Distinct modes of regulation by chromatin encoded through nucleosome positioning signals (Q33383211)

26 July 2017

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals (English)

1 reference

26 July 2017

8

1 reference

26 July 2017

Eilon Sharon

5

0 references

Noam Kaplan

object named as

Noam Kaplan

2

0 references

Yaniv Lubling

object named as

Yaniv Lubling

6

0 references

author name string

Yair Field

1

1 reference

26 July 2017

Yvonne Fondufe-Mittendorf

3

1 reference

26 July 2017

Irene K Moore

4

1 reference

26 July 2017

Jonathan Widom

7

1 reference

26 July 2017

7 November 2008

1 reference

PLOS Computational Biology

26 July 2017

1 reference

26 July 2017

4

1 reference

26 July 2017

11

1 reference

26 July 2017

e1000216

1 reference

Creative Commons Attribution 4.0 International

26 July 2017

start time

7 November 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Two strategies for gene regulation by promoter nucleosomes

21 June 2018

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

21 June 2018

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Dynamic regulation of nucleosome positioning in the human genome

21 June 2018

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Genomic sequence is highly predictive of local nucleosome depletion

21 June 2018

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Chromatin remodelling at promoters suppresses antisense transcription

21 June 2018

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A high-resolution atlas of nucleosome occupancy in yeast

21 June 2018

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Nucleosome positioning signals in genomic DNA

21 June 2018

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HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications

21 June 2018

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

DNA stretching and extreme kinking in the nucleosome core

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Hyperconserved CpG domains underlie Polycomb-binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Characterization of Z-DNA as a nucleosome-boundary element in yeast Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

A large-scale full-length cDNA analysis to explore the budding yeast transcriptome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Genome-wide characterization of fission yeast DNA replication origins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Effect of sequence-directed nucleosome disruption on cell-type-specific repression by alpha2/Mcm1 in the yeast genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

A genomic code for nucleosome positioning

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

A high-resolution map of transcription in the yeast genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Genome sequencing in microfabricated high-density picolitre reactors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Genome-scale identification of nucleosome positions in S. cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

DNA replication origins in the Schizosaccharomyces pombe genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Global position and recruitment of HATs and HDACs in the yeast genome.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Transcriptional regulatory code of a eukaryotic genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Control of stochasticity in eukaryotic gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

The structure of DNA in the nucleosome core

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Stochastic gene expression in a single cell

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

DNA replication and chromatin.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Role of DNA sequence in nucleosome stability and dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Multiple redundant sequence elements within the fission yeast ura4 replication origin enhancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Gene ontology: tool for the unification of biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Functional analysis of a homopolymeric (dA-dT) element that provides nucleosomal access to yeast and mammalian transcription factors.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Distinct frequency-distributions of homopolymeric DNA tracts in different genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

SGD: Saccharomyces Genome Database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Sequence specific cleavage of DNA by micrococcal nuclease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Sequence periodicities in chicken nucleosome core DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

The structure of an oligo(dA).oligo(dT) tract and its biological implications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Activation of yeast RNA polymerase II transcription by a thymidine-rich upstream element in vitro

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Basic local alignment search tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Poly(dA).poly(dT) rich sequences are not sufficient to exclude nucleosome formation in a constitutive yeast promoter

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

A poly(dA.dT) tract is a component of the recombination initiation site at the ARG4 locus in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

In Vitro and in Vivo nucleosome positioning on the ovine beta-lactoglobulin gene are related.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Identification and distinct regulation of yeast TATA box-containing genes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Dynamics of Replication-Independent Histone Turnover in Budding Yeast

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2570626

Structural and functional requirements for the chromatin transition at the PHO5 promoter in Saccharomyces cerevisiae upon PHO5 activation

31 October 2018

1 reference

12 December 2020

Nucleosome positions predicted through comparative genomics

1 reference

12 December 2020

Identification and characterization of genomic nucleosome-positioning sequences

1 reference

12 December 2020

Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure

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

Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1000216

Identifiers

DOI

1 reference

journals/ploscb/FieldKFMSLWS08

26 July 2017

1 reference

DBLP Dataset 2021-01-02

release_sf3kryvdczhg3pwehqaa4o6t5i

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/sf3kryvdczhg3pwehqaa4o6t5i

24 November 2022

mapped directly with Wikidata item

PMCID

2570626

1 reference

26 July 2017

1 reference