Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle (Q83226286)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

title

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

main subject

chromatin accessibility

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1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

Antonio Meireles-filho

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

Vincent Gardeux

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

Bart Deplancke

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

David Suter

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

author name string

Cédric Deluz

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

Subashika Govindan

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

language of work or name

English

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publication date

3 December 2019

1 reference

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23 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

volume

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

23 April 2020

ggplot2

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=6890464

ggplot2

2 references

10 June 2022

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

RStudio

1 reference

18 June 2022

https://europepmc.org/article/PMC/6890464

inferred from PubMed Central ID database lookup

limma

limma

2 references

22 June 2022

https://europepmc.org/article/PMC/6890464

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

ComplexHeatmap

ComplexHeatmap

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

edgeR

edgeR

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

CellProfiler

CellProfiler

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3

1 reference

12 December 2020

A third-generation lentivirus vector with a conditional packaging system

1 reference

12 December 2020

The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2.

1 reference

12 December 2020

Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells

1 reference

12 December 2020

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

1 reference

12 December 2020

Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4

1 reference

12 December 2020

The human genome browser at UCSC

1 reference

12 December 2020

Ablation of PARP-1 does not interfere with the repair of DNA double-strand breaks, but compromises the reactivation of stalled replication forks

1 reference

12 December 2020

The F-box protein TIR1 is an auxin receptor

1 reference

12 December 2020

The Arabidopsis F-box protein TIR1 is an auxin receptor

1 reference

12 December 2020

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

1 reference

12 December 2020

Core transcriptional regulatory circuitry in human embryonic stem cells

1 reference

12 December 2020

Rapid generation of stable transgenic embryonic stem cell lines using modular lentivectors

1 reference

12 December 2020

The UCSC Genome Browser Database: update 2006

1 reference

12 December 2020

CellProfiler: image analysis software for identifying and quantifying cell phenotypes

1 reference

12 December 2020

Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells.

1 reference

12 December 2020

FGF stimulation of the Erk1/2 signalling cascade triggers transition of pluripotent embryonic stem cells from self-renewal to lineage commitment.

1 reference

12 December 2020

Mediators of reprogramming: transcription factors and transitions through mitosis

1 reference

12 December 2020

Model-based analysis of ChIP-Seq (MACS)

1 reference

12 December 2020

The Sequence Alignment/Map format and SAMtools

1 reference

12 December 2020

PARP1 poly(ADP-ribosyl)ates Sox2 to control Sox2 protein levels and FGF4 expression during embryonic stem cell differentiation

1 reference

12 December 2020

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

1 reference

12 December 2020

An auxin-based degron system for the rapid depletion of proteins in nonplant cells.

1 reference

12 December 2020

Oct-4 controls cell-cycle progression of embryonic stem cells

1 reference

12 December 2020

BEDTools: a flexible suite of utilities for comparing genomic features

1 reference

12 December 2020

Tbx3 improves the germ-line competency of induced pluripotent stem cells

1 reference

12 December 2020

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

1 reference

12 December 2020

Histone H3K27ac separates active from poised enhancers and predicts developmental state

1 reference

12 December 2020

esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function

1 reference

12 December 2020

Pioneer transcription factors: establishing competence for gene expression

1 reference

12 December 2020

Fiji: an open-source platform for biological-image analysis

1 reference

12 December 2020

Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1.

1 reference

12 December 2020

An integrated encyclopedia of DNA elements in the human genome

1 reference

12 December 2020

STAR: ultrafast universal RNA-seq aligner

1 reference

12 December 2020

Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells

1 reference

12 December 2020

Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome

1 reference

12 December 2020

A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins

1 reference

12 December 2020

Master transcription factors and mediator establish super-enhancers at key cell identity genes

1 reference

12 December 2020

A defined Oct4 level governs cell state transitions of pluripotency entry and differentiation into all embryonic lineages

1 reference

12 December 2020

Reduced Oct4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct4 and Nanog

1 reference

12 December 2020

Architectural protein subclasses shape 3D organization of genomes during lineage commitment

1 reference

12 December 2020

An expanded tool kit for the auxin-inducible degron system in budding yeast

1 reference

12 December 2020

Software for computing and annotating genomic ranges

1 reference

12 December 2020

The cell-cycle state of stem cells determines cell fate propensity.

