, contribute to the regulation and structure of chromatin. Recent work has shown both condensin and cohesin extrude DNA loops and most likely work via a conserved mechanism. This review focuses on condensin complexes, highlighting recent in vitro work characterising DNA loop formation and protein structure. We discuss similarities between condensin and cohesin complexes to derive a possible mechanistic model, as well as discuss differences that exist between the different condensin isoforms found in higher eukaryotes.

scholarly journals DNA looping by protamine follows a nonuniform spatial distribution

2021 ◽  
Author(s):  
Ryan B. McMillan ◽  
Victoria D. Kuntz ◽  
Luka M. Devenica ◽  
Hilary Bediako ◽  
Ashley R. Carter
Keyword(s):  
Spatial Distribution ◽  
Dna Origami ◽  
Dna Looping ◽  
Loop Formation ◽  
Force Microscopy ◽  
Atomic Force ◽  
Multivalent Cation ◽  
Structural Maintenance Of Chromosomes

ABSTRACTDNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors like lac repressor or by structural maintenance of chromosomes (SMC) proteins such as condensin. Here, however, we are interested in a different looping method whereby multivalent cations (charge≥+3), such as protamine proteins, neutralize the DNA, causing it to form loops and toroids. We considered two previously proposed mechanisms for DNA looping by protamine. In the first mechanism, protamine stabilizes spontaneous DNA fluctuations, forming randomly distributed loops along the DNA. In the second mechanism, protamine binds and bends the DNA to form a loop, creating a distribution of loops that is biased by protamine binding. To differentiate between these mechanisms, we imaged both spontaneous and protamine-induced loops on short-length (≤ 1 μm) DNA fragments using atomic force microscopy (AFM). We then compared the spatial distribution of the loops to several model distributions. A random looping model, which describes the mechanism of spontaneous DNA folding, fit the distribution of spontaneous loops, but it did not fit the distribution of protamine-induced loops. Specifically, it overestimated the number of loops that form at the ends of the molecule and failed to predict a peak in the spatial distribution of loops at an intermediate location along the DNA. An electrostatic multibinding model, which was created to mimic the bind-and-bend mechanism of protamine, was a better fit of the distribution of protamine-induced loops. In this model, multiple protamines bind to the DNA electrostatically within a particular region along the DNA to coordinate the formation of a loop. We speculate that these findings will impact our understanding of protamine’s in vivo role for looping DNA into toroids and the mechanism of DNA condensation by multivalent cations more broadly.SIGNIFICANCEDNA looping is important in a variety of both in vivo functions (e.g. gene regulation) and in vitro applications (e.g. DNA origami). Here, we sought a mechanistic understanding of DNA looping by multivalent cations (≥+3), which condense DNA into loops and toroids. One such multivalent cation is the protein protamine, which condenses DNA in sperm. We investigated the mechanism for loop formation by protamine and found that the experimental data was consistent with an electrostatic multibinding model in which two protamines bind electrostatically to the DNA within a 50-nm region to form a loop. This model is likely general to all multivalent cations and may be helpful in applications involving toroid formation or DNA nanoengineering.

scholarly journals SMC complexes can traverse physical roadblocks bigger than their ring size

2021 ◽  
Author(s):  
Biswajit Pradhan ◽  
Roman Barth ◽  
Eugene Kim ◽  
Iain F. Davidson ◽  
Benedikt Bauer ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Single Molecule ◽  
Chromosome Organization ◽  
Ring Size ◽  
Single Chain ◽  
Dna Loops ◽  
Dna Loop ◽  
Covalently Linked ◽  
Structural Maintenance Of Chromosomes

The ring-shaped structural-maintenance-of-chromosomes (SMC) complexes condensin and cohesin extrude loops of DNA as a key motif in chromosome organization. It remains, however, unclear how these SMC motor proteins can extrude DNA loops in chromatin that is bound with proteins. Here, using in vitro single-molecule visualization, we show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to DNA loop extrusion by yeast condensin. Strikingly, we find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, can be translocated into DNA loops during condensin-driven extrusion. Similarly, human cohesin can pass 200 nm particles during loop extrusion, which even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open up to entrap DNA. These findings disqualify all common loop-extrusion models where DNA passes through the SMC rings (pseudo)topologically, and instead point to a nontopological mechanism for DNA loop extrusion.

scholarly journals Nse1, Nse2, and a Novel Subunit of the Smc5-Smc6 Complex, Nse3, Play a Crucial Role in Meiosis

