Job Dekker

Program in Gene Function and Expression, University of Massachusetts Medical School

Affiliated withUniversity of Massachusetts Medical School Howard Hughes Medical Institute

Research Area

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title Cited by 504	2010
Publication title Cited by 1	2023

Other Publications

Article	Year
Capturing chromosome conformation. Science (New York, N.Y.)\| PubMed ID: 11847345	2002
A closer look at long-range chromosomal interactions. Trends in biochemical sciences\| PubMed ID: 12826398	2003
A mechanical basis for chromosome function. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15299144	2004
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Molecular cell\| PubMed ID: 15694345	2005
The three 'C' s of chromosome conformation capture: controls, controls, controls. Nature methods\| PubMed ID: 16369547	2006
The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16891414	2006
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome research\| PubMed ID: 16954542	2006
Mapping networks of physical interactions between genomic elements using 5C technology. Nature protocols\| PubMed ID: 17446898	2007
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature\| PubMed ID: 17571346	2007
GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p. Genome biology\| PubMed ID: 17577398	2007
Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nature protocols\| PubMed ID: 17641637	2007
Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nature cell biology\| PubMed ID: 17828248	2007
Mapping chromatin interactions by chromosome conformation capture. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]\| PubMed ID: 18265379	2006
Chromosome conformation capture carbon copy technology. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]\| PubMed ID: 18265398	2007
A mechanism for Ikaros regulation of human globin gene switching. British journal of haematology\| PubMed ID: 18318763	2008
Gene regulation in the third dimension. Science (New York, N.Y.)\| PubMed ID: 18369139	2008
Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. The Journal of biological chemistry\| PubMed ID: 18930918	2008
Long-range chromosomal interactions and gene regulation. Molecular bioSystems\| PubMed ID: 18931780	2008
Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C). Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 18951182	2009
Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes & development\| PubMed ID: 19390086	2009
Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS genetics\| PubMed ID: 19424429	2009
Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization. EMBO reports\| PubMed ID: 19525922	2009
Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS genetics\| PubMed ID: 19543368	2009
Determining spatial chromatin organization of large genomic regions using 5C technology. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 19588094	2009
My5C: web tools for chromosome conformation capture studies. Nature methods\| PubMed ID: 19789528	2009
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, N.Y.)\| PubMed ID: 19815776	2009
Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic acids research\| PubMed ID: 20360044	2010
Integrating one-dimensional and three-dimensional maps of genomes. Journal of cell science\| PubMed ID: 20519580	2010
Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20616024	2010
Mediator and cohesin connect gene expression and chromatin architecture. Nature\| PubMed ID: 20720539	2010
Genomics tools for unraveling chromosome architecture. Nature biotechnology\| PubMed ID: 20944601	2010
The three-dimensional folding of the Î±-globin gene domain reveals formation of chromatin globules. Nature structural & molecular biology\| PubMed ID: 21131981	2011
Sister cohesion and structural axis components mediate homolog bias of meiotic recombination. Cell\| PubMed ID: 21145459	2010
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature\| PubMed ID: 21423168	2011
Chromatin globules: a common motif of higher order chromosome structure? Current opinion in cell biology\| PubMed ID: 21489772	2011
Translocation mapping exposes the risky lifestyle of B cells. Cell\| PubMed ID: 21962501	2011
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Molecular cell\| PubMed ID: 22017872	2011
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nature methods\| PubMed ID: 22037702	2011
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nature methods\| PubMed ID: 22037705	2011
THE STRUCTURE AND FUNCTION OF CHROMATIN AND CHROMOSOMES. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing\| PubMed ID: 22174298	2012
Evidence for transcript networks composed of chimeric RNAs in human cells. PloS one\| PubMed ID: 22238572	2012
Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell\| PubMed ID: 22341456	2012
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature\| PubMed ID: 22495304	2012
The context of gene expression regulation. F1000 biology reports\| PubMed ID: 22500194	2012
MORC family ATPases required for heterochromatin condensation and gene silencing. Science (New York, N.Y.)\| PubMed ID: 22555433	2012
CTCF and cohesin help neurons raise their self-awareness. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22615386	2012
Hi-C: a comprehensive technique to capture the conformation of genomes. Methods (San Diego, Calif.)\| PubMed ID: 22652625	2012
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome biology\| PubMed ID: 22889292	2012
