A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. (Q39706090)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

title

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

author name string

Nicholas M Luscombe

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

publication date

19 September 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

volume

22

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

page(s)

84-94

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

Predicting nucleosome positioning using a duration Hidden Markov Model

13 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Bacterial adaptation through distributed sensing of metabolic fluxes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Nucleosome positioning--what do we really know?

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Poly(dA:dT) tracts: major determinants of nucleosome organization

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Bidirectional promoters generate pervasive transcription in yeast

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

The DNA-encoded nucleosome organization of a eukaryotic genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Single-RNA counting reveals alternative modes of gene expression in yeast

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

The transcriptional landscape of the yeast genome defined by RNA sequencing

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Two strategies for gene regulation by promoter nucleosomes

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Chromatin decouples promoter threshold from dynamic range

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

GeneTrack--a genomic data processing and visualization framework.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

A high-resolution atlas of nucleosome occupancy in yeast

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Phenotypic consequences of promoter-mediated transcriptional noise

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

A genomic code for nucleosome positioning

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Noise in gene expression: origins, consequences, and control

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Genome-scale identification of nucleosome positions in S. cerevisiae

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Global nucleosome occupancy in yeast

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Transcriptional regulatory code of a eukaryotic genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Collaborative competition mechanism for gene activation in vivo

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Transcription reinitiation rate: a potential role for TATA box stabilization of the TFIID:TFIIA:DNA complex

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Nucleosome loss activates CUP1 and HIS3 promoters to fully induced levels in the yeast Saccharomyces cerevisiae

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Transcription reinitiation rate: a special role for the TATA box.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Nucleosome sequence preferences influence in vivo nucleosome organization

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Nucleosome loss activates yeast downstream promoters in vivo

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Identification and distinct regulation of yeast TATA box-containing genes

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

Evidence for nucleosome depletion at active regulatory regions genome-wide

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3246209

A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21930892

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The stability of the TFIIA-TBP-DNA complex is dependent on the sequence of the TATAAA element

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21930892

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.124099.111

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21930892 AND SRC:MED&resulttype=core&format=json

13 February 2020

PubMed publication ID

21930892

1 reference