Job Dekker

Summary

Affiliation: University of Massachusetts Medical School
Country: USA

Publications

  1. pmc Gene regulation in the third dimension
    Job Dekker
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 0103, USA
    Science 319:1793-4. 2008
  2. pmc Iterative correction of Hi-C data reveals hallmarks of chromosome organization
    Maxim Imakaev
    Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 9:999-1003. 2012
  3. pmc The context of gene expression regulation
    Johan H Gibcus
    Program in Systems Biology Program in Gene Function and Expression University of Massachusetts Medical School, Worcester, MA, USA
    F1000 Biol Rep 4:8. 2012
  4. pmc Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
    Job Dekker
    Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 2324, USA
    Nat Rev Genet 14:390-403. 2013
  5. ncbi request reprint The three 'C' s of chromosome conformation capture: controls, controls, controls
    Job Dekker
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 519, 364 Plantation Street, Worcester, Massachusetts 01605, USA
    Nat Methods 3:17-21. 2006
  6. ncbi request reprint A closer look at long-range chromosomal interactions
    Job Dekker
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Worcester 01605, USA
    Trends Biochem Sci 28:277-80. 2003
  7. pmc Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction
    Job Dekker
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 0103, USA
    J Biol Chem 283:34532-40. 2008
  8. pmc GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p
    Job Dekker
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Plantation Street, Worcester, MA 01605 4321, USA
    Genome Biol 8:R116. 2007
  9. pmc Long-range chromosomal interactions and gene regulation
    Adriana Miele
    Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 0103, USA
    Mol Biosyst 4:1046-57. 2008
  10. pmc Analysis of long-range chromatin interactions using Chromosome Conformation Capture
    Natalia Naumova
    Programs in Systems Biology and Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 0103, USA
    Methods 58:192-203. 2012

Research Grants

  1. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2003
  2. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2004
  3. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2005
  4. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2007
  5. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2009
  6. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2009
  7. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2010

