Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers. (Q33723246)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24813947%20AND%20SRC:MED&resulttype=core&format=json

18 March 2020

title

Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers (English)

1 reference

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18 March 2020

1

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18 March 2020

Marta Simonatto

2

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18 March 2020

Serena Ghisletti

6

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18 March 2020

Gioacchino Natoli

7

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18 March 2020

author name string

Silvia Bonifacio

3

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18 March 2020

Lin Yang

4

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18 March 2020

Remo Rohs

5

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18 March 2020

publication date

8 May 2014

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18 March 2020

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18 March 2020

volume

54

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18 March 2020

issue

5

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18 March 2020

page(s)

844-857

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TFBSshape: a motif database for DNA shape features of transcription factor binding sites

18 March 2020

cites work

1 reference

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Covariation between homeodomain transcription factors and the shape of their DNA binding sites

14 July 2018

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Developmental fate and cellular maturity encoded in human regulatory DNA landscapes

14 July 2018

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Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

14 July 2018

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Modification of enhancer chromatin: what, how, and why?

14 July 2018

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Determinants of nucleosome positioning

14 July 2018

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Controls of nucleosome positioning in the human genome.

14 July 2018

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CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

14 July 2018

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14 July 2018

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RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis.

14 July 2018

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The accessible chromatin landscape of the human genome

14 July 2018

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Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

14 July 2018

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

14 July 2018

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Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity

14 July 2018

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14 July 2018

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Pioneer transcription factors: establishing competence for gene expression

14 July 2018

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Master transcription factors determine cell-type-specific responses to TGF-β signaling

14 July 2018

1 reference

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Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.

14 July 2018

1 reference

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Determinants of nucleosome organization in primary human cells

14 July 2018

1 reference

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A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

A unique chromatin signature uncovers early developmental enhancers in humans

14 July 2018

1 reference

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

14 July 2018

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Maintaining cell identity through global control of genomic organization

14 July 2018

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Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

14 July 2018

1 reference

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Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

14 July 2018

1 reference

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A large fraction of extragenic RNA pol II transcription sites overlap enhancers

14 July 2018

1 reference

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Widespread transcription at neuronal activity-regulated enhancers

14 July 2018

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High nucleosome occupancy is encoded at human regulatory sequences

14 July 2018

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BEDTools: a flexible suite of utilities for comparing genomic features

14 July 2018

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Mechanisms of transcription factor selectivity

14 July 2018

1 reference

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G+C content dominates intrinsic nucleosome occupancy

14 July 2018

1 reference

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The role of DNA shape in protein-DNA recognition

14 July 2018

1 reference

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A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling

14 July 2018

1 reference

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

14 July 2018

1 reference

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

14 July 2018

1 reference

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ChIP-seq accurately predicts tissue-specific activity of enhancers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

The DNA-encoded nucleosome organization of a eukaryotic genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

Model-based analysis of ChIP-Seq (MACS)

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

Transcription factors in myeloid development: balancing differentiation with transformation.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

A genomic code for nucleosome positioning

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

Preparation of nucleosome core particle from recombinant histones

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4048654

PU.1 induces myeloid lineage commitment in multipotent hematopoietic progenitors

14 July 2018

1 reference

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The structure of an oligo(dA).oligo(dT) tract and its biological implications

14 July 2018

1 reference

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DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.

14 July 2018

1 reference

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Latent enhancers activated by stimulation in differentiated cells

30 October 2018

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Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages.

30 October 2018

1 reference

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Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages.

30 October 2018

1 reference

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Nucleosome positions predicted through comparative genomics

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24813947

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.MOLCEL.2014.04.006

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24813947%20AND%20SRC:MED&resulttype=core&format=json

18 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24813947%20AND%20SRC:MED&resulttype=core&format=json

18 March 2020

PubMed publication ID

24813947

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24813947%20AND%20SRC:MED&resulttype=core&format=json