TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity (Q35042948)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

title

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

2

1 reference

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22 February 2020

Shelley L. Berger

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

author name string

Morgan A Sammons

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

Adam M Drake

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

publication date

12 November 2014

1 reference

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22 February 2020

1 reference

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22 February 2020

volume

25

1 reference

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22 February 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

page(s)

179-188

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

Integrated high-throughput analysis identifies Sp1 as a crucial determinant of p53-mediated apoptosis

22 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=4315292

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.

8 July 2018

1 reference

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Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Unravelling mechanisms of p53-mediated tumour suppression

8 July 2018

1 reference

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An atlas of active enhancers across human cell types and 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=4315292

H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

A p53 enhancer region regulates target genes through chromatin conformations in cis and in trans.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest

8 July 2018

1 reference

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A polymorphic p53 response element in KIT ligand influences cancer risk and has undergone natural selection

8 July 2018

1 reference

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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Genome-wide profiling reveals stimulus-specific functions of p53 during differentiation and DNA damage of human embryonic stem cells

8 July 2018

1 reference

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eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Transcription factor-induced enhancer modulations during cell fate conversions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Characterization of the p53 cistrome--DNA binding cooperativity dissects p53's tumor suppressor functions.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and 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=4315292

SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer 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=4315292

Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Models incorporating chromatin modification data identify functionally important p53 binding sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 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=4315292

H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

p63 steps into the limelight: crucial roles in the suppression of tumorigenesis and metastasis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

eRNAs are required for p53-dependent enhancer activity and gene transcription

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

STAR: ultrafast universal RNA-seq aligner

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

The accessible chromatin landscape of the human 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=4315292

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression 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=4315292

Enhancers: emerging roles in cell fate specification

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

p53-mediated heterochromatin reorganization regulates its cell fate decisions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Fast gapped-read alignment with Bowtie 2

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Distinct regulatory mechanisms and functions for p53-activated and p53-repressed DNA damage response genes in embryonic stem 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=4315292

ChromHMM: automating chromatin-state discovery and characterization

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

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=4315292

p53 binding to nucleosomes within the p21 promoter in vivo leads to nucleosome loss and transcriptional activation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

A user's guide to the encyclopedia of DNA elements (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=4315292

Mapping and analysis of chromatin state dynamics in nine human cell types

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

TAp63 suppresses metastasis through coordinate regulation of Dicer and miRNAs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

The NIH Roadmap Epigenomics Mapping Consortium

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

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=4315292

Transcriptional regulation by p53.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Basal dynamics of p53 reveal transcriptionally attenuated pulses in cycling 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=4315292

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Posttranslational modification of p53: cooperative integrators of function

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

p53-family proteins and their regulators: hubs and spokes in tumor suppression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Clinical outcomes and correlates of TP53 mutations and cancer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

BEDTools: a flexible suite of utilities for comparing genomic features

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Tumor suppressive functions of p53

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

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=4315292

Two mammalian MOF complexes regulate transcription activation by distinct mechanisms

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

p53--a Jack of all trades but master of none

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Redefining the p53 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=4315292

Blinded by the Light: The Growing Complexity of p53

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Modifications of p53: competing for the lysines

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Model-based analysis of ChIP-Seq (MACS)

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Characterization of genome-wide p53-binding sites upon stress response.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Recurrent initiation: a mechanism for triggering p53 pulses in response to DNA damage.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Modulation of p53 function by SET8-mediated methylation at lysine 382

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

The landscape of histone modifications across 1% of the human genome in five human cell lines

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

p53 in health and disease

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Tip60-dependent acetylation of p53 modulates the decision between cell-cycle arrest and apoptosis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Repression of p53 activity by Smyd2-mediated methylation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

In vivo activation of the p53 pathway by small-molecule antagonists of MDM2

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Active genes are tri-methylated at K4 of histone H3

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Live or let die: the cell's response to p53

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Methylation of histone H3 Lys 4 in coding regions of active genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

AP-1 in cell proliferation and survival

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

p63 is essential for regenerative proliferation in limb, craniofacial and epithelial 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=4315292

p63 is a p53 homologue required for limb and epidermal morphogenesis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

p53 sites acetylated in vitro by PCAF and p300 are acetylated in vivo in response to DNA damage

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

SnapShot: p53 posttranslational modifications

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

Acetylation of the p53 DNA-binding domain regulates apoptosis induction

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4315292

25 October 2018

Identifiers

DOI

10.1101/GR.181883.114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

PubMed publication ID

25391375

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25391375%20AND%20SRC:MED&resulttype=core&format=json