Integrating one-dimensional and three-dimensional maps of genomes (Q33891295)

29 July 2017

title

Integrating one-dimensional and three-dimensional maps of genomes (English)

1 reference

29 July 2017

2

Job Dekker

1 reference

29 July 2017

Natalia Naumova

1

1 reference

29 July 2017

language of work or name

English

0 references

publication date

1 June 2010

1 reference

29 July 2017

published in

Journal of Cell Science

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29 July 2017

volume

123

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29 July 2017

issue

Pt 12

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29 July 2017

page(s)

1979-1988

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

29 July 2017

cites work

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5 July 2018

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Nuclear neighborhoods and gene expression

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5 July 2018

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Long-range chromosomal interactions and gene regulation

5 July 2018

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Global reorganization of replication domains during embryonic stem cell differentiation

5 July 2018

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Association between active genes occurs at nuclear speckles and is modulated by chromatin environment

5 July 2018

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Chromatin loops in gene regulation

5 July 2018

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5 July 2018

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5 July 2018

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Global chromatin domain organization of the Drosophila genome

5 July 2018

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Gene regulation in the third dimension

5 July 2018

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The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions

5 July 2018

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The genome landscape of ERalpha- and ERbeta-binding DNA regions

5 July 2018

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High-resolution mapping and characterization of open chromatin across the genome

5 July 2018

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Coordinate gene regulation during hematopoiesis is related to genomic organization

5 July 2018

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An evaluation of 3C-based methods to capture DNA interactions

5 July 2018

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5 July 2018

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Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex.

5 July 2018

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Domain-wide regulation of gene expression in the human genome

5 July 2018

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Beyond repair foci: subnuclear domains and the cellular response to DNA damage

5 July 2018

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5 July 2018

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Identification of higher-order functional domains in the human ENCODE regions

5 July 2018

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5 July 2018

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5 July 2018

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Nuclear organization of the genome and the potential for gene regulation

5 July 2018

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High-resolution profiling of histone methylations in the human genome

5 July 2018

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Mapping networks of physical interactions between genomic elements using 5C technology

5 July 2018

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

5 July 2018

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Beyond the sequence: cellular organization of genome function

5 July 2018

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5 July 2018

The mammalian epigenome

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Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping.

5 July 2018

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

5 July 2018

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

5 July 2018

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Genome-wide analysis of estrogen receptor binding sites

5 July 2018

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

5 July 2018

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Transcriptional control thrown for a loop

5 July 2018

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The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications

5 July 2018

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Interchromosomal interactions and olfactory receptor choice

5 July 2018

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CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2

5 July 2018

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Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories

5 July 2018

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DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

5 July 2018

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Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes

5 July 2018

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The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding

5 July 2018

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Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations

5 July 2018

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The role of chromatin structure in regulating the expression of clustered genes.

5 July 2018

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Interchromosomal associations between alternatively expressed loci

5 July 2018

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Temporal profile of replication of human chromosomes

5 July 2018

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Remote control of gene transcription

5 July 2018

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DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise.

5 July 2018

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Control of globin gene expression during development and erythroid differentiation

5 July 2018

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

5 July 2018

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The profile of repeat-associated histone lysine methylation states in the mouse epigenome

5 July 2018

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

5 July 2018

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Polytene chromosomes: 70 years of genetic research.

5 July 2018

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The ENCODE (ENCyclopedia Of DNA Elements) Project

5 July 2018

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Active genes dynamically colocalize to shared sites of ongoing transcription

5 July 2018

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Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers

5 July 2018

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Does looping and clustering in the nucleus regulate gene expression?

5 July 2018

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The evolutionary dynamics of eukaryotic gene order

5 July 2018

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Genome-wide identification of high-affinity estrogen response elements in human and mouse

5 July 2018

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Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites

5 July 2018

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Inheritance of Polycomb-dependent chromosomal interactions in Drosophila

5 July 2018

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Transcription factories: quantitative studies of nanostructures in the mammalian nucleus

5 July 2018

1 reference

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Spatial organization of gene expression: the active chromatin hub.

5 July 2018

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The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes

5 July 2018

1 reference

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A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus

5 July 2018

1 reference

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A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Integration of the cytogenetic map with the draft human genome sequence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Evidence for large domains of similarly expressed genes in the Drosophila genome

5 July 2018

1 reference

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Clustering of housekeeping genes provides a unified model of gene order in the human genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Capturing chromosome conformation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells

5 July 2018

1 reference

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The concept of self-organization in cellular architecture

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

The human transcriptome map: clustering of highly expressed genes in chromosomal domains

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Genome-wide location and function of DNA binding proteins

5 July 2018

1 reference

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A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression

5 July 2018

1 reference

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Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase

5 July 2018

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Isochores and the evolutionary genomics of vertebrates

5 July 2018

1 reference

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Differences in the localization and morphology of chromosomes in the human nucleus.

5 July 2018

1 reference

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Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei.

5 July 2018

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The topology of transcription by immobilized polymerases.

5 July 2018

1 reference

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Replication structure of the human beta-globin gene domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Chromosome bands, their chromatin flavors, and their functional features

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Entropic organization of interphase chromosomes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

A gene-centered C. elegans protein-DNA interaction network

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Predicting three-dimensional genome structure from transcriptional activity.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

A unification of mosaic structures in the human genome

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Active RNA polymerases are localized within discrete transcription "factories' in human nuclei

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2880011

Long-range intrachromosomal interactions in the T helper type 2 cytokine locus

10 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20519580

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20519580

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1242/JCS.051631

1 reference

29 July 2017

1 reference

29 July 2017

1 reference