(Q34785860)

4 August 2017

title

Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding (English)

1 reference

4 August 2017

author

John Stamatoyannopoulos

8

object named as

John A Stamatoyannopoulos

1 reference

4 August 2017

9

Gordon L Hager

1 reference

4 August 2017

Ximiao He

1

1 reference

4 August 2017

Raghunath Chatterjee

2

1 reference

4 August 2017

Sam John

3

1 reference

4 August 2017

Hector Bravo

4

1 reference

4 August 2017

B K Sathyanarayana

5

1 reference

4 August 2017

Simon C Biddie

6

1 reference

4 August 2017

Peter C FitzGerald

7

1 reference

4 August 2017

Charles Vinson

10

1 reference

4 August 2017

language of work or name

English

0 references

publication date

28 June 2013

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4 August 2017

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4 August 2017

volume

14

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4 August 2017

page(s)

428

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Immunology. Cooperative transcription factor complexes in control

4 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

The UCSC Genome Browser database: extensions and updates 2013.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

The UCSC genome browser and associated tools

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

An encyclopedia of mouse DNA elements (Mouse ENCODE).

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Genome-wide occupancy links Hoxa2 to Wnt-β-catenin signaling in mouse embryonic development

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

DNA methylation status predicts cell type-specific enhancer activity.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Determinants of nucleosome organization in primary human cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Nucleosome-mediated cooperativity between transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

High nucleosome occupancy is encoded at human regulatory sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

G+C content dominates intrinsic nucleosome occupancy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Different gene regulation strategies revealed by analysis of binding motifs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

MEME SUITE: tools for motif discovery and searching

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

The DNA-encoded nucleosome organization of a eukaryotic genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Design and analysis of ChIP-seq experiments for DNA-binding proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Two strategies for gene regulation by promoter nucleosomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Interaction of the glucocorticoid receptor with the chromatin landscape

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Comparative genomics of Drosophila and human core promoters

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Transcriptional control in the segmentation gene network of Drosophila

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

UCSF Chimera--a visualization system for exploratory research and analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Clustering of DNA sequences in human promoters

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Collaborative competition mechanism for gene activation in vivo

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Repbase update: a database and an electronic journal of repetitive elements

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

A dominant negative to activation protein-1 (AP1) that abolishes DNA binding and inhibits oncogenesis.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Specific glucocorticoid receptor binding to DNA reconstituted in a nucleosome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3700821

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

8 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-14-428

Transcription factor binding sites and other features in human and Drosophila proximal promoters.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-14-428

Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation

21 January 2018

1 reference

12 December 2020

A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites

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

Nucleosome positions predicted through comparative genomics

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2164-14-428

1 reference

4 August 2017

1 reference

4 August 2017

1 reference