Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions (Q21145294)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

3

Yevhen Vainshtein

Yevhen

Vainshtein

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Vladimir B. Teif

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Vladimir B. Teif

series ordinal

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Daria A Beshnova

1

Daria A

Beshnova

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

PLOS Computational Biology

11 June 2020

language of work or name

English

0 references

publication date

July 2014

0 references

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

page(s)

e1003698

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

11 June 2020

copyright license

start time

3 July 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

19 March 2017

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A genomic code for nucleosome positioning

19 March 2017

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H1 histones: current perspectives and challenges

19 March 2017

1 reference

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The role of chromatin insulators in nuclear architecture and genome function

19 March 2017

1 reference

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Genome-wide nucleosome positioning during embryonic stem cell development

19 March 2017

1 reference

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Chromatin Structure: A Repeating Unit of Histones and DNA

19 March 2017

1 reference

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General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage

19 March 2017

1 reference

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A map of the cis-regulatory sequences in the mouse genome

6 April 2017

1 reference

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The biology of chromatin remodeling complexes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Ubiquitous nucleosome crowding in the yeast genome.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Canonical nucleosome organization at promoters forms during genome activation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Structural insights into the histone H1-nucleosome complex

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Taking into account nucleosomes for predicting gene expression

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Toward a unified physical model of nucleosome patterns flanking transcription start sites

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Nonspecific transcription-factor-DNA binding influences nucleosome occupancy in yeast

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Calculating transcription factor binding maps for chromatin.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Determinants of nucleosome organization in primary human cells

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Statistical-mechanical lattice models for protein-DNA binding in chromatin

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Nucleosome-mediated cooperativity between transcription factors

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Condensed DNA: condensing the concepts.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

The DNA-encoded nucleosome organization of a eukaryotic genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

nuScore: a web-interface for nucleosome positioning predictions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Physicochemical analysis of electrostatic foundation for DNA-protein interactions in chromatin transformations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

The pitch of chromatin DNA is reflected in its nucleotide sequence

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Spheroid chromatin units (v bodies).

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Mobile nucleosomes--a general behavior

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

The nucleosome repeat length increases during erythropoiesis in the chick

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

On the occurrence of nucleosome phasing in chromatin

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Quantifying the role of steric constraints in nucleosome positioning

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Visible periodicity of strong nucleosome DNA sequences.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

On the structure and dynamics of the complex of the nucleosome and the linker histone

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

A novel strategy of transcription regulation by intragenic nucleosome ordering

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

The biochemical and phenotypic characterization of Hho1p, the putative linker histone H1 of Saccharomyces cerevisiae

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Electrostatic mechanism of nucleosome spacing.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

A lattice model for transcription factor access to nucleosomal DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Linker histone subtypes differ in their effect on nucleosomal spacing in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Beitrag zur Theorie des Ferromagnetismus

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Peeling and sliding in nucleosome repositioning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Short-range interactions and size of ligands bound to DNA strongly influence adsorptive phase transition caused by long-range interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Long-Range Interactions between Ligands Bound to a DNA Molecule Give Rise to Adsorption with the Character of Phase Transition of the First Kind

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Chromatin Remodeling and Nucleosome Positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Electrostatic effect of H1-histone protein binding on nucleosome repeat length.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Strong nucleosomes of mouse genome including recovered centromeric sequences

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081033

The length of nucleosome-associated DNA is the same in both transcribed and nontranscribed regions of chromatin

29 November 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

Nucleosomes are positioned on mouse satellite DNA in multiple highly specific frames that are correlated with a diverged subrepeat of nine base-pairs

21 January 2018

1 reference

12 December 2020

Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae

1 reference

12 December 2020

Nucleosome positioning and nucleosome stacking: two faces of the same coin

1 reference

12 December 2020

The roles of the monomer length and nucleotide context of plant tandem repeats in nucleosome positioning

1 reference

12 December 2020

[Anticooperative interactions between the nearest neighbor chromatosomes]

1 reference

12 December 2020

DNA spools under tension

1 reference

12 December 2020

Thermodynamics of intragenic nucleosome ordering

1 reference

12 December 2020

Stochastic nucleosome positioning in a yeast chromatin region is not dependent on histone H1

1 reference

12 December 2020

Kinetic Control of Nucleosome Displacement by ISWI/ACF Chromatin Remodelers

1 reference

12 December 2020

FineStr: a web server for single-base-resolution nucleosome positioning

1 reference

12 December 2020

Simple model for overcharging of a sphere by a wrapped oppositely charged asymmetrically neutralized polyelectrolyte: Possible effects of helical charge distribution

1 reference

12 December 2020

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003698

1 reference

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003698

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

4239869

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/BeshnovaCVT14

11 June 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_dothyik3hvcczlwvr5iiad645y

28 January 2021

Fatcat ID

0 references

OpenCitations bibliographic resource ID

4239869

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

PubMed publication ID

24992723

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24992723%20AND%20SRC:MED&resulttype=core&format=json