Results 21 to 30 of about 9,982 (202)

Chromosome organization by one-sided and two-sided loop extrusion

eLife, 2020
SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops.
Edward J Banigan, Aafke A van den Berg, Hugo B Brandão, John F Marko, Leonid A Mirny   +4 more
doaj   +1 more source

CTCF is a DNA-tension-dependent barrier to cohesin-mediated DNA loop extrusion

, 2022
Abstract In eukaryotes, genomic DNA is extruded into loops by cohesin 1 . By restraining this process, the DNA-binding protein CTCF generates topologically associating domains (TADs) 2-4 that play key roles in gene regulation and recombination ...
Davidson IF, Barth R, Zaczek M, van der Torre J, Tang W, Nagasaka K, Janissen R, Kerssemakers J, Wutz G, Dekker C, Peters J.   +10 more
europepmc   +2 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

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

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

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

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

eLife, 2020
Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL.
Gordana Wutz, Rene Ladurner, Brian Glenn St Hilaire, Roman R Stocsits, Kota Nagasaka, Benoit Pignard, Adrian Sanborn, Wen Tang, Csilla Várnai, Miroslav P Ivanov, Stefan Schoenfelder, Petra van der Lelij, Xingfan Huang, Gerhard Dürnberger, Elisabeth Roitinger, Karl Mechtler, Iain Finley Davidson, Peter Fraser, Erez Lieberman-Aiden, Jan-Michael Peters   +19 more
doaj   +1 more source

DNA Damage Response and Repair in Adaptive Immunity

Frontiers in Cell and Developmental Biology, 2022
The diversification of B-cell receptor (BCR), as well as its secreted product, antibody, is a hallmark of adaptive immunity, which has more specific roles in fighting against pathogens.
Sha Luo, Sha Luo, Ruolin Qiao, Ruolin Qiao, Xuefei Zhang   +4 more
doaj   +1 more source