Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA (Q58611949)

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scientific article published on 05 November 2018

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English	Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA	scientific article published on 05 November 2018

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scholarly article

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Europe PubMed Central

PMC publication ID

6237416

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30395604%20AND%20SRC:MED&resulttype=core&format=json

retrieved

1 May 2020

title

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA (English)

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Europe PubMed Central

PMC publication ID

6237416

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30395604%20AND%20SRC:MED&resulttype=core&format=json

retrieved

1 May 2020

author

Shoji Takada

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2

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Europe PubMed Central

PMC publication ID

6237416

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30395604%20AND%20SRC:MED&resulttype=core&format=json

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1 May 2020

author name string

Giovanni B Brandani

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1

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Europe PubMed Central

PMC publication ID

6237416

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30395604%20AND%20SRC:MED&resulttype=core&format=json

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1 May 2020

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English

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publication date

5 November 2018

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Europe PubMed Central

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6237416

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1 May 2020

published in

PLOS Computational Biology

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Europe PubMed Central

PMC publication ID

6237416

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1 May 2020

volume

14

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Europe PubMed Central

PMC publication ID

6237416

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1 May 2020

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11

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Europe PubMed Central

PMC publication ID

6237416

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1 May 2020

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e1006512

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Europe PubMed Central

PMC publication ID

6237416

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1 May 2020

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Creative Commons Attribution 4.0 International

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5 November 2018

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cites work

Mobile nucleosomes--a general behavior

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Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals

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Crystal structure of the nucleosome core particle at 2.8 A resolution

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New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning

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DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

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12 December 2020

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Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism

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Polymer reptation and nucleosome repositioning

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Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

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The structure of DNA in the nucleosome core

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Chromatin Dynamics: Nucleosomes go Mobile through Twist Defects

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Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities

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Removal of promoter nucleosomes by disassembly rather than sliding in vivo

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Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex

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Nucleosomes in solution exist as a mixture of twist-defect states

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Chromatin remodeling through directional DNA translocation from an internal nucleosomal site

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Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome

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Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase

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The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing

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DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.

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Dynamic regulation of nucleosome positioning in the human genome

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12 December 2020

based on heuristic

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Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation

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https://pubmed.ncbi.nlm.nih.gov/30395604

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

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Poly(dA:dT) tracts: major determinants of nucleosome organization

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Kinetic proofreading of gene activation by chromatin remodeling

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https://pubmed.ncbi.nlm.nih.gov/30395604

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Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

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12 December 2020

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Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence

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based on heuristic

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A proposal for kinetic proof reading by ISWI family chromatin remodeling motors

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Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations.

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Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations

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Markov models of molecular kinetics: generation and validation

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based on heuristic

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

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanisms for ATP-dependent chromatin remodelling: the means to the end

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based on heuristic

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The dynamics of the nucleosome: thermal effects, external forces and ATP.

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Identification of a rapidly formed nonnucleosomal histone-DNA intermediate that is converted into chromatin by ACF

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12 December 2020

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A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization

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PubMed

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12 December 2020

based on heuristic

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Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain

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12 December 2020

based on heuristic

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Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

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based on heuristic

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Genome-wide nucleosome positioning during embryonic stem cell development

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based on heuristic

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Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler

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based on heuristic

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ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps

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https://pubmed.ncbi.nlm.nih.gov/30395604

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based on heuristic

inferred from PubMed ID database lookup

Determinants of nucleosome positioning

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https://pubmed.ncbi.nlm.nih.gov/30395604

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleosome sliding mechanisms: new twists in a looped history.

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains.

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DNA shape dominates sequence affinity in nucleosome formation.

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based on heuristic

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Coarse-grained modeling of DNA curvature.

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Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions

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based on heuristic

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

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based on heuristic

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Molecular mechanisms of ribosomal protein gene coregulation.

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based on heuristic

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Chromatin-remodeling and the initiation of transcription

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12 December 2020

based on heuristic

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Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins

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based on heuristic

inferred from PubMed ID database lookup

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work.

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stepwise nucleosome translocation by RSC remodeling complexes

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https://pubmed.ncbi.nlm.nih.gov/30395604

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12 December 2020

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Exploring the Free Energy Landscape of Nucleosomes.

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based on heuristic

inferred from PubMed ID database lookup

Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics.

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanisms of ATP-Dependent Chromatin Remodeling Motors

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dynamics of Nucleosome Positioning Maturation following Genomic Replication

1 reference

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reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genomic Nucleosome Organization Reconstituted with Pure Proteins

1 reference

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PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Sequence of Nucleosomal DNA Modulates Sliding by the Chd1 Chromatin Remodeler.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

1 reference

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reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

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Understanding nucleosome dynamics and their links to gene expression and DNA replication

1 reference

stated in

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reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers

1 reference

stated in

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleosome-Chd1 structure and implications for chromatin remodelling

1 reference

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https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

In silico evidence for sequence-dependent nucleosome sliding.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DNA topology in chromatin is defined by nucleosome spacing.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural rearrangements of the histone octamer translocate DNA.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure and regulation of the human INO80-nucleosome complex.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.

1 reference

stated in

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reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA.

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/30395604

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

DOI

10.1371/JOURNAL.PCBI.1006512

1 reference

stated in

Europe PubMed Central

PMC publication ID

6237416

reference URL

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30395604%20AND%20SRC:MED&resulttype=core&format=json

retrieved

1 May 2020

DBLP publication ID

journals/ploscb/BrandaniT18

1 reference

stated in

DBLP Dataset 2021-01-02

retrieved

28 January 2021

PMC publication ID

6237416

1 reference

stated in

Europe PubMed Central

PMC publication ID

6237416

reference URL

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30395604%20AND%20SRC:MED&resulttype=core&format=json

retrieved

1 May 2020

PubMed publication ID

30395604

1 reference

stated in

Europe PubMed Central

PMC publication ID

6237416

reference URL

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30395604%20AND%20SRC:MED&resulttype=core&format=json

retrieved

1 May 2020

 

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