Results 31 to 40 of about 2,219,993 (156)

Current working models of SMC-driven DNA-loop extrusion

Biochemical Society Transactions, 2023
Structural maintenance of chromosome (SMC) proteins play a key roles in the chromosome organization by condensing two meters of DNA into cell-sized structures considered as the SMC protein extrudes DNA loop. Recent sequencing-based high-throughput chromosome conformation capture technique (Hi-C) and single-molecule experiments have provided direct ...
Kyoung-Wook Moon, Je-Kyung Ryu
openaire   +2 more sources

Reeling it in: how DNA topology drives loop extrusion by condensin

Nature Structural & Molecular Biology, 2022
Structural maintenance of chromosomes (SMC) complexes such as condensin regulate chromosome organization by extruding loops. A new study uses single-molecule imaging of condensin on supercoiled DNA to understand how condensins navigate the under- and overwound DNA states common throughout the genome.
Domenic N. Narducci, Anders S. Hansen
openaire   +3 more sources

Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy.

PLoS Computational Biology, 2021
The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding ...
Hiroki Koide, Noriyuki Kodera, Shveta Bisht, Shoji Takada, Tsuyoshi Terakawa   +4 more
doaj   +1 more source

Three-Dimensional Loop Extrusion [PDF]

, 2021
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations showing that ...
Michieletto, Davide, Bonato, Andrea, Andrea Bonato, Davide Michieletto   +3 more
core   +1 more source

Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries

Nature Communications, 2023
Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered ...
Li-Hsin Chang, Sourav Ghosh, Andrea Papale, Jennifer M. Luppino, Mélanie Miranda, Vincent Piras, Jéril Degrouard, Joanne Edouard, Mallory Poncelet, Nathan Lecouvreur, Sébastien Bloyer, Amélie Leforestier, Eric F. Joyce, David Holcman, Daan Noordermeer   +14 more
doaj   +1 more source

A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis

eLife, 2021
SMC complexes are widely conserved ATP-powered DNA-loop-extrusion motors indispensable for organizing and faithfully segregating chromosomes. How SMC complexes translocate along DNA for loop extrusion and what happens when two complexes meet on the same ...
Anna Anchimiuk, Virginia S Lioy, Florian Patrick Bock, Anita Minnen, Frederic Boccard, Stephan Gruber   +5 more
doaj   +1 more source

TAD cliques predict key features of chromatin organization

BMC Genomics, 2021
Background Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and interactions with the nuclear ...
Tharvesh M. Liyakat Ali, Annaël Brunet, Philippe Collas, Jonas Paulsen   +3 more
doaj   +1 more source

Custom code accompanying Davidson, Barth, Zaczek et al. - CTCF is a DNA-tension-dependent barrier to cohesin-mediated DNA loop extrusion

, 2022
Accompanying custom code for the manuscript "CTCF is a DNA-tension-dependent barrier to cohesin-mediated DNA loop extrusion" by Davidson, Barth, Zaczek, et ...
Roman Barth, Maciej Zaczek, Cees Dekker, Kota Nagasaka, Gordana Wutz, Richard Janissen, Jacob Kerssemakers, Jaco van der Torre, Wen Tang, Iain F. Davidson, Jan-Michael Peters   +10 more
core   +1 more source

The Smc5/6 complex is a DNA loop extruding motor

, 2022
Structural Maintenance of Chromosomes (SMC) protein complexes are essential for the spatial organization of chromosomes. While cohesin and condensin organize chromosomes by extruding DNA loops, the molecular functions of the third eukaryotic SMC complex,
Baaske, MD, Pradhan, B, Igarashi, MU, Kei, Wong JS, Björkegren, C, Kim, E, Kanno, T, Jeppsson, K   +7 more
core   +2 more sources

Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization

eLife, 2021
DNA loop extrusion by condensins and decatenation by DNA topoisomerase II (topo II) are thought to drive mitotic chromosome compaction and individualization. Here, we reveal that the linker histone H1.8 antagonizes condensins and topo II to shape mitotic
Pavan Choppakatla, Bastiaan Dekker, Erin E Cutts, Alessandro Vannini, Job Dekker, Hironori Funabiki   +5 more
doaj   +1 more source