Analysis of long-range chromatin interactions using Chromosome Conformation Capture. Methods (San Diego, Calif.)\| PubMed ID: 22903059	2012
HiTC: exploration of high-throughput 'C' experiments. Bioinformatics (Oxford, England)\| PubMed ID: 22923296	2012
Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature methods\| PubMed ID: 22941365	2012
The accessible chromatin landscape of the human genome. Nature\| PubMed ID: 22955617	2012
The long-range interaction landscape of gene promoters. Nature\| PubMed ID: 22955621	2012
From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods (San Diego, Calif.)\| PubMed ID: 23137922	2012
Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome. Genome research\| PubMed ID: 23152449	2013
3C-based technologies to study the shape of the genome. Methods (San Diego, Calif.)\| PubMed ID: 23199640	2012
The hierarchy of the 3D genome. Molecular cell\| PubMed ID: 23473598	2013
Nuclear biology: what's been most surprising? Cell\| PubMed ID: 23616995	2013
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nature reviews. Genetics\| PubMed ID: 23657480	2013
Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell\| PubMed ID: 23706625	2013
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome research\| PubMed ID: 24002784	2013
Organization of the mitotic chromosome. Science (New York, N.Y.)\| PubMed ID: 24200812	2013
Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny. Genes & development\| PubMed ID: 24240234	2013
High-throughput genome scaffolding from in vivo DNA interaction frequency. Nature biotechnology\| PubMed ID: 24270850	2013
Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 24753594	2014
Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell\| PubMed ID: 24813616	2014
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25275169	2014
Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature\| PubMed ID: 25307058	2014
Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture. Epigenetics & chromatin\| PubMed ID: 25435919	2014
The Hitchhiker's guide to Hi-C analysis: practical guidelines. Methods (San Diego, Calif.)\| PubMed ID: 25448293	2015
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin. Genome research\| PubMed ID: 25677180	2015
Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature\| PubMed ID: 26030525	2015
Chromosome Conformation Capture (3C) in Budding Yeast. Cold Spring Harbor protocols\| PubMed ID: 26034304	2015
Randomized ligation control for chromosome conformation capture. Cold Spring Harbor protocols\| PubMed ID: 26034305	2015
Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. Cold Spring Harbor protocols\| PubMed ID: 26034306	2015
Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell\| PubMed ID: 26119342	2015
Hi-C in Budding Yeast. Cold Spring Harbor protocols\| PubMed ID: 26134906	2015
Measuring Chromatin Structure in Budding Yeast. Cold Spring Harbor protocols\| PubMed ID: 26134912	2015
The yeast genome undergoes significant topological reorganization in quiescence. Nucleic acids research\| PubMed ID: 26202961	2015
Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis. Genes & development\| PubMed ID: 26253537	2015
Structural and functional diversity of Topologically Associating Domains. FEBS letters\| PubMed ID: 26348399	2015
Genome-wide maps of nuclear lamina interactions in single human cells. Cell\| PubMed ID: 26365489	2015
Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome biology\| PubMed ID: 26415882	2015
Long-Range Chromatin Interactions. Cold Spring Harbor perspectives in biology\| PubMed ID: 26430217	2015
High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. Molecular cell\| PubMed ID: 26431028	2015
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome biology\| PubMed ID: 26619908	2015
The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer. Cell reports\| PubMed ID: 26655901	2015
Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus. American journal of human genetics\| PubMed ID: 26748519	2016
Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire. Cell reports\| PubMed ID: 26804913	2016
Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science (New York, N.Y.)\| PubMed ID: 26940867	2016
The 3D Genome as Moderator of Chromosomal Communication. Cell\| PubMed ID: 26967279	2016
TAD disruption as oncogenic driver. Current opinion in genetics & development\| PubMed ID: 27111891	2016
Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Cell stem cell\| PubMed ID: 27152443	2016
Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. American journal of respiratory and critical care medicine\| PubMed ID: 27367781	2016
SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells. Genome research\| PubMed ID: 27435934	2016
Structural organization of the inactive X chromosome in the mouse. Nature\| PubMed ID: 27437574	2016
RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells. Biochimica et biophysica acta\| PubMed ID: 27514584	2016
Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 27791029	2016
Mapping the 3D genome: Aiming for consilience. Nature reviews. Molecular cell biology\| PubMed ID: 27869158	2016
CTCF-mediated topological boundaries during development foster appropriate gene regulation. Genes & development\| PubMed ID: 28087711	2016
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Molecular cell\| PubMed ID: 28157505	2017
Epigenetic characteristics of the mitotic chromosome in 1D and 3D. Critical reviews in biochemistry and molecular biology\| PubMed ID: 28228067	2017
