Literature DB >> 22831768

Structural dynamics of nucleosomes at single-molecule resolution.

John S Choy1, Tae-Hee Lee.   

Abstract

The detailed mechanisms of how DNA that is assembled around a histone core can be accessed by DNA-binding proteins for transcription, replication, or repair, remain elusive nearly 40 years after Kornberg's nucleosome model was proposed. Uncovering the structural dynamics of nucleosomes is a crucial step in elucidating the mechanisms regulating genome accessibility. This requires the deconvolution of multiple structural states within an ensemble. Recent advances in single-molecule methods enable unprecedented efficiency in examining subpopulation dynamics. In this review, we summarize studies of nucleosome structure and dynamics from single-molecule approaches and how they advance our understanding of the mechanisms that govern DNA transactions. Published by Elsevier Ltd.

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Year:  2012        PMID: 22831768      PMCID: PMC3669752          DOI: 10.1016/j.tibs.2012.06.006

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  82 in total

1.  Role of direct interactions between the histone H4 Tail and the H2A core in long range nucleosome contacts.

Authors:  Divya Sinha; Michael A Shogren-Knaak
Journal:  J Biol Chem       Date:  2010-03-29       Impact factor: 5.157

2.  Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation.

Authors:  Darren Yang; Gaurav Arya
Journal:  Phys Chem Chem Phys       Date:  2010-12-15       Impact factor: 3.676

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.  Effects of histone acetylation by Piccolo NuA4 on the structure of a nucleosome and the interactions between two nucleosomes.

Authors:  Ju Yeon Lee; Sijie Wei; Tae-Hee Lee
Journal:  J Biol Chem       Date:  2011-01-31       Impact factor: 5.157

Review 5.  Recognizing and remodeling the nucleosome.

Authors:  Sebastian Glatt; Claudio Alfieri; Christoph W Müller
Journal:  Curr Opin Struct Biol       Date:  2011-03-04       Impact factor: 6.809

6.  The histone chaperone Nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone DNA interactions.

Authors:  Andrew J Andrews; Xu Chen; Alexander Zevin; Laurie A Stargell; Karolin Luger
Journal:  Mol Cell       Date:  2010-03-26       Impact factor: 17.970

7.  DNA methylation increases nucleosome compaction and rigidity.

Authors:  John S Choy; Sijie Wei; Ju Yeon Lee; Song Tan; Steven Chu; Tae-Hee Lee
Journal:  J Am Chem Soc       Date:  2010-02-17       Impact factor: 15.419

8.  Nucleosome accessibility governed by the dimer/tetramer interface.

Authors:  Vera Böhm; Aaron R Hieb; Andrew J Andrews; Alexander Gansen; Andrea Rocker; Katalin Tóth; Karolin Luger; Jörg Langowski
Journal:  Nucleic Acids Res       Date:  2010-12-21       Impact factor: 16.971

9.  The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association.

Authors:  Abdollah Allahverdi; Renliang Yang; Nikolay Korolev; Yanping Fan; Curt A Davey; Chuan-Fa Liu; Lars Nordenskiöld
Journal:  Nucleic Acids Res       Date:  2010-11-02       Impact factor: 16.971

10.  The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation.

Authors:  Andrew Bowman; Richard Ward; Nicola Wiechens; Vijender Singh; Hassane El-Mkami; David George Norman; Tom Owen-Hughes
Journal:  Mol Cell       Date:  2011-02-18       Impact factor: 17.970

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  13 in total

Review 1.  Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells.

Authors:  Olivier Cuvier; Beat Fierz
Journal:  Nat Rev Genet       Date:  2017-05-22       Impact factor: 53.242

2.  Preparation of mononucleosomal templates for analysis of transcription with RNA polymerase using spFRET.

Authors:  Kseniya S Kudryashova; Oleg V Chertkov; Dmitry V Nikitin; Nikolai A Pestov; Olga I Kulaeva; Anastasija V Efremenko; Alexander S Solonin; Mikhail P Kirpichnikov; Vasily M Studitsky; Alexey V Feofanov
Journal:  Methods Mol Biol       Date:  2015

3.  Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.

Authors:  Alexey K Shaytan; Grigoriy A Armeev; Alexander Goncearenco; Victor B Zhurkin; David Landsman; Anna R Panchenko
Journal:  J Mol Biol       Date:  2015-12-14       Impact factor: 5.469

Review 4.  A guide for single-particle chromatin tracking in live cell nuclei.

Authors:  Mengdi Zhang; Clayton Seitz; Garrick Chang; Fadil Iqbal; Hua Lin; Jing Liu
Journal:  Cell Biol Int       Date:  2022-01-30       Impact factor: 4.473

5.  Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II.

Authors:  Jaehyoun Lee; J Brooks Crickard; Joseph C Reese; Tae-Hee Lee
Journal:  Methods       Date:  2019-01-17       Impact factor: 3.608

Review 6.  Anti-DNA antibodies--quintessential biomarkers of SLE.

Authors:  David S Pisetsky
Journal:  Nat Rev Rheumatol       Date:  2015-11-19       Impact factor: 20.543

7.  Nucleosomes impede Cas9 access to DNA in vivo and in vitro.

Authors:  Max A Horlbeck; Lea B Witkowsky; Benjamin Guglielmi; Joseph M Replogle; Luke A Gilbert; Jacqueline E Villalta; Sharon E Torigoe; Robert Tjian; Jonathan S Weissman
Journal:  Elife       Date:  2016-03-17       Impact factor: 8.140

Review 8.  Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics.

Authors:  Orkide Ordu; Alexandra Lusser; Nynke H Dekker
Journal:  Biophys Rev       Date:  2016-10-18

9.  Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations.

Authors:  Hiroo Kenzaki; Shoji Takada
Journal:  PLoS Comput Biol       Date:  2015-08-11       Impact factor: 4.475

10.  The Use of Poly-L-Lysine as a Capture Agent to Enhance the Detection of Antinuclear Antibodies by ELISA.

Authors:  Nancy A Stearns; Shuxia Zhou; Michelle Petri; Steven R Binder; David S Pisetsky
Journal:  PLoS One       Date:  2016-09-09       Impact factor: 3.240

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