(Q34043829)

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Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

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scholarly article

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Europe PubMed Central

PubMed publication ID

30 July 2017

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast (English)

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Federica Battistini

object named as

Federica Battistini

3

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6

object named as

Modesto Orozco

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

0 references

author name string

Ozgen Deniz

1

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Oscar Flores

2

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Alberto Pérez

4

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

Montserrat Soler-López

5

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

language of work or name

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publication date

7 October 2011

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

12

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

489

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

The effect of micrococcal nuclease digestion on nucleosome positioning data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

High-throughput sequencing reveals a simple model of nucleosome energetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Self-organization of G-quadruplex structures in the hTERT core promoter stabilized by polyaminic side chain perylene derivatives

1 reference

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5 July 2018

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Gene regulation by nucleosome positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Structure of RCC1 chromatin factor bound to the nucleosome core particle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing

1 reference

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5 July 2018

Origins of specificity in protein-DNA recognition.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

A structural perspective on the where, how, why, and what of nucleosome positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

DNA architecture, deformability, and nucleosome positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

The DNA sequence-dependence of nucleosome positioning in vivo and in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

The role of DNA shape in protein-DNA recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

From DNA sequence to transcriptional behaviour: a quantitative approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Nucleosome positioning and gene regulation: advances through genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

The DNA-encoded nucleosome organization of a eukaryotic genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

DNA physical properties determine nucleosome occupancy from yeast to fly.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Nucleosome organization in the Drosophila genome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Towards a molecular dynamics consensus view of B-DNA flexibility

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

High-resolution mapping and characterization of open chromatin across the genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Generic eukaryotic core promoter prediction using structural features of DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Determining promoter location based on DNA structure first-principles calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

A high-resolution atlas of nucleosome occupancy in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Sequence-dependent DNA deformability studied using molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Nucleosome positioning signals in genomic DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Rules and regulation in the primary structure of chromatin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

A genomic code for nucleosome positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Genome-scale identification of nucleosome positions in S. cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

The structure of DNA in the nucleosome core

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Gene ontology: tool for the unification of biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Crystal structure of the nucleosome core particle at 2.8 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Unusual DNA structures, chromatin and transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Sequence specific cleavage of DNA by micrococcal nuclease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

The pitch of chromatin DNA is reflected in its nucleotide sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Micrococcal nuclease as a DNA structural probe: its recognition sequences, their genomic distribution and correlation with DNA structure determinants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224377

5 July 2018

Interactions between upstream and core promoter sequences determine gene expression and nucleosome positioning in tobacco PR-1a promoter.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-489

21 January 2018

Intrinsic variability of gene expression encoded in nucleosome positioning sequences.

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21 January 2018

Sequence-dependent nucleosome positioning

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21 January 2018

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

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21 January 2018

Nucleosome positioning by sequence, state of the art and apparent finale

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21 January 2018

DNAlive: a tool for the physical analysis of DNA at the genomic scale

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21 January 2018

A generalized conformational energy function of DNA derived from molecular dynamics simulations.

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21 January 2018

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

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https://api.crossref.org/works/10.1186%2F1471-2164-12-489

21 January 2018

nucleR: a package for non-parametric nucleosome positioning.

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21 January 2018

The purification and properties of micrococcal nuclease.

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28 October 2018

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

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https://api.crossref.org/works/10.1186%2F1471-2164-12-489

21 January 2018

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/21981773

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleosome positions predicted through comparative genomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/21981773

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches

1 reference

https://pubmed.ncbi.nlm.nih.gov/21981773

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1471-2164-12-489

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

30 July 2017

ResearchGate publication ID

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