Literature DB >> 23514142

Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experiments.

Rosana Collepardo-Guevara1, Tamar Schlick.   

Abstract

The detailed structure and dynamics of the chromatin fibre and their relation to gene regulation represent important open biological questions. Recent advances in single-molecule force spectroscopy experiments have addressed these questions by directly measuring the forces that stabilize and alter the folded states of chromatin, and by investigating the mechanisms of fibre unfolding. We present examples that demonstrate how complementary modelling approaches have helped not only to interpret the experimental findings, but also to advance our knowledge of force-induced events such as unfolding of chromatin with dynamically bound linker histones and nucleosome unwrapping.

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Year:  2013        PMID: 23514142      PMCID: PMC3683968          DOI: 10.1042/BST20120349

Source DB:  PubMed          Journal:  Biochem Soc Trans        ISSN: 0300-5127            Impact factor:   5.407


  64 in total

1.  Mechanical unfolding intermediates in titin modules.

Authors:  P E Marszalek; H Lu; H Li; M Carrion-Vazquez; A F Oberhauser; K Schulten; J M Fernandez
Journal:  Nature       Date:  1999-11-04       Impact factor: 49.962

2.  Rapid exchange of histone H1.1 on chromatin in living human cells.

Authors:  M A Lever; J P Th'ng; X Sun; M J Hendzel
Journal:  Nature       Date:  2000-12-14       Impact factor: 49.962

3.  Reversible unfolding of single RNA molecules by mechanical force.

Authors:  J Liphardt; B Onoa; S B Smith; I Tinoco; C Bustamante
Journal:  Science       Date:  2001-04-27       Impact factor: 47.728

4.  Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures.

Authors:  J R Daban
Journal:  Biochemistry       Date:  2000-04-11       Impact factor: 3.162

5.  Pulling chromatin fibers: computer simulations of direct physical micromanipulations.

Authors:  V Katritch; C Bustamante; W K Olson
Journal:  J Mol Biol       Date:  2000-01-07       Impact factor: 5.469

6.  Replication by a single DNA polymerase of a stretched single-stranded DNA.

Authors:  B Maier; D Bensimon; V Croquette
Journal:  Proc Natl Acad Sci U S A       Date:  2000-10-24       Impact factor: 11.205

7.  Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

Authors:  D A Beard; T Schlick
Journal:  Biopolymers       Date:  2001-01       Impact factor: 2.505

8.  Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers.

Authors:  M L Bennink; S H Leuba; G H Leno; J Zlatanova; B G de Grooth; J Greve
Journal:  Nat Struct Biol       Date:  2001-07

9.  Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions.

Authors:  Sergei A Grigoryev; Gaurav Arya; Sarah Correll; Christopher L Woodcock; Tamar Schlick
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-27       Impact factor: 11.205

10.  Dynamic binding of histone H1 to chromatin in living cells.

Authors:  T Misteli; A Gunjan; R Hock; M Bustin; D T Brown
Journal:  Nature       Date:  2000-12-14       Impact factor: 49.962

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  7 in total

1.  Changing chromatin fiber conformation by nucleosome repositioning.

Authors:  Oliver Müller; Nick Kepper; Robert Schöpflin; Ramona Ettig; Karsten Rippe; Gero Wedemann
Journal:  Biophys J       Date:  2014-11-04       Impact factor: 4.033

2.  Forced unraveling of chromatin fibers with nonuniform linker DNA lengths.

Authors:  Gungor Ozer; Rosana Collepardo-Guevara; Tamar Schlick
Journal:  J Phys Condens Matter       Date:  2015-01-07       Impact factor: 2.333

3.  Chromatin fiber polymorphism triggered by variations of DNA linker lengths.

Authors:  Rosana Collepardo-Guevara; Tamar Schlick
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-20       Impact factor: 11.205

4.  Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin.

Authors:  Antoni Luque; Gungor Ozer; Tamar Schlick
Journal:  Biophys J       Date:  2016-06-07       Impact factor: 4.033

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

6.  Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes.

Authors:  Mary Pitman; Yamini Dalal; Garegin A Papoian
Journal:  Biophys J       Date:  2020-02-12       Impact factor: 4.033

Review 7.  The chromatin fiber: multiscale problems and approaches.

Authors:  Gungor Ozer; Antoni Luque; Tamar Schlick
Journal:  Curr Opin Struct Biol       Date:  2015-06-05       Impact factor: 6.809

  7 in total

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