(Q34360725)

1 August 2017

title

Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro (English)

1 reference

1 August 2017

Feng Cui

1

1 reference

1 August 2017

Victor B Zhurkin

series ordinal

2

1 reference

1 August 2017

publication date

1 June 2010

1 reference

Journal of Biomolecular Structure and Dynamics

1 August 2017

published in

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1 August 2017

volume

27

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1 August 2017

issue

6

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1 August 2017

page(s)

821-841

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Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II.

1 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

The role of DNA shape in protein-DNA recognition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

The DNA-encoded nucleosome organization of a eukaryotic genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

nuScore: a web-interface for nucleosome positioning predictions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Nucleosome organization in the Drosophila genome.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

A high-resolution atlas of nucleosome occupancy in yeast

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

A genomic code for nucleosome positioning

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Genome-scale identification of nucleosome positions in S. cerevisiae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

A determining influence for CpG dinucleotides on nucleosome positioning in vitro

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

What positions nucleosomes?--A model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Differential nucleosome positioning on Xenopus oocyte and somatic 5 S RNA genes determines both TFIIIA and H1 binding: a mechanism for selective H1 repression.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Unique translational positioning of nucleosomes on synthetic DNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

DNA bending: the prevalence of kinkiness and the virtues of normality

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Crystal structure of the nucleosome core particle at 2.8 A resolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Crystal structure of CATGGCCATG and its implications for A-tract bending models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Crystal structure of a yeast TBP/TATA-box complex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Stereochemical basis of DNA bending by transcription factors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Periodicity in DNA primary structure is defined by secondary structure of the coded protein

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

The pitch of chromatin DNA is reflected in its nucleotide sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

A random-walk model for helix bending in B-DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Sequence-dependent anisotropic flexibility of B-DNA. A conformational study

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Sequence-dependent bending of DNA and phasing of nucleosomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Sequence periodicities in chicken nucleosome core DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Calibration of DNA curvature and a unified description of sequence-directed bending

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Asymmetry and polarity of nucleosomes in chicken erythrocyte chromatin.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Crystallographic study of one turn of G/C-rich B-DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Analysis of local helix geometry in three B-DNA decamers and eight dodecamers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Static and statistical bending of DNA evaluated by Monte Carlo simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Organization of DNA in chromatin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

Anisotropic flexibility of DNA and the nucleosomal structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2993692

High-throughput mapping of the chromatin structure of human promoters.

6 July 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

Sequence-dependent nucleosome positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

Sequence-Dependent Variability of B-DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

Sequence structure of hidden 10.4-base repeat in the nucleosomes of C. elegans

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

A translational signature for nucleosome positioning in vivo.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F073911010010524947

Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure

21 January 2018

1 reference

12 December 2020

Mechanics of sequence-dependent stacking of bases in B-DNA

1 reference

12 December 2020

Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine-pyrimidine and pyrimidine-purine dimers

1 reference

12 December 2020

Effects of DNA sequence and histone-histone interactions on nucleosome placement

1 reference

12 December 2020

B-DNA twisting correlates with base-pair morphology.

1 reference

12 December 2020

Positioning and stability of nucleosomes on MMTV 3'LTR sequences

1 reference

12 December 2020

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

1 reference

12 December 2020

Sequence structure of human nucleosome DNA

1 reference

12 December 2020

Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II

1 reference

12 December 2020

Nucleosome positioning determinants

1 reference

12 December 2020

Nucleosome DNA bendability matrix (C. elegans)

1 reference

12 December 2020

Modeling DNA deformations

1 reference

12 December 2020

10.1080/073911010010524947

Identifiers

DOI

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1 August 2017

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1 August 2017

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