(Q34435301)

2 August 2017

title

In search of the determinants of enhancer-promoter interaction specificity (English)

1 reference

2 August 2017

2

Bas van Steensel

0 references

author name string

Joris van Arensbergen

series ordinal

1

1 reference

2 August 2017

Harmen J Bussemaker

series ordinal

3

1 reference

2 August 2017

publication date

24 August 2014

1 reference

2 August 2017

published in

Trends in Cell Biology

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2 August 2017

volume

24

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2 August 2017

issue

11

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2 August 2017

page(s)

695-702

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Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

2 August 2017

cites work

1 reference

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6 July 2018

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6 July 2018

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6 July 2018

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6 July 2018

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Effective blocking of the white enhancer requires cooperation between two main mechanisms suggested for the insulator function

6 July 2018

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Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

6 July 2018

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6 July 2018

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

6 July 2018

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Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

6 July 2018

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Single-cell dynamics of genome-nuclear lamina interactions

6 July 2018

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CTCF and cohesin: linking gene regulatory elements with their targets

6 July 2018

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Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

6 July 2018

1 reference

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Genome-wide quantitative enhancer activity maps identified by STARR-seq

6 July 2018

1 reference

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

6 July 2018

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Complex effects of nucleotide variants in a mammalian cis-regulatory element.

6 July 2018

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Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains

6 July 2018

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The long-range interaction landscape of gene promoters

6 July 2018

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The accessible chromatin landscape of the human genome

6 July 2018

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ChIA-PET analysis of transcriptional chromatin interactions.

6 July 2018

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Transcription factors: from enhancer binding to developmental control

6 July 2018

1 reference

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

6 July 2018

1 reference

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

6 July 2018

1 reference

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Developmental regulation of chromatin conformation by Hox proteins in Drosophila

6 July 2018

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

6 July 2018

1 reference

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

6 July 2018

1 reference

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Metazoan promoters: emerging characteristics and insights into transcriptional regulation

6 July 2018

1 reference

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Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

6 July 2018

1 reference

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Massively parallel functional dissection of mammalian enhancers in vivo

6 July 2018

1 reference

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Transcription factories: genetic programming in three dimensions

6 July 2018

1 reference

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Higher-order chromatin structure: bridging physics and biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

CTCF: insights into insulator function during development

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Variegated gene expression caused by cell-specific long-range DNA interactions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

CTCF-mediated functional chromatin interactome in pluripotent cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

An embryonic stage-specific enhancer within the murine β-globin locus mediates domain-wide histone hyperacetylation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Functional and mechanistic diversity of distal transcription enhancers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

A unique chromatin signature uncovers early developmental enhancers in humans

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Histone H3K27ac separates active from poised enhancers and predicts developmental state

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Genomics tools for unraveling chromosome architecture

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Systematic protein location mapping reveals five principal chromatin types in Drosophila cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Mediator and cohesin connect gene expression and chromatin architecture

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Chromatin insulators: lessons from the fly.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Enhancer-promoter communication at the Drosophila engrailed locus.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Close encounters of the 3C kind: long-range chromatin interactions and transcriptional regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

ChIP-seq accurately predicts tissue-specific activity of enhancers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Caudal, a key developmental regulator, is a DPE-specific transcriptional factor

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

A novel promoter-tethering element regulates enhancer-driven gene expression at the bithorax complex in the Drosophila embryo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Interchromosomal interactions and olfactory receptor choice

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Long-range control of gene expression: emerging mechanisms and disruption in disease

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Bystander gene activation by a locus control region

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Looping and interaction between hypersensitive sites in the active beta-globin locus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

POU/TBP cooperativity: a mechanism for enhancer action from a distance

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Capturing chromosome conformation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Different core promoters possess distinct regulatory activities in the Drosophila embryo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Interphase chromosomes undergo constrained diffusional motion in living cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Promoter specificity mediates the independent regulation of neighboring genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Cis-regulation of achaete and scute: shared enhancer-like elements drive their coexpression in proneural clusters of the imaginal discs.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Bidirectional control of the chicken beta- and epsilon-globin genes by a shared enhancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

A position-effect assay for boundaries of higher order chromosomal domains

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

A group of scs elements function as domain boundaries in an enhancer-blocking assay

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

The Drosophila sloppy paired locus encodes two proteins involved in segmentation that show homology to mammalian transcription factors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Enhancer loops appear stable during development and are associated with paused polymerase.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Chromatin position effects assayed by thousands of reporters integrated in parallel

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Flexible and dynamic nucleosome fiber in living mammalian cells

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

A switch between topological domains underlies HoxD genes collinearity in mouse limbs

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Chromatin folding--from biology to polymer models and back

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

Chromatin motion is constrained by association with nuclear compartments in human cells.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4252644

10.1016/J.TCB.2014.07.004

27 October 2018

Identifiers

DOI

1 reference

2 August 2017

1 reference

2 August 2017

1 reference