Literature DB >> 24606138

Regulating the chromatin landscape: structural and mechanistic perspectives.

Blaine Bartholomew1.   

Abstract

A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).

Entities:  

Keywords:  ATRX; CHD; INO80; ISWI; SWI/SNF; SWR1; cancer; differentiation; epigenetics; histone; nucleosome; transcription

Mesh:

Substances:

Year:  2014        PMID: 24606138      PMCID: PMC4332854          DOI: 10.1146/annurev-biochem-051810-093157

Source DB:  PubMed          Journal:  Annu Rev Biochem        ISSN: 0066-4154            Impact factor:   23.643


  164 in total

1.  The INO80 ATP-dependent chromatin remodeling complex is a nucleosome spacing factor.

Authors:  Maheshi Udugama; Abdellah Sabri; Blaine Bartholomew
Journal:  Mol Cell Biol       Date:  2010-12-06       Impact factor: 4.272

2.  Structural biochemistry of nuclear actin-related proteins 4 and 8 reveals their interaction with actin.

Authors:  Sebastian Fenn; Dennis Breitsprecher; Christian B Gerhold; Gregor Witte; Jan Faix; Karl-Peter Hopfner
Journal:  EMBO J       Date:  2011-04-15       Impact factor: 11.598

3.  The RSC chromatin remodelling ATPase translocates DNA with high force and small step size.

Authors:  George Sirinakis; Cedric R Clapier; Ying Gao; Ramya Viswanathan; Bradley R Cairns; Yongli Zhang
Journal:  EMBO J       Date:  2011-05-06       Impact factor: 11.598

4.  SnapShot: Chromatin remodeling: CHD.

Authors:  Jennifer K Sims; Paul A Wade
Journal:  Cell       Date:  2011-02-18       Impact factor: 41.582

5.  Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP.

Authors:  Petra Wollmann; Sheng Cui; Ramya Viswanathan; Otto Berninghausen; Melissa N Wells; Manuela Moldt; Gregor Witte; Agata Butryn; Petra Wendler; Roland Beckmann; David T Auble; Karl-Peter Hopfner
Journal:  Nature       Date:  2011-07-06       Impact factor: 49.962

6.  The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes.

Authors:  Christian J Wippo; Lars Israel; Shinya Watanabe; Andreas Hochheimer; Craig L Peterson; Philipp Korber
Journal:  EMBO J       Date:  2011-02-22       Impact factor: 11.598

7.  Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin.

Authors:  Sebastian Eustermann; Ji-Chun Yang; Martin J Law; Rachel Amos; Lynda M Chapman; Clare Jelinska; David Garrick; David Clynes; Richard J Gibbons; Daniela Rhodes; Douglas R Higgs; David Neuhaus
Journal:  Nat Struct Mol Biol       Date:  2011-06-12       Impact factor: 15.369

8.  Altered telomeres in tumors with ATRX and DAXX mutations.

Authors:  Christopher M Heaphy; Roeland F de Wilde; Yuchen Jiao; Alison P Klein; Barish H Edil; Chanjuan Shi; Chetan Bettegowda; Fausto J Rodriguez; Charles G Eberhart; Sachidanand Hebbar; G Johan Offerhaus; Roger McLendon; B Ahmed Rasheed; Yiping He; Hai Yan; Darell D Bigner; Sueli Mieko Oba-Shinjo; Suely Kazue Nagahashi Marie; Gregory J Riggins; Kenneth W Kinzler; Bert Vogelstein; Ralph H Hruban; Anirban Maitra; Nickolas Papadopoulos; Alan K Meeker
Journal:  Science       Date:  2011-06-30       Impact factor: 47.728

9.  Structure and mechanism of the chromatin remodelling factor ISW1a.

Authors:  Kazuhiro Yamada; Timothy D Frouws; Brigitte Angst; Daniel J Fitzgerald; Carl DeLuca; Kyoko Schimmele; David F Sargent; Timothy J Richmond
Journal:  Nature       Date:  2011-04-28       Impact factor: 49.962

10.  The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains.

Authors:  Daniel P Ryan; Ramasubramanian Sundaramoorthy; David Martin; Vijender Singh; Tom Owen-Hughes
Journal:  EMBO J       Date:  2011-05-27       Impact factor: 11.598

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  93 in total

Review 1.  Epigenetic regulation of ageing: linking environmental inputs to genomic stability.

Authors:  Bérénice A Benayoun; Elizabeth A Pollina; Anne Brunet
Journal:  Nat Rev Mol Cell Biol       Date:  2015-09-16       Impact factor: 94.444

2.  SWI/SNF chromatin remodeling complex regulates a non-chromatin substrate.

Authors:  Prabodh Kapoor; Xuetong Shen
Journal:  Cell Cycle       Date:  2015-08-03       Impact factor: 4.534

Review 3.  Touch, act and go: landing and operating on nucleosomes.

Authors:  Valentina Speranzini; Simona Pilotto; Titia K Sixma; Andrea Mattevi
Journal:  EMBO J       Date:  2016-01-19       Impact factor: 11.598

4.  Emerging Chemistry Strategies for Engineering Native Chromatin.

Authors:  Yael David; Tom W Muir
Journal:  J Am Chem Soc       Date:  2017-06-27       Impact factor: 15.419

5.  Histone core phosphorylation regulates DNA accessibility.

Authors:  Matthew Brehove; Tao Wang; Justin North; Yi Luo; Sarah J Dreher; John C Shimko; Jennifer J Ottesen; Karolin Luger; Michael G Poirier
Journal:  J Biol Chem       Date:  2015-07-13       Impact factor: 5.157

6.  TRIM29 regulates the assembly of DNA repair proteins into damaged chromatin.

Authors:  Yasushi Masuda; Hidehisa Takahashi; Shigeo Sato; Chieri Tomomori-Sato; Anita Saraf; Michael P Washburn; Laurence Florens; Ronald C Conaway; Joan W Conaway; Shigetsugu Hatakeyama
Journal:  Nat Commun       Date:  2015-06-22       Impact factor: 14.919

7.  A SMARCD2-containing mSWI/SNF complex is required for granulopoiesis.

Authors:  Brittany C Michel; Cigall Kadoch
Journal:  Nat Genet       Date:  2017-04-26       Impact factor: 38.330

Review 8.  Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes.

Authors:  Cedric R Clapier; Janet Iwasa; Bradley R Cairns; Craig L Peterson
Journal:  Nat Rev Mol Cell Biol       Date:  2017-05-17       Impact factor: 94.444

9.  Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair.

Authors:  Avinash Srivastava; Rakesh K Mishra
Journal:  J Biosci       Date:  2020       Impact factor: 1.826

10.  INO80 Chromatin Remodeler Facilitates Release of RNA Polymerase II from Chromatin for Ubiquitin-Mediated Proteasomal Degradation.

Authors:  Anne Lafon; Surayya Taranum; Federico Pietrocola; Florent Dingli; Damarys Loew; Sandipan Brahma; Blaine Bartholomew; Manolis Papamichos-Chronakis
Journal:  Mol Cell       Date:  2015-11-19       Impact factor: 17.970

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