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods (San Diego, Calif.)\| PubMed ID: 28435001	2017
Shelterin components mediate genome reorganization in response to replication stress. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 28490498	2017
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell\| PubMed ID: 28525758	2017
SMC complexes differentially compact mitotic chromosomes according to genomic context. Nature cell biology\| PubMed ID: 28825700	2017
The 4D nucleome project. Nature\| PubMed ID: 28905911	2017
The cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes & development\| PubMed ID: 29273679	2017
A pathway for mitotic chromosome formation. Science (New York, N.Y.)\| PubMed ID: 29348367	2018
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Nature methods\| PubMed ID: 29735996	2018
CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell\| PubMed ID: 29958106	2018
Integrative detection and analysis of structural variation in cancer genomes. Nature genetics\| PubMed ID: 30202056	2018
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nature genetics\| PubMed ID: 30374068	2018
Higher-Order Organization Principles of Pre-translational mRNPs. Molecular cell\| PubMed ID: 30415953	2018
The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome. Nature communications\| PubMed ID: 30604745	2019
CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning. Genome research\| PubMed ID: 30655336	2019
Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Cell\| PubMed ID: 30799036	2019
Measuring the reproducibility and quality of Hi-C data. Genome biology\| PubMed ID: 30890172	2019
Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature\| PubMed ID: 31168090	2019
Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment. Stem cell reports\| PubMed ID: 31231024	2019
Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature\| PubMed ID: 31375785	2019
Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. Cell stem cell\| PubMed ID: 31495782	2019
The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nature communications\| PubMed ID: 31582744	2019
Highly structured homolog pairing reflects functional organization of the Drosophila genome. Nature communications\| PubMed ID: 31582763	2019
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. Nature cell biology\| PubMed ID: 31685986	2019
Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts. Molecular cell\| PubMed ID: 31704182	2020
SPEN integrates transcriptional and epigenetic control of X-inactivation. Nature\| PubMed ID: 32025035	2020
Ultrastructural Details of Mammalian Chromosome Architecture. Molecular cell\| PubMed ID: 32213324	2020
Mechanisms and Functions of Chromosome Compartmentalization. Trends in biochemical sciences\| PubMed ID: 32311333	2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature\| PubMed ID: 32728249	2020
Large domains of heterochromatin direct the formation of short mitotic chromosome loops. eLife\| PubMed ID: 32915140	2020
Multi-contact 3C reveals that the human genome during interphase is largely not entangled. Nature structural & molecular biology\| PubMed ID: 32929283	2020
Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. The EMBO journal\| PubMed ID: 32935369	2020
Detecting chromatin interactions between and along sister chromatids with SisterC. Nature methods\| PubMed ID: 32968250	2020
Is Involved in Corneal Stroma Development by Regulating Neural Crest Migration. International journal of molecular sciences\| PubMed ID: 33096935	2020
Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. JCI insight\| PubMed ID: 33351783	2021
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nature genetics\| PubMed ID: 33574602	2021
Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum. Nature genetics\| PubMed ID: 33927399	2021
Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. Genome biology and evolution\| PubMed ID: 33964136	2021
Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. Current protocols\| PubMed ID: 34286910	2021
Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization. eLife\| PubMed ID: 34406118	2021
Systematic evaluation of chromosome conformation capture assays. Nature methods\| PubMed ID: 34480151	2021
Symbiodinium microadriaticum (coral microalgal endosymbiont). Trends in genetics : TIG\| PubMed ID: 34518054	2021
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harbor perspectives in biology\| PubMed ID: 34518339	2022
Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nature communications\| PubMed ID: 34716321	2021
Spatial organization of transcribed eukaryotic genes. Nature cell biology\| PubMed ID: 35177821	2022
Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling. Scientific reports\| PubMed ID: 35304523	2022
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature\| PubMed ID: 35474001	2022
Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis. BMC biology\| PubMed ID: 35549698	2022
CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity. Nature cell biology\| PubMed ID: 36202971	2022
Regulation of the mitotic chromosome folding machines. The Biochemical journal\| PubMed ID: 36268993	2022
A cohesin traffic pattern genetically linked to gene regulation. Nature structural & molecular biology\| PubMed ID: 36482254	2022
Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nature structural & molecular biology\| PubMed ID: 36550219	2023
Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nature structural & molecular biology\| PubMed ID: 36564591	2023