Literature DB >> 22172540

Recent advances in single molecule studies of nucleosomes.

Jessica L Killian1, Ming Li, Maxim Y Sheinin, Michelle D Wang.   

Abstract

As the fundamental packing units of DNA in eukaryotes, nucleosomes play a central role in governing DNA accessibility in a variety of cellular processes. Our understanding of the mechanisms underlying this complex regulation has been aided by unique structural and dynamic perspectives offered by single molecule techniques. Recent years have witnessed remarkable advances achieved using these techniques, including the generation of a detailed histone-DNA energy landscape, elucidation of nucleosome disassembly processes, and real-time monitoring of molecular motors interacting with nucleosomes. These and other highlights of single molecule nucleosome studies will be discussed in this review. Copyright Â
© 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 22172540      PMCID: PMC5515226          DOI: 10.1016/j.sbi.2011.11.003

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  68 in total

1.  RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones.

Authors:  Olga I Kulaeva; Fu-Kai Hsieh; Vasily M Studitsky
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-07       Impact factor: 11.205

2.  Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection.

Authors:  Christopher Deufel; Scott Forth; Chad R Simmons; Siavash Dejgosha; Michelle D Wang
Journal:  Nat Methods       Date:  2007-02-25       Impact factor: 28.547

3.  Nucleosome chiral transition under positive torsional stress in single chromatin fibers.

Authors:  Aurélien Bancaud; Gaudeline Wagner; Natalia Conde E Silva; Christophe Lavelle; Hua Wong; Julien Mozziconacci; Maria Barbi; Andrei Sivolob; Eric Le Cam; Liliane Mouawad; Jean-Louis Viovy; Jean-Marc Victor; Ariel Prunell
Journal:  Mol Cell       Date:  2007-07-06       Impact factor: 17.970

Review 4.  The histone variant CENP-A and centromere specification.

Authors:  Ben E Black; Emily A Bassett
Journal:  Curr Opin Cell Biol       Date:  2008-01-15       Impact factor: 8.382

5.  Transcription within condensed chromatin: Steric hindrance facilitates elongation.

Authors:  Christophe Bécavin; Maria Barbi; Jean-Marc Victor; Annick Lesne
Journal:  Biophys J       Date:  2010-03-03       Impact factor: 4.033

6.  Crystal structure of the human centromeric nucleosome containing CENP-A.

Authors:  Hiroaki Tachiwana; Wataru Kagawa; Tatsuya Shiga; Akihisa Osakabe; Yuta Miya; Kengo Saito; Yoko Hayashi-Takanaka; Takashi Oda; Mamoru Sato; Sam-Yong Park; Hiroshi Kimura; Hitoshi Kurumizaka
Journal:  Nature       Date:  2011-07-10       Impact factor: 49.962

7.  Salt-induced release of DNA from nucleosome core particles.

Authors:  T D Yager; C T McMurray; K E van Holde
Journal:  Biochemistry       Date:  1989-03-07       Impact factor: 3.162

8.  DNA curtains for high-throughput single-molecule optical imaging.

Authors:  Eric C Greene; Shalom Wind; Teresa Fazio; Jason Gorman; Mari-Liis Visnapuu
Journal:  Methods Enzymol       Date:  2010       Impact factor: 1.600

9.  Direct observation of DNA distortion by the RSC complex.

Authors:  Giuseppe Lia; Elise Praly; Helder Ferreira; Chris Stockdale; Yuk Ching Tse-Dinh; David Dunlap; Vincent Croquette; David Bensimon; Tom Owen-Hughes
Journal:  Mol Cell       Date:  2006-02-03       Impact factor: 17.970

10.  Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3.

Authors:  Zheng Zhou; Hanqiao Feng; Bing-Rui Zhou; Rodolfo Ghirlando; Kaifeng Hu; Adam Zwolak; Lisa M Miller Jenkins; Hua Xiao; Nico Tjandra; Carl Wu; Yawen Bai
Journal:  Nature       Date:  2011-03-16       Impact factor: 49.962

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  24 in total

Review 1.  New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

Authors:  Karolin Luger; Mekonnen L Dechassa; David J Tremethick
Journal:  Nat Rev Mol Cell Biol       Date:  2012-06-22       Impact factor: 94.444

2.  Structural basis of histone H2A-H2B recognition by the essential chaperone FACT.

Authors:  Maria Hondele; Tobias Stuwe; Markus Hassler; Felix Halbach; Andrew Bowman; Elisa T Zhang; Bianca Nijmeijer; Christiane Kotthoff; Vladimir Rybin; Stefan Amlacher; Ed Hurt; Andreas G Ladurner
Journal:  Nature       Date:  2013-05-22       Impact factor: 49.962

Review 3.  Histones: at the crossroads of peptide and protein chemistry.

Authors:  Manuel M Müller; Tom W Muir
Journal:  Chem Rev       Date:  2014-10-20       Impact factor: 60.622

Review 4.  Nucleosome mobility and the regulation of gene expression: Insights from single-molecule studies.

Authors:  Sergei Rudnizky; Omri Malik; Adaiah Bavly; Lilach Pnueli; Philippa Melamed; Ariel Kaplan
Journal:  Protein Sci       Date:  2017-04-02       Impact factor: 6.725

Review 5.  Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.

Authors:  Karissa Y Sanbonmatsu
Journal:  Curr Opin Struct Biol       Date:  2019-05-21       Impact factor: 6.809

Review 6.  Overcoming the nucleosome barrier during transcript elongation.

Authors:  Steven J Petesch; John T Lis
Journal:  Trends Genet       Date:  2012-03-31       Impact factor: 11.639

7.  Biophysics of protein-DNA interactions and chromosome organization.

Authors:  John F Marko
Journal:  Physica A       Date:  2015-01-15       Impact factor: 3.263

Review 8.  Recent developments in single-molecule DNA mechanics.

Authors:  Zev Bryant; Florian C Oberstrass; Aakash Basu
Journal:  Curr Opin Struct Biol       Date:  2012-05-31       Impact factor: 6.809

Review 9.  Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics.

Authors:  Carlos A Aguilar; Harold G Craighead
Journal:  Nat Nanotechnol       Date:  2013-10       Impact factor: 39.213

10.  Force-induced melting of DNA--evidence for peeling and internal melting from force spectra on short synthetic duplex sequences.

Authors:  Niklas Bosaeus; Afaf H El-Sagheer; Tom Brown; Björn Åkerman; Bengt Nordén
Journal:  Nucleic Acids Res       Date:  2014-05-16       Impact factor: 16.971

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