Detail Information

Publications44

  1. pmc Gene regulation in the third dimension
    Job Dekker
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 0103, USA
    Science 319:1793-4. 2008
    ..Major challenges now include deciphering the mechanisms by which loci come together and understanding the functional consequences of these often transient associations...
  2. pmc Iterative correction of Hi-C data reveals hallmarks of chromosome organization
    Maxim Imakaev
    Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 9:999-1003. 2012
    ....
  3. pmc The context of gene expression regulation
    Johan H Gibcus
    Program in Systems Biology Program in Gene Function and Expression University of Massachusetts Medical School, Worcester, MA, USA
    F1000 Biol Rep 4:8. 2012
    ..In this perspective, we propose a structural and functional hierarchy, in which the DNA code, proteins and non-coding RNAs act as context creators to fold chromosomes and regulate genes...
  4. pmc Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
    Job Dekker
    Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 2324, USA
    Nat Rev Genet 14:390-403. 2013
    ..Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data...
  5. ncbi request reprint The three 'C' s of chromosome conformation capture: controls, controls, controls
    Job Dekker
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 519, 364 Plantation Street, Worcester, Massachusetts 01605, USA
    Nat Methods 3:17-21. 2006
    ..The general guidelines presented here should help experimental design and minimize misinterpretation of 3C experiments...
  6. ncbi request reprint A closer look at long-range chromosomal interactions
    Job Dekker
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Worcester 01605, USA
    Trends Biochem Sci 28:277-80. 2003
    ....
  7. pmc Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction
    Job Dekker
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 0103, USA
    J Biol Chem 283:34532-40. 2008
    ..Our approach should be widely applicable to scale 3C data to real spatial dimensions, which will facilitate the quantification of the effects of chromatin modifications and transcription on chromatin fiber organization...
  8. pmc GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p
    Job Dekker
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Plantation Street, Worcester, MA 01605 4321, USA
    Genome Biol 8:R116. 2007
    ..Isochore domains differ in gene expression levels, replication timing, levels of meiotic recombination and chromatin structure. The molecular basis for these differences is poorly understood...
  9. pmc Long-range chromosomal interactions and gene regulation
    Adriana Miele
    Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 0103, USA
    Mol Biosyst 4:1046-57. 2008
    ..Finally, we propose that a genome-wide network analysis may provide new insights into the logic of long-range gene regulation...
  10. pmc Analysis of long-range chromatin interactions using Chromosome Conformation Capture
    Natalia Naumova
    Programs in Systems Biology and Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 0103, USA
    Methods 58:192-203. 2012
    ..This paper represents a complete resource and detailed guide for anyone who desires to perform 3C...
  11. pmc Hi-C: a comprehensive technique to capture the conformation of genomes
    Jon Matthew Belton
    Programs in Systems Biology and Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Methods 58:268-76. 2012
    ..This spatial context will provide a new perspective to studies of chromatin and its role in genome regulation in normal conditions and in disease...
  12. pmc Organization of the mitotic chromosome
    Natalia Naumova
    Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School UMMS, 368 Plantation Street, Worcester, MA 01605 0103, USA
    Science 342:948-53. 2013
    ..Using polymer simulations, we found that metaphase Hi-C data are inconsistent with classic hierarchical models and are instead best described by a linearly organized longitudinally compressed array of consecutive chromatin loops. ..
  13. pmc Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome
    Rachel Patton McCord
    Program in Systems Biology, Department of Biochemistry and Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 23:260-9. 2013
    ..These changes may result in transcriptional misregulation and eventually trigger the global loss of spatial chromatin compartmentalization in late passage HGPS fibroblasts...
  14. doi request reprint Mapping chromatin interactions by chromosome conformation capture
    Adriana Miele
    University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Curr Protoc Mol Biol . 2006
    ..This unit describes detailed protocols for performing 3C with yeast Saccharomyces cerevisiae and mammalian cells...
  15. pmc The long-range interaction landscape of gene promoters
    Amartya Sanyal
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 0103, USA
    Nature 489:109-13. 2012
    ..Our results start to place genes and regulatory elements in three-dimensional context, revealing their functional relationships...
  16. pmc Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery
    Pranav Oza
    Program in Molecular Medicine, Interdisciplinary Graduate Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 23:912-27. 2009
    ..Based on these findings, we propose that sequestration of unrepaired or slowly repaired DSBs to the nuclear periphery reflects a competition between alternative repair pathways...
  17. pmc Integrating one-dimensional and three-dimensional maps of genomes
    Natalia Naumova
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 0103, USA
    J Cell Sci 123:1979-88. 2010
    ....
  18. pmc Mediator and cohesin connect gene expression and chromatin architecture
    Michael H Kagey
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 467:430-5. 2010
    ..Mediator and cohesin co-occupy different promoters in different cells, thus generating cell-type-specific DNA loops linked to the gene expression program of each cell...
  19. ncbi request reprint Capturing chromosome conformation
    Job Dekker
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Science 295:1306-11. 2002
    ..Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring...
  20. pmc A mechanical basis for chromosome function
    Nancy Kleckner
    Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 101:12592-7. 2004
    ..We propose that chromosome function is governed by internal mechanical forces generated by programmed tendencies for expansion of the DNA/chromatin fiber against constraining features...
  21. pmc The hierarchy of the 3D genome
    Johan H Gibcus
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 0103, USA
    Mol Cell 49:773-82. 2013
    ..Here, we review the experimental and theoretical data on this hierarchy of structures and propose a key role for the recently discovered topologically associating domains...
  22. ncbi request reprint Chromosome conformation capture carbon copy technology
    Josee Dostie
    University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Curr Protoc Mol Biol . 2007
    ..g., by identifying relationships between regulatory elements and their target genes. This unit describes 5C for large-scale analysis of cis- and trans-chromatin interactions in mammalian cells...
  23. pmc Yeast one-hybrid assays for gene-centered human gene regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1050-2. 2011
    ..We present Y1H resources, including clones for 988 of 1,434 (69%) predicted human transcription factors, that can be used to detect both known and new interactions between human DNA regions and transcription factors...
  24. pmc Chromatin globules: a common motif of higher order chromosome structure?
    Amartya Sanyal
    Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 01605 2324 Worcester, MA, USA
    Curr Opin Cell Biol 23:325-31. 2011
    ..This process would yield a compartmentalized chromosome conformation, consistent with recent observations obtained with genome-wide chromatin interaction mapping...
  25. ncbi request reprint Mapping networks of physical interactions between genomic elements using 5C technology
