The role of nucleosome positioning in the evolution of gene regulation (Q33964627)

30 July 2017

title

The role of nucleosome positioning in the evolution of gene regulation (English)

1 reference

30 July 2017

Aviv Regev

1 reference

30 July 2017

Oliver J Rando

0 references

Alexander M Tsankov

1 reference

30 July 2017

Dawn Anne Thompson

series ordinal

1 reference

30 July 2017

Amanda Socha

series ordinal

1 reference

30 July 2017

language of work or name

English

0 references

publication date

6 July 2010

1 reference

30 July 2017

1 reference

30 July 2017

1 reference

30 July 2017

1 reference

30 July 2017

page(s)

e1000414

1 reference

Creative Commons Attribution 4.0 International

30 July 2017

start time

6 July 2010

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

Evolutionary tinkering with conserved components of a transcriptional regulatory network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Gene duplication and the evolution of ribosomal protein gene regulation in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

G+C content dominates intrinsic nucleosome occupancy

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Fungal regulatory evolution: cis and trans in the balance

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

From elements to modules: regulatory evolution in Ascomycota fungi

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Defining mechanisms that regulate RNA polymerase II transcription in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

What controls nucleosome positions?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Nucleosome positioning: how is it established, and why does it matter?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Mechanisms that specify promoter nucleosome location and identity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The biology of chromatin remodeling complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Genome-wide views of chromatin structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Nucleosome positioning and gene regulation: advances through genomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Bidirectional promoters generate pervasive transcription in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

High-resolution DNA-binding specificity analysis of yeast transcription factors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The impact of the nucleosome code on protein-coding sequence evolution in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Two strategies for gene regulation by promoter nucleosomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Chromatin decouples promoter threshold from dynamic range

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Nucleosome organization in the Drosophila genome.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The asexual yeast Candida glabrata maintains distinct a and alpha haploid mating types

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Transcription factor substitution during the evolution of fungal ribosome regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Dynamic regulation of nucleosome positioning in the human genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The evolution of combinatorial gene regulation in fungi

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Chromatin remodelling at promoters suppresses antisense transcription

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Natural history and evolutionary principles of gene duplication in fungi

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Increased glycolytic flux as an outcome of whole-genome duplication in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Emerging principles of regulatory evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The pattern and evolution of yeast promoter bendability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The role of chromatin during transcription

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Evolution of primate gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Genome-scale identification of nucleosome positions in S. cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Conservation and evolution of cis-regulatory systems in ascomycete fungi

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Transcriptional regulatory code of a eukaryotic genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The evolution of genetic regulatory systems in bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The Gene Ontology (GO) database and informatics resource

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

BLAT—The BLAST-Like Alignment Tool

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Genetic dissection of transcriptional regulation in budding yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

MIPS: a database for genomes and protein sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Genomic expression programs in the response of yeast cells to environmental changes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

KEGG: Kyoto Encyclopedia of Genes and Genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

The nucleosome repeat length of Kluyveromyces lactis is 16 bp longer than that of Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

DNA bending and its relation to nucleosome positioning.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

Evolution at two levels in humans and chimpanzees

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2897762

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome

5 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

A yeast hybrid provides insight into the evolution of gene expression regulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

On the relation between promoter divergence and gene expression evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

Evolutionary footprints of nucleosome positions in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

Intrinsic variability of gene expression encoded in nucleosome positioning sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

Modifying gene expression programs by altering core promoter chromatin architecture.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

CIS: compound importance sampling method for protein-DNA binding site p-value estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000414

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

21 January 2018

1 reference

12 December 2020

RNA polymerase II initiation factor interactions and transcription start site selection

1 reference

12 December 2020

A genetic signature of interspecies variations in gene expression

1 reference

12 December 2020

Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast

1 reference

12 December 2020

10.1371/JOURNAL.PBIO.1000414

Identifiers

DOI

1 reference

30 July 2017

1 reference

30 July 2017

1 reference