(Q34711883)

4 August 2017

A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription (English)

1 reference

4 August 2017

1

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4 August 2017

6

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4 August 2017

Kyle Tsui

2

1 reference

4 August 2017

Marinella Gebbia

series ordinal

3

1 reference

4 August 2017

Sanie Mnaimneh

series ordinal

4

1 reference

4 August 2017

Timothy R Hughes

series ordinal

5

1 reference

4 August 2017

2 May 2013

1 reference

4 August 2017

1 reference

4 August 2017

9

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4 August 2017

5

1 reference

4 August 2017

e1003479

1 reference

Creative Commons Attribution 4.0 International

4 August 2017

start time

2 May 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3642058/fullTextXML

inferred from PubMed Central ID database lookup

ImageQuant

object named as

ImageQuant

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

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Systematic dissection of roles for chromatin regulators in a yeast stress response

7 July 2018

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In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae

7 July 2018

1 reference

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Genome-wide nucleosome specificity and directionality of chromatin remodelers.

7 July 2018

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Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function

7 July 2018

1 reference

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Genomic approaches for determining nucleosome occupancy in yeast

7 July 2018

1 reference

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Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein.

7 July 2018

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Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner

7 July 2018

1 reference

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

7 July 2018

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Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes

7 July 2018

1 reference

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Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output

7 July 2018

1 reference

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H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway

7 July 2018

1 reference

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Trait variation in yeast is defined by population history

7 July 2018

1 reference

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A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome

7 July 2018

1 reference

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Control of chromatin structure by spt6: different consequences in coding and regulatory regions

7 July 2018

1 reference

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Spt10 and Spt21 are required for transcriptional silencing in Saccharomyces cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

The role of nucleosome positioning in the evolution of gene regulation

7 July 2018

1 reference

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The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae.

7 July 2018

1 reference

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Widespread remodeling of mid-coding sequence nucleosomes by Isw1.

7 July 2018

1 reference

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Chromatin 'programming' by sequence--is there more to the nucleosome code than %GC?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome

7 July 2018

1 reference

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The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

7 July 2018

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Quantification of the yeast transcriptome by single-molecule sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Mechanisms that specify promoter nucleosome location and identity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Bidirectional promoters generate pervasive transcription in yeast

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

The DNA-encoded nucleosome organization of a eukaryotic genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

The transcriptional landscape of the yeast genome defined by RNA sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Chromatin remodelling at promoters suppresses antisense transcription

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

A high-resolution atlas of nucleosome occupancy in yeast

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Transcriptional repression by Tup1-Ssn6.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

A genomic code for nucleosome positioning

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Antagonistic forces that position nucleosomes in vivo.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

A high-resolution map of transcription in the yeast genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Genome-scale identification of nucleosome positions in S. cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

The histone chaperone anti-silencing function 1 is a global regulator of transcription independent of passage through S phase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Bioconductor: open software development for computational biology and bioinformatics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Exploration of essential gene functions via titratable promoter alleles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Promoter-dependent roles for the Srb10 cyclin-dependent kinase and the Hda1 deacetylase in Tup1-mediated repression in Saccharomyces cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Chromatin dynamics at DNA replication, transcription and repair

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Transcription elongation factors repress transcription initiation from cryptic sites.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

The structure of DNA in the nucleosome core

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Multiple factors prevent transcriptional interference at the yeast ARO4-HIS7 locus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Specific distribution of the Saccharomyces cerevisiae linker histone homolog HHO1p in the chromatin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

An activation-independent role of transcription factors in insulator function

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Turning genes off by Ssn6-Tup1: a conserved system of transcriptional repression in eukaryotes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Crystal structure of the nucleosome core particle at 2.8 A resolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

The AFT1 transcriptional factor is differentially required for expression of high-affinity iron uptake genes in Saccharomyces cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Rgt1p of Saccharomyces cerevisiae, a key regulator of glucose-induced genes, is both an activator and a repressor of transcription

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

SPT10 and SPT21 are required for transcription of particular histone genes in Saccharomyces cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Chromatin structure; oligomers of the histones

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Depletion of histone H4 and nucleosomes activates the PHO5 gene in Saccharomyces cerevisiae.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Effects of histone H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Chromatin assembly during SV40 DNA replication in vitro

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Nucleosome loss activates yeast downstream promoters in vivo

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Stepwise assembly of chromatin during DNA replication in vitro

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Ferric reductase of Saccharomyces cerevisiae: molecular characterization, role in iron uptake, and transcriptional control by iron

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3642058

Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1.

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003479

Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003479

Histone chaperone spt16 promotes redeposition of the original h3-h4 histones evicted by elongating RNA polymerase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003479

Computational analysis of nucleosome positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003479

Potential role of the histone chaperone, CAF-1, in transcription.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003479

A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003479

6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae

21 January 2018

1 reference

12 December 2020

Nucleosome sliding via TBP DNA binding in vivo

1 reference

12 December 2020

General regulatory factors (GRFs) as genome partitioners

1 reference

12 December 2020

A preoccupied position on nucleosomes

1 reference

12 December 2020

10.1371/JOURNAL.PGEN.1003479

Identifiers

DOI

1 reference

4 August 2017

1 reference

4 August 2017

1 reference