Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. (Q39983632)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17053089%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

title

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection (English)

1 reference

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20 December 2019

main subject

whole genome sequencing

1 reference

1

1 reference

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20 December 2019

Joshua A Granek

3

1 reference

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20 December 2019

author name string

Cheol-Koo Lee

2

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20 December 2019

Neil D Clarke

4

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20 December 2019

Jason D Lieb

5

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20 December 2019

publication date

19 October 2006

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20 December 2019

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20 December 2019

volume

16

1 reference

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20 December 2019

issue

12

1 reference

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20 December 2019

page(s)

1517-1528

1 reference

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Genome-wide patterns of histone modifications in yeast.

20 December 2019

cites work

1 reference

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A genomic code for nucleosome positioning

22 September 2017

1 reference

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Control of transcription through intragenic patterns of nucleosome composition

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Explicit equilibrium modeling of transcription-factor binding and gene regulation.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Genome-wide map of nucleosome acetylation and methylation in yeast

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

The dynamics of chromatin remodeling at promoters

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Genome-scale identification of nucleosome positions in S. cerevisiae

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Histone modifications: combinatorial complexity or cumulative simplicity?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

DIP-chip: rapid and accurate determination of DNA-binding specificity.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Transcriptional regulatory code of a eukaryotic genome

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Global analysis of protein expression in yeast

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Transcriptional regulatory networks in Saccharomyces cerevisiae

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Genome-wide location and function of DNA binding proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Preferential accessibility of the yeast his3 promoter is determined by a general property of the DNA sequence, not by specific elements

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Detection of leucine-independent DNA site occupancy of the yeast Leu3p transcriptional activator in vivo

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

LEU3 of Saccharomyces cerevisiae activates multiple genes for branched-chain amino acid biosynthesis by binding to a common decanucleotide core sequence

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Sequence logos: a new way to display consensus sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Evidence for nucleosome depletion at active regulatory regions genome-wide

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1665635

Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17053089

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Yeast transcriptional regulator Leu3p. Self-masking, specificity of masking, and evidence for regulation by the intracellular level of Leu3p

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17053089

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17053089

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.5655606

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17053089%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17053089%20AND%20SRC:MED&resulttype=core&format=json

20 December 2019

PubMed publication ID

17053089

1 reference