Capturing Chromosome Conformation

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A Transcription-Independent Role for TFIIB in Gene Looping

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Interactions among Polycomb Domains Are Guided by Chromosome Architecture

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PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory elementPreprint

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Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

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Genetics and Epigenetics of the Multifunctional Protein CTCF

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Epigenomics

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The Nuclear Receptor PPARγ Controls Progressive Macrophage Polarization as a Ligand-Insensitive Epigenomic Ratchet of Transcriptional Memory

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Subtype-specific regulatory network rewiring in acute myeloid leukemia

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Chromatin Dynamics

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Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

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In search of the determinants of enhancer–promoter interaction specificity

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Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale

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Higher-order chromatin structure: bridging physics and biology

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Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle

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Analysis methods for studying the 3D architecture of the genome

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High-quality genome (re)assembly using chromosomal contact data

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Direct observation of a condensate effect on super-enhancer controlled gene bursting

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Genome-Wide Analysis of Protein-DNA Interactions

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Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming

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Does CTCF mediate between nuclear organization and gene expression?

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STAT3, STAT4, NFATc1, and CTCF Regulate PD-1 through Multiple Novel Regulatory Regions in Murine T Cells

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Enhancer Logic and Mechanics in Development and Disease

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Multiple interactions between regulatory regions are required to stabilize an active chromatin hub

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Genomics of Long-Range Regulatory Elements

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Electrostatic interactions in biological DNA-related systems

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Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

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Predicting three-dimensional genome structure from transcriptional activity

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On a chromosome far, far away: LCRs and gene expression

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Enhancers Located within Two Introns of the Vitamin D Receptor Gene Mediate Transcriptional Autoregulation by 1,25-Dihydroxyvitamin D3

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Architecture of the Escherichia coli nucleoid

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Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

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Human tRNA genes function as chromatin insulators

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Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

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A supervised learning framework for chromatin loop detection in genome-wide contact maps

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Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

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Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity

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Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes

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Epigenetic regulation: A new frontier for biomedical engineers

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Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

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Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression

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Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling

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Pericentric Chromatin Is Organized into an Intramolecular Loop in Mitosis

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The class E floral homeotic protein SEPALLATA3 is sufficient to loop DNA in ‘floral quartet’-like complexes in vitro

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Chromatin Dynamics and Gene Positioning

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Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA

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The transcriptional interactome: gene expression in 3D

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A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

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A Functional Variant at a Prostate Cancer Predisposition Locus at 8q24 Is Associated with PVT1 Expression

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Identification of β-catenin binding regions in colon cancer cells using ChIP-Seq

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A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies

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Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

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Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

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Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene

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Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres

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A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae

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Mapping in Vivo Chromatin Interactions in Yeast Suggests an Extended Chromatin Fiber with Regional Variation in Compaction

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Developmental Control of Polycomb Subunit Composition by GATA Factors Mediates a Switch to Non-Canonical Functions

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AP‐2γ regulates oestrogen receptor‐mediated long‐range chromatin interaction and gene transcription

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Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

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Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase

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Chromatin Organization in the Mammalian Nucleus

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Epigenetic regulation of Kiss1 gene expression mediating estrogen-positive feedback action in the mouse brain

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Genome organization and long-range regulation of gene expression by enhancers

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How best to identify chromosomal interactions: a comparison of approaches

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From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics

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The spatial organization of transcriptional control

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Looking beyond the genes: the role of non-coding variants in human disease

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Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology

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A Downstream Intergenic Cluster of Regulatory Enhancers Contributes to the Induction of CYP24A1 Expression by 1α,25-Dihydroxyvitamin D3

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Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences

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Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

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A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)

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“Cat’s Cradling” the 3D Genome by the Act of LncRNA Transcription

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TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

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Stable Chromosome Condensation Revealed by Chromosome Conformation Capture

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Epigenetic mechanisms regulating T-cell responses

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Tissue- and Expression Level–Specific Chromatin Looping at Maizeb1Epialleles

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Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

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Similar active genes cluster in specialized transcription factories

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Genome‐wide Hi‐C analysis reveals extensive hierarchical chromatin interactions in rice

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The three-dimensional architecture of Hox cluster silencing

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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

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