    Josee Dostie
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Room 519, Worcester, Massachusetts 01605 4321, USA
    Nat Protoc 2:988-1002. 2007
    ..The resulting 5C library of ligated primers is analyzed using either microarray detection or ultra-high-throughput DNA sequencing. The 5C protocol described here can be completed in 13 d...
  26. pmc Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C)
    Adriana Miele
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
    Methods Mol Biol 464:105-21. 2009
    ..This chapter describes detailed protocols for 3C analysis of chromatin interactions in the yeast Saccharomyces cerevisiae and in mammalian cells...
  27. pmc Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions
    Adriana Miele
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA
    PLoS Genet 5:e1000478. 2009
    ....
  28. pmc Sister cohesion and structural axis components mediate homolog bias of meiotic recombination
    Keun P Kim
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 143:924-37. 2010
    ..These domains could comprise complementary environments that integrate inputs from DSB repair and mitotic chromosome morphogenesis into the complete meiotic program...
  29. pmc Determining spatial chromatin organization of large genomic regions using 5C technology
    Nynke L van Berkum
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
    Methods Mol Biol 567:189-213. 2009
    ..The power of the 5C technique described in this chapter is the high-throughput, high-resolution, and quantitative way in which the spatial organization of chromatin can be examined...
  30. pmc The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications
    Nele Gheldof
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
    Proc Natl Acad Sci U S A 103:12463-8. 2006
    ..The described approaches are widely applicable to the study of conformational changes of any locus of interest...
  31. pmc Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements
    Josee Dostie
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 0103, USA
    Genome Res 16:1299-309. 2006
    ..5C should be widely applicable for large-scale mapping of cis- and trans- interaction networks of genomic elements and for the study of higher-order chromosome structure...
  32. pmc Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene
    Nele Gheldof
    Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 0103, USA
    Nucleic Acids Res 38:4325-36. 2010
    ..Our results reveal novel long-range acting elements that control expression of CFTR and suggest that 3C-based approaches can be used for discovery of novel regulatory elements...
  33. pmc Defining functional DNA elements in the human genome
    Manolis Kellis
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
    Proc Natl Acad Sci U S A 111:6131-8. 2014
    ..Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease. ..
  34. pmc Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1059-64. 2011
    ..eY1H assays will be an important tool for mapping gene regulatory networks in Caenorhabditis elegans and other model organisms as well as in humans...
  35. ncbi request reprint Translocation mapping exposes the risky lifestyle of B cells
    Rachel Patton McCord
    Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 0103, USA
    Cell 147:20-2. 2011
    ..2011) and Klein et al. (2011) characterize the genome-wide spectrum of translocations that form from a single double-stranded break, revealing that specific loci have an intrinsic predisposition for frequent chromosomal rearrangements...
  36. pmc High-throughput genome scaffolding from in vivo DNA interaction frequency
    Noam Kaplan
    Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Biotechnol 31:1143-7. 2013
    ..Our approach can theoretically bridge any gap size and should be applicable to any species for which global chromatin interaction data can be generated. ..
  37. pmc Architectural protein subclasses shape 3D organization of genomes during lineage commitment
    Jennifer E Phillips-Cremins
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Cell 153:1281-95. 2013
    ..We conclude that cell-type-specific chromatin organization occurs at the submegabase scale and that architectural proteins shape the genome in hierarchical length scales...
  38. pmc HiTC: exploration of high-throughput 'C' experiments
    Nicolas Servant
    Institut Curie, F 75248 Paris, France
    Bioinformatics 28:2843-4. 2012
    ..Availability and implementation: The R package HiTC is available from the Bioconductor website. A detailed vignette provides additional documentation and help for using the package...
  39. ncbi request reprint Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1
    Christopher R Vakoc
    Division of Hematology, The Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
    Mol Cell 17:453-62. 2005
    ..Together, these data demonstrate that GATA-1 and FOG-1 are essential anchors for a tissue-specific chromatin loop, providing general insights into long-range enhancer function...
  40. ncbi request reprint Quantitative analysis of chromosome conformation capture assays (3C-qPCR)
    Hélène Hagège
    UMR5535 CNRS UMII, IFR122, Institut de Genetique Moleculaire de Montpellier, IGMM, 1919, route de Mende, 34293 Montpellier Cedex 5, France
    Nat Protoc 2:1722-33. 2007
    ..Here, we provide a detailed protocol for this method, which we have named 3C-qPCR. Once preliminary controls and optimizations have been performed, the whole procedure (3C assays and quantitative analyses) can be completed in 7-9 days...
  41. doi request reprint A mechanism for Ikaros regulation of human globin gene switching
    Janelle R Keys
    Institute for Molecular Bioscience, Queensland Bioscience Precinct, University of Queensland, Queensland, Australia
    Br J Haematol 141:398-406. 2008
    ..This study provides new insights into the mechanism of stage-specific assembly of the beta-globin ACH, and HPFH...
  42. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  43. ncbi request reprint Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex
    Chiara Lanzuolo
    Dulbecco Telethon Institute at IGB CNR, Epigenetics and Genome Reprogramming, Via Pietro Castellino 111, 80131 Naples, Italy
    Nat Cell Biol 9:1167-74. 2007
    ....

Research Grants8

  1. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2003
    ..Analysis of the data obtained and integration of these data with results derived from other ENCODE projects is expected to provide information regarding the suitability of this chromosome structural approach to find functional elements. ..
  2. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2004
    ..Analysis of the data obtained and integration of these data with results derived from other ENCODE projects is expected to provide information regarding the suitability of this chromosome structural approach to find functional elements. ..
  3. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2005
    ..Analysis of the data obtained and integration of these data with results derived from other ENCODE projects is expected to provide information regarding the suitability of this chromosome structural approach to find functional elements. ..
  4. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2007
    ..These studies will map the network of connections between genes and regulatory elements and will reveal new insights into the mechanisms that underlie long-range gene regulation. ..
  5. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2009
    ..These studies will map the network of connections between genes and regulatory elements and will reveal new insights into the mechanisms that underlie long-range gene regulation. ..
  6. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2009
    ..These studies will map the network of connections between genes and regulatory elements and will reveal new insights into the mechanisms that underlie long-range gene regulation. ..
  7. Structural Annotation of the Human Genome
    Job Dekker; Fiscal Year: 2010
    ..These studies will map the network of connections between genes and regulatory elements and will reveal new insights into the mechanisms that underlie long-range gene regulation. ..