Literature DB >> 25980611

A brief review of nucleosome structure.

Amber R Cutter1, Jeffrey J Hayes2.   

Abstract

The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial ∼7-fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA-dependent activities by restricting binding of trans-acting factors to cognate DNA sequences. Conversely they are engineered to be nearly meta-stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher-order chromatin structures. Thus, in order to provide a foundation for understanding these functions, we present a review of the basic elements of nucleosome structure and stability, including the association of linker histones.
Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Chromatin structure; Histone; Nucleosome structure

Mesh:

Substances:

Year:  2015        PMID: 25980611      PMCID: PMC4598263          DOI: 10.1016/j.febslet.2015.05.016

Source DB:  PubMed          Journal:  FEBS Lett        ISSN: 0014-5793            Impact factor:   4.124


  118 in total

1.  N- and C-terminal domains determine differential nucleosomal binding geometry and affinity of linker histone isotypes H1(0) and H1c.

Authors:  Payal Vyas; David T Brown
Journal:  J Biol Chem       Date:  2012-02-10       Impact factor: 5.157

2.  Complex of linker histone H5 with the nucleosome and its implications for chromatin packing.

Authors:  Li Fan; Victoria A Roberts
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-22       Impact factor: 11.205

3.  Nucleosome linker DNA contacts and induces specific folding of the intrinsically disordered H1 carboxyl-terminal domain.

Authors:  Tamara L Caterino; He Fang; Jeffrey J Hayes
Journal:  Mol Cell Biol       Date:  2011-04-04       Impact factor: 4.272

4.  A mutational mimic analysis of histone H3 post-translational modifications: specific sites influence the conformational state of H3/H4, causing either positive or negative supercoiling of DNA.

Authors:  Rachel H White; Melissa Keberlein; Vaughn Jackson
Journal:  Biochemistry       Date:  2012-10-08       Impact factor: 3.162

5.  Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure.

Authors:  Yunhe Bao; Cindy L White; Karolin Luger
Journal:  J Mol Biol       Date:  2006-07-05       Impact factor: 5.469

6.  Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping.

Authors:  Tatiana Nikitina; Difei Wang; Misha Gomberg; Sergei A Grigoryev; Victor B Zhurkin
Journal:  J Mol Biol       Date:  2013-02-28       Impact factor: 5.469

7.  Linker histone H1.0 interacts with an extensive network of proteins found in the nucleolus.

Authors:  Anna A Kalashnikova; Duane D Winkler; Steven J McBryant; Ryan K Henderson; Jacob A Herman; Jennifer G DeLuca; Karolin Luger; Jessica E Prenni; Jeffrey C Hansen
Journal:  Nucleic Acids Res       Date:  2013-02-21       Impact factor: 16.971

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.  DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain.

Authors:  He Fang; David J Clark; Jeffrey J Hayes
Journal:  Nucleic Acids Res       Date:  2011-10-22       Impact factor: 16.971

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  96 in total

1.  Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.

Authors:  Mehmet Ali Öztürk; Georgi V Pachov; Rebecca C Wade; Vlad Cojocaru
Journal:  Nucleic Acids Res       Date:  2016-06-07       Impact factor: 16.971

Review 2.  Towards quantitative analysis of gene regulation by enhancers.

Authors:  Ekaterina V Nizovtseva; Stefjord Todolli; Wilma K Olson; Vasily M Studitsky
Journal:  Epigenomics       Date:  2017-08-11       Impact factor: 4.778

3.  Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast.

Authors:  Yan Zheng; Hong Li; Yue Wang; Hu Meng; Qiang Zhang; Xiaoqing Zhao
Journal:  Chromosome Res       Date:  2017-02-09       Impact factor: 5.239

4.  Variable impact of conformationally distinct DNA lesions on nucleosome structure and dynamics: Implications for nucleotide excision repair.

Authors:  Yuqin Cai; Nicholas E Geacintov; Suse Broyde
Journal:  DNA Repair (Amst)       Date:  2019-12-28

Review 5.  Histones on fire: the effect of Dun1 and Mrc1 on origin firing and replication of hyper-acetylated genomes.

Authors:  Lihi Gershon; Martin Kupiec
Journal:  Curr Genet       Date:  2021-03-14       Impact factor: 3.886

6.  Canonical and Variant Forms of Histone H3 Are Deposited onto the Human Cytomegalovirus Genome during Lytic and Latent Infections.

Authors:  Emily R Albright; Robert F Kalejta
Journal:  J Virol       Date:  2016-10-28       Impact factor: 5.103

7.  Unique Dynamics in Asymmetric macroH2A-H2A Hybrid Nucleosomes Result in Increased Complex Stability.

Authors:  Samuel Bowerman; Robert J Hickok; Jeff Wereszczynski
Journal:  J Phys Chem B       Date:  2019-01-08       Impact factor: 2.991

Review 8.  Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies.

Authors:  Catherine A Musselman; Tatiana G Kutateladze
Journal:  ACS Chem Biol       Date:  2019-03-12       Impact factor: 5.100

9.  Acetylation-modulated communication between the H3 N-terminal tail domain and the intrinsically disordered H1 C-terminal domain.

Authors:  Fanfan Hao; Kevin J Murphy; Tomoya Kujirai; Naoki Kamo; Junko Kato; Masako Koyama; Akimitsu Okamato; Gosuke Hayashi; Hitoshi Kurumizaka; Jeffrey J Hayes
Journal:  Nucleic Acids Res       Date:  2020-11-18       Impact factor: 16.971

10.  Probing Nucleosome Stability with a DNA Origami Nanocaliper.

Authors:  Jenny V Le; Yi Luo; Michael A Darcy; Christopher R Lucas; Michelle F Goodwin; Michael G Poirier; Carlos E Castro
Journal:  ACS Nano       Date:  2016-07-06       Impact factor: 15.881

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