Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture (Q33557596)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

title

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

Caelin Cubeñas-Potts

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

Xiaowen Lyu

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

Ge Li

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

Elissa P Lei

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

Victor G Corces

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

language of work or name

English

0 references

publication date

1 February 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

published in

Nucleic Acids Research

1 reference

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28 March 2020

volume

1 reference

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28 March 2020

issue

1 reference

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28 March 2020

page(s)

1714-1730

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 4.0 International

28 March 2020

start time

2 December 2016

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

describes a project that uses

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila

1 reference

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Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex

21 June 2018

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The Hierarchy of Transcriptional Activation: From Enhancer to Promoter

21 June 2018

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Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

21 June 2018

1 reference

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Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

21 June 2018

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Architectural and Functional Commonalities between Enhancers and Promoters

21 June 2018

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Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution

21 June 2018

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Absence of canonical marks of active chromatin in developmentally regulated genes

21 June 2018

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CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

21 June 2018

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Architectural proteins, transcription, and the three-dimensional organization of the genome

21 June 2018

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Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions

21 June 2018

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Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.

21 June 2018

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High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.

21 June 2018

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Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing

21 June 2018

1 reference

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CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation

21 June 2018

1 reference

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Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

21 June 2018

1 reference

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A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

21 June 2018

1 reference

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Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes

21 June 2018

1 reference

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In search of the determinants of enhancer-promoter interaction specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Insulator function and topological domain border strength scale with architectural protein occupancy

21 June 2018

1 reference

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ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

21 June 2018

1 reference

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Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Cohesin-mediated interactions organize chromosomal domain architecture

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Distinct isoforms of the Drosophila Brd4 homologue are present at enhancers, promoters and insulator sites

21 June 2018

1 reference

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Chromatin insulators: linking genome organization to cellular function

21 June 2018

1 reference

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Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.

21 June 2018

1 reference

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

21 June 2018

1 reference

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Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle

21 June 2018

1 reference

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Precise maps of RNA polymerase reveal how promoters direct initiation and pausing

21 June 2018

1 reference

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

21 June 2018

1 reference

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Poised RNA polymerase II changes over developmental time and prepares genes for future expression

21 June 2018

1 reference

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Defining the status of RNA polymerase at promoters

21 June 2018

1 reference

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

21 June 2018

1 reference

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The chromatin fingerprint of gene enhancer elements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Transcriptional repression via antilooping in the Drosophila embryo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Topological domains in mammalian genomes identified by analysis of chromatin interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Regulation of chromatin organization and inducible gene expression by a Drosophila insulator

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

H3K4 tri-methylation provides an epigenetic signature of active enhancers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

CTCF-mediated functional chromatin interactome in pluripotent cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Integrative genomics viewer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Aligning Short Sequencing Reads with Bowtie

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

BEDTools: a flexible suite of utilities for comparing genomic features

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Genome-wide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Active promoters and insulators are marked by the centrosomal protein 190.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

BEAF regulates cell-cycle genes through the controlled deposition of H3K9 methylation marks into its conserved dual-core binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Model-based analysis of ChIP-Seq (MACS)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

The Drosophila transcription factor tramtrack (TTK) interacts with Trithorax-like (GAGA) and represses GAGA-mediated activation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Selectivity, sharing and competitive interactions in the regulation of Hoxb genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Different core promoters possess distinct regulatory activities in the Drosophila embryo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Promoter specificity mediates the independent regulation of neighboring genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

Protein encoding by both DNA strands.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1114

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389536

31 October 2018

Identifiers

DOI

10.1093/NAR/GKW1114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

release_cya5flqnsfdsvj3bmtjxemfhl4

28 March 2020

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/cya5flqnsfdsvj3bmtjxemfhl4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json

28 March 2020

PubMed publication ID

27899590

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27899590%20AND%20SRC:MED&resulttype=core&format=json