Literature DB >> 35103965

A Robust Protocol for Investigating the Cohesin Complex by ChIP-Sequencing.

Macarena Moronta Gines1, Kerstin S Wendt2.   

Abstract

The investigation of cohesin binding sites throughout different mammalian genomes by ChIP-sequencing has been fundamental to discover how cohesin and CTCF collaborate to form chromatin loops and to gain insight in the intricate regulation of cohesin. Here we describe a detailed ChIP protocol that has been successfully used for different cohesin subunits and cohesin regulators in various cell lines.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  ChIP; Chromatin immunoprecipitation; Cohesin

Mesh：

Substances：

Year:  2022        PMID： 35103965     DOI： 10.1007/978-1-0716-2140-0_7

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  15 in total

Review 1.  Cohesion and cohesin-dependent chromatin organization.

Authors:  Tomoko Nishiyama
Journal:  Curr Opin Cell Biol       Date:  2018-12-11       Impact factor: 8.382

Review 2.  On the choreography of genome folding: A grand pas de deux of cohesin and CTCF.

Authors:  Marjon S van Ruiten; Benjamin D Rowland
Journal:  Curr Opin Cell Biol       Date:  2021-02-02       Impact factor: 8.382

3.  CTCF and cohesin regulate chromatin loop stability with distinct dynamics.

Authors:  Anders S Hansen; Iryna Pustova; Claudia Cattoglio; Robert Tjian; Xavier Darzacq
Journal:  Elife       Date:  2017-05-03       Impact factor: 8.140

4.  Cohesin Loss Eliminates All Loop Domains.

Authors:  Suhas S P Rao; Su-Chen Huang; Brian Glenn St Hilaire; Jesse M Engreitz; Elizabeth M Perez; Kyong-Rim Kieffer-Kwon; Adrian L Sanborn; Sarah E Johnstone; Gavin D Bascom; Ivan D Bochkov; Xingfan Huang; Muhammad S Shamim; Jaeweon Shin; Douglass Turner; Ziyi Ye; Arina D Omer; James T Robinson; Tamar Schlick; Bradley E Bernstein; Rafael Casellas; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2017-10-05       Impact factor: 41.582

5.  Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.

Authors:  Gordana Wutz; Csilla Várnai; Kota Nagasaka; David A Cisneros; Roman R Stocsits; Wen Tang; Stefan Schoenfelder; Gregor Jessberger; Matthias Muhar; M Julius Hossain; Nike Walther; Birgit Koch; Moritz Kueblbeck; Jan Ellenberg; Johannes Zuber; Peter Fraser; Jan-Michael Peters
Journal:  EMBO J       Date:  2017-12-07       Impact factor: 11.598

6.  Cohesin mediates transcriptional insulation by CCCTC-binding factor.

Authors:  Kerstin S Wendt; Keisuke Yoshida; Takehiko Itoh; Masashige Bando; Birgit Koch; Erika Schirghuber; Shuichi Tsutsumi; Genta Nagae; Ko Ishihara; Tsuyoshi Mishiro; Kazuhide Yahata; Fumio Imamoto; Hiroyuki Aburatani; Mitsuyoshi Nakao; Naoko Imamoto; Kazuhiro Maeshima; Katsuhiko Shirahige; Jan-Michael Peters
Journal:  Nature       Date:  2008-01-30       Impact factor: 49.962

7.  Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.

Authors:  Aaron D Viny; Robert L Bowman; Yu Liu; Vincent-Philippe Lavallée; Shira E Eisman; Wenbin Xiao; Benjamin H Durham; Anastasia Navitski; Jane Park; Stephanie Braunstein; Besmira Alija; Abdul Karzai; Isabelle S Csete; Matthew Witkin; Elham Azizi; Timour Baslan; Christopher J Ott; Dana Pe'er; Job Dekker; Richard Koche; Ross L Levine
Journal:  Cell Stem Cell       Date:  2019-09-05       Impact factor: 24.633

8.  Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl.

Authors:  Georg A Busslinger; Roman R Stocsits; Petra van der Lelij; Elin Axelsson; Antonio Tedeschi; Niels Galjart; Jan-Michael Peters
Journal:  Nature       Date:  2017-04-19       Impact factor: 49.962

9.  Two independent modes of chromatin organization revealed by cohesin removal.

Authors:  Wibke Schwarzer; Nezar Abdennur; Anton Goloborodko; Aleksandra Pekowska; Geoffrey Fudenberg; Yann Loe-Mie; Nuno A Fonseca; Wolfgang Huber; Christian H Haering; Leonid Mirny; Francois Spitz
Journal:  Nature       Date:  2017-09-27       Impact factor: 49.962

10.  CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention.

Authors:  Elena M Pugacheva; Naoki Kubo; Dmitri Loukinov; Md Tajmul; Sungyun Kang; Alexander L Kovalchuk; Alexander V Strunnikov; Gabriel E Zentner; Bing Ren; Victor V Lobanenkov
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-14       Impact factor: 11.205
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