(Q34723685)

4 August 2017

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast (English)

1 reference

4 August 2017

Mythily Ganapathi

1

1 reference

4 August 2017

Michael J Palumbo

2

1 reference

4 August 2017

Suraiya A Ansari

3

1 reference

4 August 2017

Qiye He

4

1 reference

4 August 2017

Kyle Tsui

5

1 reference

4 August 2017

Corey Nislow

6

1 reference

4 August 2017

Randall H Morse

7

1 reference

4 August 2017

language of work or name

English

0 references

publication date

16 November 2010

1 reference

4 August 2017

13

1 reference

based on heuristic

inferred from page(s)

published in

Nucleic Acids Research

1 reference

4 August 2017

39

1 reference

4 August 2017

2032-2044

1 reference

4 August 2017

6

1 reference

Creative Commons Attribution-NonCommercial 2.5 Generic

4 August 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Nucleosome sequence preferences influence in vivo nucleosome organization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

The role of nucleosome positioning in the evolution of gene regulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

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=3064788

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

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=3064788

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

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=3064788

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=3064788

The UCSC Genome Browser Database: update 2009

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across 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=3064788

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=3064788

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=3064788

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation 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=3064788

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

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=3064788

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=3064788

Transcription factor access to promoter 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=3064788

Assembly of regulatory factors on rRNA and ribosomal protein 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=3064788

Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 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=3064788

Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Extensive low-affinity transcriptional interactions 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=3064788

An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus 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=3064788

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=3064788

An improved map of conserved regulatory sites for 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=3064788

Scanning chromatin: a new paradigm?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

The YEASTRACT database: a tool for the analysis of transcription regulatory associations 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=3064788

T-profiler: scoring the activity of predefined groups of genes using gene expression data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

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=3064788

Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast 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=3064788

Genomic analysis of regulatory network dynamics reveals large topological changes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Global 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=3064788

Transcriptional regulatory code 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=3064788

Genome-wide analysis of ARS (autonomously replicating sequence) binding factor 1 (Abf1p)-mediated transcriptional regulation 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=3064788

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Getting into chromatin: how do transcription factors get past 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=3064788

Regulatory sequence analysis tools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

RAP, RAP, open up! New wrinkles for RAP1 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=3064788

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Chromatin opening and transactivator potentiation by RAP1 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=3064788

Molecular model for telomeric heterochromatin 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=3064788

Activation mechanism of the multifunctional transcription factor repressor-activator protein 1 (Rap1p)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

RAP1: a protean regulator 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=3064788

Experimental analysis of chromatin function in transcription control.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Sequence periodicities in chicken nucleosome core DNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

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=3064788

Nucleosome positioning: occurrence, mechanisms, and functional consequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

7 July 2018

Nucleosome positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064788

Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin 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=3064788

Local protein–DNA interactions may determine nucleosome positions on yeast plasmids

7 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1161

Nucleosome disruption by transcription factor binding in yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1161

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1161

The N-terminal and C-terminal domains of RAP1 are dispensable for chromatin opening and GCN4-mediated HIS4 activation in budding yeast.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1161

Genetic tests of the role of Abf1p in driving transcription of the yeast TATA box bindng protein-encoding gene, SPT15.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1161

The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1161

Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1161

Nucleosome positions predicted through comparative genomics

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21081559

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Non-random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21081559

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKQ1161

1 reference

4 August 2017

1 reference

4 August 2017

1 reference