2004 ◽  
Vol 15 (11) ◽  
pp. 4866-4876 ◽  
Author(s):  
Stephanie Pebernard ◽  
W. Hayes McDonald ◽  
Yelena Pavlova ◽  
John R. Yates ◽  
Michael N. Boddy
Keyword(s):  
Homologous Recombination ◽  
Chromosome Segregation ◽  
Replication Fork ◽  
Mitotic Chromosome ◽  
Nuclear Protein ◽  
Genetic Interactions ◽  
Cellular Resistance ◽  
Spore Viability ◽  
Sister Chromatids ◽  
Structural Maintenance Of Chromosomes

The structural maintenance of chromosomes (SMC) family of proteins play key roles in the organization, packaging, and repair of chromosomes. Cohesin (Smc1+3) holds replicated sister chromatids together until mitosis, condensin (Smc2+4) acts in chromosome condensation, and Smc5+6 performs currently enigmatic roles in DNA repair and chromatin structure. The SMC heterodimers must associate with non-SMC subunits to perform their functions. Using both biochemical and genetic methods, we have isolated a novel subunit of the Smc5+6 complex, Nse3. Nse3 is an essential nuclear protein that is required for normal mitotic chromosome segregation and cellular resistance to a number of genotoxic agents. Epistasis with Rhp51 (Rad51) suggests that like Smc5+6, Nse3 functions in the homologous recombination based repair of DNA damage. We previously identified two non-SMC subunits of Smc5+6 called Nse1 and Nse2. Analysis of nse1-1, nse2-1, and nse3-1 mutants demonstrates that they are crucial for meiosis. The Nse1 mutant displays meiotic DNA segregation and homologous recombination defects. Spore viability is reduced by nse2-1 and nse3-1, without affecting interhomolog recombination. Finally, genetic interactions shared by the nse mutants suggest that the Smc5+6 complex is important for replication fork stability.

Cohesin dependent compaction of mitotic chromosomes

2016 ◽  
Author(s):  
Stephanie A Schalbetter ◽  
Anton Goloborodko ◽  
Geoffrey Fudenberg ◽  
Jon M Belton ◽  
Catrina Miles ◽  
...  
Keyword(s):  
Sister Chromatid ◽  
Mitotic Chromosome ◽  
Protein Complexes ◽  
Budding Yeast ◽  
Mitotic Chromosomes ◽  
Chromosome Conformation ◽  
Sister Chromatids ◽  
Chromatid Cohesion ◽  
Structural Maintenance Of Chromosomes

Structural Maintenance of Chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply-conserved SMC complexes, organize chromosomes in budding yeast. The canonical role of cohesins is to co-align sister chromatids whilst condensins generally compact mitotic chromosomes. We find strikingly different roles in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosomes arms, independent of and in addition to its role in sister-chromatid cohesion. Cohesin dependent mitotic chromosome compaction can be fully accounted for through cis-looping of chromatin by loop extrusion. Second, condensin is dispensable for compaction along chromosomal arms and instead plays a specialized role, structuring rDNA and peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that SMC-dependent looping is readily deployed in a range of contexts to functionally organize chromosomes.

The thermodynamics of DNA loop formation, from J to Z

2013 ◽  
Vol 41 (2) ◽  
pp. 513-518 ◽  
Author(s):  
Stephen D. Levene ◽  
Stefan M. Giovan ◽  
Andreas Hanke ◽  
Massa J. Shoura
Keyword(s):  
Dna Looping ◽  
Biological Processes ◽  
Loop Formation ◽  
Base Pairs ◽  
Dna Molecule ◽  
Dna Loop ◽  
Sensitive Function ◽  
Statistical Mechanical ◽  
Single Dna Molecule ◽  
Dna Cyclization

The formation of DNA loops is a ubiquitous theme in biological processes, including DNA replication, recombination and repair, and gene regulation. These loops are mediated by proteins bound at specific sites along the contour of a single DNA molecule, in some cases many thousands of base pairs apart. Loop formation incurs a thermodynamic cost that is a sensitive function of the length of looped DNA as well as the geometry and elastic properties of the DNA-bound protein. The free energy of DNA looping is logarithmically related to a generalization of the Jacobson–Stockmayer factor for DNA cyclization, termed the J factor. In the present article, we review the thermodynamic origins of this quantity, discuss how it is measured experimentally and connect the macroscopic interpretation of the J factor with a statistical-mechanical description of DNA looping and cyclization.

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