1 reference

12 December 2020

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

1 reference

12 December 2020

Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells

1 reference

12 December 2020

Single-molecule dynamics of enhanceosome assembly in embryonic stem cells

1 reference

12 December 2020

Klf4 and Klf5 differentially inhibit mesoderm and endoderm differentiation in embryonic stem cells.

1 reference

12 December 2020

Defining an essential transcription factor program for naïve pluripotency

1 reference

12 December 2020

Genome accessibility is widely preserved and locally modulated during mitosis

1 reference

12 December 2020

CpG island-mediated global gene regulatory modes in mouse embryonic stem cells

1 reference

12 December 2020

Pioneer transcription factors in cell reprogramming

1 reference

12 December 2020

limma powers differential expression analyses for RNA-sequencing and microarray studies

1 reference

12 December 2020

Enhancers, enhancers - from their discovery to today's universe of transcription enhancers

1 reference

12 December 2020

Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming

1 reference

12 December 2020

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells.

1 reference

12 December 2020

GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler

1 reference

12 December 2020

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

1 reference

12 December 2020

deepTools2: a next generation web server for deep-sequencing data analysis

1 reference

12 December 2020

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.

1 reference

12 December 2020

Proliferation, survival and metabolism: the role of PI3K/AKT/mTOR signalling in pluripotency and cell fate determination.

1 reference

12 December 2020

Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective: Multiple transcription factors can effect chromatin pioneer functions through dynamic interactions with ATP-dependent chromatin remodeling factor

1 reference

12 December 2020

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

1 reference

12 December 2020

Cooperative Action between SALL4A and TET Proteins in Stepwise Oxidation of 5-Methylcytosine.

1 reference

12 December 2020

A dynamic mode of mitotic bookmarking by transcription factors

1 reference

12 December 2020

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

1 reference

12 December 2020

Cooperative Binding of Transcription Factors Orchestrates Reprogramming

1 reference

12 December 2020

Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci.

1 reference

12 December 2020

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells.

1 reference

12 December 2020

3D structures of individual mammalian genomes studied by single-cell Hi-C.

1 reference

12 December 2020

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

1 reference

12 December 2020

Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells

1 reference

12 December 2020

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

1 reference

12 December 2020

Profiling of Single-Cell Transcriptomes.

1 reference

12 December 2020

Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability.

1 reference

12 December 2020

Synergistic gene expression during the acute phase response is characterized by transcription factor assisted loading

1 reference

12 December 2020

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing.

1 reference

12 December 2020

Distinct SoxB1 networks are required for naïve and primed pluripotency

1 reference

12 December 2020

Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate.

1 reference

12 December 2020

An Mll4/COMPASS-Lsd1 epigenetic axis governs enhancer function and pluripotency transition in embryonic stem cells.

1 reference

12 December 2020

Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming.

1 reference

12 December 2020

Dynamic changes in Sox2 spatio-temporal expression promote the second cell fate decision through Fgf4/Fgfr2 signalling in preimplantation mouse embryos.

1 reference

12 December 2020

The dTAG system for immediate and target-specific protein degradation.

1 reference

12 December 2020

TFAP2C regulates transcription in human naive pluripotency by opening enhancers.

1 reference

12 December 2020

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

1 reference

12 December 2020

Coactivator condensation at super-enhancers links phase separation and gene control

1 reference

12 December 2020

Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a.

1 reference

12 December 2020

Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates

1 reference

12 December 2020

CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning

1 reference

12 December 2020

Transcription factor activity and nucleosome organization in mitosis

1 reference

12 December 2020

Mitotic chromosome binding predicts transcription factor properties in interphase

1 reference

12 December 2020

Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation

1 reference

12 December 2020

Zfp281 Shapes the Transcriptome of Trophoblast Stem Cells and Is Essential for Placental Development

1 reference

12 December 2020

Transcription Restart Establishes Chromatin Accessibility after DNA Replication

1 reference

12 December 2020

Determining cellular CTCF and cohesin abundances to constrain 3D genome models

1 reference

12 December 2020

Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening

1 reference

12 December 2020

Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors

1 reference

12 December 2020

Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions

1 reference

12 December 2020

https://opencitations.net/index/coci/api/v1/references/10.7554/ELIFE.50087

1 reference

13 October 2023

Identifiers

DOI

10.7554/ELIFE.50087

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31794382%20AND%20SRC:MED&resulttype=core&format=json

23 April 2020

1 reference