Organization and function of the 3D genome (Q38980344)

8 September 2017

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title

Organization and function of the 3D genome. (English)

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8 September 2017

Boyan Bonev

1

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Giacomo Cavalli

object named as

Giacomo Cavalli

series ordinal

2

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publication date

1 October 2016

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8 September 2017

Nature Reviews Genetics

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8 September 2017

17

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8 September 2017

11

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8 September 2017

661-678

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https://scigraph.springernature.com/pub.10.1038/nrg.2016.112

8 September 2017

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Organization of the mitotic chromosome

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

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Gene loops juxtapose promoters and terminators in yeast

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Gene loops enhance transcriptional directionality

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

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Stable Chromosome Condensation Revealed by Chromosome Conformation Capture

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

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Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

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Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries

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31 March 2020

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31 March 2020

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

31 March 2020

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31 March 2020

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Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

31 March 2020

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31 March 2020

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31 March 2020

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Cohesin-mediated interactions organize chromosomal domain architecture

31 March 2020

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CTCF: an architectural protein bridging genome topology and function

31 March 2020

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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

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRG.2016.112

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

31 March 2020

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The chromatin insulator CTCF and the emergence of metazoan diversity

31 March 2020

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Functional analysis of CTCF during mammalian limb development

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRG.2016.112

Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

CTCF-mediated functional chromatin interactome in pluripotent cells

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Widespread plasticity in CTCF occupancy linked to DNA methylation

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

CTCF Binding Polarity Determines Chromatin Looping.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Transcription factor trapping by RNA in gene regulatory elements

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Bipartite structure of the inactive mouse X chromosome

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Structural organization of the inactive X chromosome in the mouse.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Condensin-driven remodelling of X chromosome topology during dosage compensation.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

A novel role for the Aurora B kinase in epigenetic marking of silent chromatin in differentiated postmitotic cells.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

LBR and lamin A/C sequentially tether peripheral heterochromatin and inversely regulate differentiation.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Chromosomal variation in neurons of the developing and adult mammalian nervous system

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

The yeast genome undergoes significant topological reorganization in quiescence

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Global reorganization of the nuclear landscape in senescent cells

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

A regulatory archipelago controls Hox genes transcription in digits

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRG.2016.112

Single-cell dynamics of genome-nuclear lamina interactions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Reactivation of developmentally silenced globin genes by forced chromatin looping.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Insulator dysfunction and oncogene activation in IDH mutant gliomas

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Activation of proto-oncogenes by disruption of chromosome neighborhoods.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Chromatin insulators: linking genome organization to cellular function

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Chromosomal contact permits transcription between coregulated genes

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

A three-dimensional model of the yeast genome

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

High-resolution mapping of the spatial organization of a bacterial chromosome

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Recurring genomic breaks in independent lineages support genomic fragility

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

The 3D organization of chromatin explains evolutionary fragile genomic regions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Genome-wide chromatin state transitions associated with developmental and environmental cues

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Imaging intracellular fluorescent proteins at nanometer resolution

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Scoring and manipulating gene position and dynamics using FROS in budding yeast

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

DNA dynamics during early double-strand break processing revealed by non-intrusive imaging of living cells

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Interaction between transcription regulatory regions of prolactin chromatin

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Capturing chromosome conformation

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

An oestrogen-receptor-α-bound human chromatin interactome

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Chromosome conformation capture technologies and their impact in understanding genome function

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.112

Open and closed domains in the mouse genome are configured as 10-nm chromatin fibres

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27739532

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27739532

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG.2016.112

1 reference

PubMed ID

27739532

Dimensions Publication ID

8 September 2017

1029513141

0 references

Fatcat ID

release_gmftbpgcafaslkvfpri7loyqrm

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/gmftbpgcafaslkvfpri7loyqrm

mapped directly with Wikidata item

24 November 2022

based on heuristic

PubMed ID

27739532

1 reference

PubMed ID

27739532