The 3D genome in transcriptional regulation and pluripotency

An integrated encyclopedia of DNA elements in the human genome

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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High-Resolution Profiling of Histone Methylations in the Human Genome

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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Super-enhancers in the control of cell identity and disease

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Capturing Chromosome Conformation

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Discovery and saturation analysis of cancer genes across 21 tumour types

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

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Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

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

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

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Mediator and cohesin connect gene expression and chromatin architecture

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The NIH Roadmap Epigenomics Mapping Consortium

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

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An oestrogen-receptor-α-bound human chromatin interactome

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Long Noncoding RNAs with Enhancer-like Function in Human Cells

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

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

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CTCF: Master Weaver of the Genome

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The long-range interaction landscape of gene promoters

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

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

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Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus

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Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

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Obesity-associated variants within FTO form long-range functional connections with IRX3

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A high-resolution map of the three-dimensional chromatin interactome in human cells

Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208 · see citing works

Cohesin mediates transcriptional insulation by CCCTC-binding factor

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

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

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

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Chromosome TerritoriesPreprint

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The protein CTCF is required for the enhancer blocking activity of vertebrate insulators

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

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Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

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Active genes dynamically colocalize to shared sites of ongoing transcription

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CTCF: an architectural protein bridging genome topology and function

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Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

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Hyperdynamic Plasticity of Chromatin Proteins in Pluripotent Embryonic Stem Cells

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Organization of the mitotic chromosome

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The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

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Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

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Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

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Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes

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Distinct epigenomic landscapes of pluripotent and lineage-committed human cells

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Transcriptional repression mediated by repositioning of genes to the nuclear lamina

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

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An expansive human regulatory lexicon encoded in transcription factor footprints

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

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Subnuclear Compartmentalization of Immunoglobulin Loci During Lymphocyte Development

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Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

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

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A decade of 3C technologies: insights into nuclear organizationPreprint

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The Hierarchy of the 3D Genome

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Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations

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Interphase chromosomes undergo constrained diffusional motion in living cells

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Long-range chromatin regulatory interactions in vivo

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Characterization of the Drosophila melanogaster genome at the nuclear lamina

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Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

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

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Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcriptionPreprint

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Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

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CTCF-mediated functional chromatin interactome in pluripotent cells

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Genomic views of distant-acting enhancers

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Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

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Defining mechanisms that regulate RNA polymerase II transcription in vivo

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Open chromatin in pluripotency and reprogramming

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Ring1B Compacts Chromatin Structure and Represses Gene Expression Independent of Histone Ubiquitination

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Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

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

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

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

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Topology of mammalian developmental enhancers and their regulatory landscapes

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CTCF physically links cohesin to chromatin

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Proximity among Distant Regulatory Elements at the β-Globin Locus Requires GATA-1 and FOG-1

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A Regulatory Archipelago Controls Hox Genes Transcription in Digits

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

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

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Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

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Functional and topological characteristics of mammalian regulatory domains

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Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

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Functional implications of genome topology

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A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

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Chromatin dynamics during cellular reprogramming

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