The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. (Q35573905)

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2 March 2020

title

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements (English)

1 reference

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2 March 2020

1 reference

2

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2 March 2020

Borbala Mifsud

3

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2 March 2020

Filipe Tavares-Cadete

4

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2 March 2020

Biola M. Javierre

6

1 reference

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2 March 2020

Steven W Wingett

10

1 reference

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2 March 2020

Andrew Dimond

12

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2 March 2020

Cameron S. Osborne

21

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2 March 2020

Peter Fraser

24

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2 March 2020

author name string

Stefan Schoenfelder

1

1 reference

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2 March 2020

Robert Sugar

5

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2 March 2020

Takashi Nagano

7

1 reference

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2 March 2020

Yulia Katsman

8

1 reference

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2 March 2020

Moorthy Sakthidevi

9

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2 March 2020

Emilia Dimitrova

11

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2 March 2020

Lucas B Edelman

13

1 reference

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2 March 2020

Sarah Elderkin

14

1 reference

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2 March 2020

Kristina Tabbada

15

1 reference

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2 March 2020

Elodie Darbo

16

1 reference

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2 March 2020

Simon Andrews

17

1 reference

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2 March 2020

Bram Herman

18

1 reference

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2 March 2020

Andy Higgs

19

1 reference

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2 March 2020

Emily LeProust

20

1 reference

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2 March 2020

Jennifer A Mitchell

22

1 reference

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2 March 2020

Nicholas M Luscombe

23

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2 March 2020

publication date

9 March 2015

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2 March 2020

1 reference

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2 March 2020

volume

25

1 reference

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2 March 2020

issue

4

1 reference

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2 March 2020

page(s)

582-597

1 reference

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A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential

2 March 2020

cites work

1 reference

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Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C.

27 July 2018

1 reference

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Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.

27 July 2018

1 reference

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Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations

27 July 2018

1 reference

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Fine tuning of craniofacial morphology by distant-acting enhancers

27 July 2018

1 reference

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Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

27 July 2018

1 reference

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Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization

27 July 2018

1 reference

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The pluripotent genome in three dimensions is shaped around pluripotency factors

27 July 2018

1 reference

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

27 July 2018

1 reference

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Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming

27 July 2018

1 reference

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

27 July 2018

1 reference

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

27 July 2018

1 reference

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The hierarchy of the 3D genome

27 July 2018

1 reference

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Impaired in vitro erythropoiesis following deletion of the Scl (Tal1) +40 enhancer is largely compensated for in vivo despite a significant reduction in expression

27 July 2018

1 reference

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The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation

27 July 2018

1 reference

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Robust 4C-seq data analysis to screen for regulatory DNA interactions.

27 July 2018

1 reference

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The long-range interaction landscape of gene promoters

27 July 2018

1 reference

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An integrated encyclopedia of DNA elements in the human genome

27 July 2018

1 reference

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Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor

27 July 2018

1 reference

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Hi-C: a comprehensive technique to capture the conformation of genomes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Spatial partitioning of the regulatory landscape of the X-inactivation centre

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Topological domains in mammalian genomes identified by analysis of chromatin interactions

27 July 2018

1 reference

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The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Spatial organization of the mouse genome and its role in recurrent chromosomal translocations

27 July 2018

1 reference

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Three-dimensional folding and functional organization principles of the Drosophila genome

27 July 2018

1 reference

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A regulatory archipelago controls Hox genes transcription in digits

27 July 2018

1 reference

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CTCF-mediated functional chromatin interactome in pluripotent cells

27 July 2018

1 reference

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Mammalian genes are transcribed with widely different bursting kinetics

27 July 2018

1 reference

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Functional and mechanistic diversity of distal transcription enhancers

27 July 2018

1 reference

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Mediator and cohesin connect gene expression and chromatin architecture

27 July 2018

1 reference

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Active RNA polymerases: mobile or immobile molecular machines?

27 July 2018

1 reference

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Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation

27 July 2018

1 reference

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Phenotypic robustness conferred by apparently redundant transcriptional enhancers

27 July 2018

1 reference

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Lineage-specific combinatorial action of enhancers regulates mouse erythroid Gata1 expression

27 July 2018

1 reference

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Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

27 July 2018

1 reference

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An oestrogen-receptor-α-bound human chromatin interactome

27 July 2018

1 reference

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Comprehensive mapping of long-range interactions reveals folding principles of the human genome

27 July 2018

1 reference

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Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus

27 July 2018

1 reference

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ChIP-seq accurately predicts tissue-specific activity of enhancers

27 July 2018

1 reference

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Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

27 July 2018

1 reference

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Shadow enhancers as a source of evolutionary novelty

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression

27 July 2018

1 reference

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Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

27 July 2018

1 reference

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Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells

27 July 2018

1 reference

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Deletion of ultraconserved elements yields viable mice

27 July 2018

1 reference

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Myc dynamically and preferentially relocates to a transcription factory occupied by Igh

27 July 2018

1 reference

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Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression

27 July 2018

1 reference

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In vivo enhancer analysis of human conserved non-coding sequences

27 July 2018

1 reference

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Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.

27 July 2018

1 reference

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Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

27 July 2018

1 reference

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Long-range downstream enhancers are essential for Pax6 expression

27 July 2018

1 reference

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Interchromosomal associations between alternatively expressed loci

27 July 2018

1 reference

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Active genes dynamically colocalize to shared sites of ongoing transcription

27 July 2018

1 reference

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A global control region defines a chromosomal regulatory landscape containing the HoxD cluster

27 July 2018

1 reference

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Long-range chromatin regulatory interactions in vivo

27 July 2018

1 reference

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Deletion of the mouse alpha-globin regulatory element (HS -26) has an unexpectedly mild phenotype

27 July 2018

1 reference

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Capturing chromosome conformation

27 July 2018

1 reference

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A BAC transgenic analysis of the Mrf4/Myf5 locus reveals interdigitated elements that control activation and maintenance of gene expression during muscle development

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Chromosomal contact permits transcription between coregulated genes

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Klf4 organizes long-range chromosomal interactions with the oct4 locus in reprogramming and pluripotency.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Exploring long-range genome interactions using the WashU Epigenome Browser

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

A map of the cis-regulatory sequences in the mouse genome

26 September 2018

1 reference

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DNA-binding factors shape the mouse methylome at distal regulatory regions

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

A cluster of three long-range enhancers directs regional Shh expression in the epithelial linings.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Transcription factories are nuclear subcompartments that remain in the absence of transcription

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Targeted deletion of 5'HS1 and 5'HS4 of the beta-globin locus control region reveals additive activity of the DNaseI hypersensitive sites

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4381529

Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25752748

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.185272.114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25752748%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25752748%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

PubMed publication ID

25752748

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25752748%20AND%20SRC:MED&resulttype=core&format=json