Research Topics
| Job DekkerSummaryAffiliation: University of Massachusetts Medical School Country: USA Publications
Research Grants
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Detail Information
Publications
Gene regulation in the third dimensionJob 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...- Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compactionJob 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... 
A closer look at long-range chromosomal interactionsJob 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....- GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3pJob 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... - The three 'C' s of chromosome conformation capture: controls, controls, controlsJob 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... - Long-range chromosomal interactions and gene regulationAdriana 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... - Mapping chromatin interactions by chromosome conformation captureAdriana 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... - Mechanisms that regulate localization of a DNA double-strand break to the nuclear peripheryPranav 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... - Chromosome conformation capture carbon copy technologyJosee 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... - Mapping networks of physical interactions between genomic elements using 5C technologyJosee 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... - The long-range interaction landscape of gene promotersAmartya 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... 
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...- Integrating one-dimensional and three-dimensional maps of genomesNatalia Naumova
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 0103, USA
J Cell Sci 123:1979-88. 2010.... - Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactionsAdriana Miele
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA
PLoS Genet 5:e1000478. 2009.... - Yeast one-hybrid assays for gene-centered human gene regulatory network mappingJohn 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... - Determining spatial chromatin organization of large genomic regions using 5C technologyNynke 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... - 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... - Hi-C: a comprehensive technique to capture the conformation of genomesJon 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... - Analysis of long-range chromatin interactions using Chromosome Conformation CaptureNatalia 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... - Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elementsJosee 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... - Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR geneNele 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... - Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndromeRachel 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... - Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mappingJohn 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... - The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modificationsNele 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... - HiTC: exploration of high-throughput 'C' experimentsNicolas 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... - 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... - Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1Christopher 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... - A mechanical basis for chromosome functionNancy 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... - Capturing chromosome conformationJob 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... - Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complexChiara 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.... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - A mechanism for Ikaros regulation of human globin gene switchingJanelle 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...
Research Grants
- Structural Annotation of the Human GenomeJob 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. ..
- Structural Annotation of the Human GenomeJob 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. ..
- Structural Annotation of the Human GenomeJob 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. ..