Job Dekker

Capturing chromosome conformation.

A closer look at long-range chromosomal interactions.

A mechanical basis for chromosome function.

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

The three 'C' s of chromosome conformation capture: controls, controls, controls.

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

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

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

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p.

Quantitative analysis of chromosome conformation capture assays (3C-qPCR).

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

Mapping chromatin interactions by chromosome conformation capture.

Chromosome conformation capture carbon copy technology.

A mechanism for Ikaros regulation of human globin gene switching.

Gene regulation in the third dimension.

Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction.

Long-range chromosomal interactions and gene regulation.

Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C).

Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery.

Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions.

Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization.

Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening.

Determining spatial chromatin organization of large genomic regions using 5C technology.

My5C: web tools for chromosome conformation capture studies.

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

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.

Integrating one-dimensional and three-dimensional maps of genomes.

Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease.

Mediator and cohesin connect gene expression and chromatin architecture.

Genomics tools for unraveling chromosome architecture.

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.

Sister cohesion and structural axis components mediate homolog bias of meiotic recombination.

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.

Chromatin globules: a common motif of higher order chromosome structure?

Translocation mapping exposes the risky lifestyle of B cells.

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.

Yeast one-hybrid assays for gene-centered human gene regulatory network mapping.

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping.

THE STRUCTURE AND FUNCTION OF CHROMATIN AND CHROMOSOMES.

Evidence for transcript networks composed of chimeric RNAs in human cells.

Spatial organization of the mouse genome and its role in recurrent chromosomal translocations.

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

The context of gene expression regulation.

MORC family ATPases required for heterochromatin condensation and gene silencing.

CTCF and cohesin help neurons raise their self-awareness.

Hi-C: a comprehensive technique to capture the conformation of genomes.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Analysis of long-range chromatin interactions using Chromosome Conformation Capture.

HiTC: exploration of high-throughput 'C' experiments.

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

The accessible chromatin landscape of the human genome.

The long-range interaction landscape of gene promoters.

From cells to chromatin: capturing snapshots of genome organization with 5C technology.

Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.

3C-based technologies to study the shape of the genome.

The hierarchy of the 3D genome.

Nuclear biology: what's been most surprising?

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

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

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

Organization of the mitotic chromosome.

Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny.

High-throughput genome scaffolding from in vivo DNA interaction frequency.

Defining functional DNA elements in the human genome.

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

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

Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture.

The Hitchhiker's guide to Hi-C analysis: practical guidelines.

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.

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

Chromosome Conformation Capture (3C) in Budding Yeast.

Randomized ligation control for chromosome conformation capture.

Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast.

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.

Hi-C in Budding Yeast.

Measuring Chromatin Structure in Budding Yeast.

The yeast genome undergoes significant topological reorganization in quiescence.

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis.

Structural and functional diversity of Topologically Associating Domains.

Genome-wide maps of nuclear lamina interactions in single human cells.

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.

Long-Range Chromatin Interactions.

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

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.

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

Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire.

Activation of proto-oncogenes by disruption of chromosome neighborhoods.

The 3D Genome as Moderator of Chromosomal Communication.

TAD disruption as oncogenic driver.

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.

Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma.

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells.

Structural organization of the inactive X chromosome in the mouse.

RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.

Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.

Mapping the 3D genome: Aiming for consilience.

CTCF-mediated topological boundaries during development foster appropriate gene regulation.

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.

Epigenetic characteristics of the mitotic chromosome in 1D and 3D.

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.

Shelterin components mediate genome reorganization in response to replication stress.

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

SMC complexes differentially compact mitotic chromosomes according to genomic context.

The 4D nucleome project.

The cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes.

A pathway for mitotic chromosome formation.

C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.

CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia.

Integrative detection and analysis of structural variation in cancer genomes.

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.

Higher-Order Organization Principles of Pre-translational mRNPs.

The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome.

CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning.

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.

Measuring the reproducibility and quality of Hi-C data.

Heterochromatin drives compartmentalization of inverted and conventional nuclei.

Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment.

Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei.

Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.

Highly structured homolog pairing reflects functional organization of the Drosophila genome.

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.

SPEN integrates transcriptional and epigenetic control of X-inactivation.

Ultrastructural Details of Mammalian Chromosome Architecture.

Mechanisms and Functions of Chromosome Compartmentalization.

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Large domains of heterochromatin direct the formation of short mitotic chromosome loops.

Multi-contact 3C reveals that the human genome during interphase is largely not entangled.

Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain.

Detecting chromatin interactions between and along sister chromatids with SisterC.

Is Involved in Corneal Stroma Development by Regulating Neural Crest Migration.

Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML.

Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.

Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.

Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation.

Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture.

Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization.

Systematic evaluation of chromosome conformation capture assays.

Symbiodinium microadriaticum (coral microalgal endosymbiont).

Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions.

Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture.

Spatial organization of transcribed eukaryotic genes.

Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling.

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis.

CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity.

Regulation of the mitotic chromosome folding machines.

A cohesin traffic pattern genetically linked to gene regulation.

Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.

Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.