Literature DB >> 33295869

The interplay between asymmetric and symmetric DNA loop extrusion.

Edward J Banigan1, Leonid A Mirny1.   

Abstract

Chromosome compaction is essential for reliable transmission of genetic information. Experiments suggest that ∼1000-fold compaction is driven by condensin complexes that extrude chromatin loops, by progressively collecting chromatin fiber from one or both sides of the complex to form a growing loop. Theory indicates that symmetric two-sided loop extrusion can achieve such compaction, but recent single-molecule studies (Golfier et al., 2020) observed diverse dynamics of condensins that perform one-sided, symmetric two-sided, and asymmetric two-sided extrusion. We use simulations and theory to determine how these molecular properties lead to chromosome compaction. High compaction can be achieved if even a small fraction of condensins have two essential properties: a long residence time and the ability to perform two-sided (not necessarily symmetric) extrusion. In mixtures of condensins I and II, coupling two-sided extrusion and stable chromatin binding by condensin II promotes compaction. These results provide missing connections between single-molecule observations and chromosome-scale organization.
© 2020, Banigan and Mirny.

Entities:  

Keywords:  SMC complexes; chromosome compaction; chromosomes; condensin; gene expression; human; loop extrusion; mitosis; physics of living systems; simulation; xenopus

Mesh:

Substances:

Year:  2020        PMID: 33295869      PMCID: PMC7793625          DOI: 10.7554/eLife.63528

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.713


  72 in total

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Authors:  Tatsuya Hirano
Journal:  Cell       Date:  2016-02-25       Impact factor: 41.582

2.  DNA loop extrusion by human cohesin.

Authors:  Iain F Davidson; Benedikt Bauer; Daniela Goetz; Wen Tang; Gordana Wutz; Jan-Michael Peters
Journal:  Science       Date:  2019-11-21       Impact factor: 47.728

3.  Three-dimensional folding and functional organization principles of the Drosophila genome.

Authors:  Tom Sexton; Eitan Yaffe; Ephraim Kenigsberg; Frédéric Bantignies; Benjamin Leblanc; Michael Hoichman; Hugues Parrinello; Amos Tanay; Giacomo Cavalli
Journal:  Cell       Date:  2012-01-19       Impact factor: 41.582

4.  The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics.

Authors:  Shinya Ohta; Jimi-Carlo Bukowski-Wills; Luis Sanchez-Pulido; Flavia de Lima Alves; Laura Wood; Zhuo A Chen; Melpi Platani; Lutz Fischer; Damien F Hudson; Chris P Ponting; Tatsuo Fukagawa; William C Earnshaw; Juri Rappsilber
Journal:  Cell       Date:  2010-09-03       Impact factor: 41.582

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

Authors:  Edward J Banigan; Aafke A van den Berg; Hugo B Brandão; John F Marko; Leonid A Mirny
Journal:  Elife       Date:  2020-04-06       Impact factor: 8.713

6.  Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.

Authors:  Matteo Vietri Rudan; Christopher Barrington; Stephen Henderson; Christina Ernst; Duncan T Odom; Amos Tanay; Suzana Hadjur
Journal:  Cell Rep       Date:  2015-02-26       Impact factor: 9.423

7.  Absolute quantification of cohesin, CTCF and their regulators in human cells.

Authors:  Johann Holzmann; Antonio Z Politi; Kota Nagasaka; Merle Hantsche-Grininger; Nike Walther; Birgit Koch; Johannes Fuchs; Gerhard Dürnberger; Wen Tang; Rene Ladurner; Roman R Stocsits; Georg A Busslinger; Béla Novák; Karl Mechtler; Iain Finley Davidson; Jan Ellenberg; Jan-Michael Peters
Journal:  Elife       Date:  2019-06-17       Impact factor: 8.140

8.  Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging.

Authors:  Martial Marbouty; Antoine Le Gall; Diego I Cattoni; Axel Cournac; Alan Koh; Jean-Bernard Fiche; Julien Mozziconacci; Heath Murray; Romain Koszul; Marcelo Nollmann
Journal:  Mol Cell       Date:  2015-08-20       Impact factor: 17.970

9.  Compaction and segregation of sister chromatids via active loop extrusion.

Authors:  Anton Goloborodko; Maxim V Imakaev; John F Marko; Leonid Mirny
Journal:  Elife       Date:  2016-05-18       Impact factor: 8.140

10.  A quantitative map of human Condensins provides new insights into mitotic chromosome architecture.

Authors:  Nike Walther; M Julius Hossain; Antonio Z Politi; Birgit Koch; Moritz Kueblbeck; Øyvind Ødegård-Fougner; Marko Lampe; Jan Ellenberg
Journal:  J Cell Biol       Date:  2018-04-09       Impact factor: 10.539

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  1 in total

1.  Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells.

Authors:  Sarah G Swygert; Dejun Lin; Stephanie Portillo-Ledesma; Po-Yen Lin; Dakota R Hunt; Cheng-Fu Kao; Tamar Schlick; William S Noble; Toshio Tsukiyama
Journal:  Elife       Date:  2021-11-04       Impact factor: 8.140

  1 in total

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