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    Job Dekker PhD

    TitleProfessor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentBiochemistry and Molecular Pharmacology
    AddressUniversity of Massachusetts Medical School
    364 Plantation Street, LRB-509
    Worcester MA 01605
    Phone508-856-4371
      Other Positions
      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBiochemistry and Molecular Pharmacology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBioinformatics and Computational Biology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentInterdisciplinary Graduate Program

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentBioinformatics and Integrative Biology

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentProgram in Gene Function and Expression

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentSystems Biology

        Biography 
        awards and honors
        2007W.M. Keck Foundation Distinguished Young Scholar in Medical Research Award
        2011American Society for Biochemistry and Molecular Biology Young Investigator Award
        2014Elected Fellow of the American Association for the Advancement of Science (AAAS)
        Overview 
        Narrative
        ?

        Academic Background

        Job Dekker received his B.S. (1993) and his Ph.D. (1997) from the University of Utrecht, The Netherlands. From 1998 to 2003, he was a post-doctoral fellow at Harvard University during which time he was awarded an NWO-TALENT stipendium, an EMBO long-term fellowship and a fellowship from The Medical Foundation / Charles A. King Trust. Dr. Dekker joined the University of Massachusetts Medical School as an Assistant Professor in the Program of Gene Function and Expression in the spring of 2003. In 2008 he was promoted to Associate Professor, and in 2011 to Professor. He is a recipient of a 2007 W. M. Keck Foundation Distinguished Young Scholar in Medical Research Award, and the 2011 ASBMB Young Investigator Award. In 2011 he became co-director (with Dr. Marian Walhout) of the newly established Program in Systems Biology.

        For more information about the Dekker lab, to access tools and view and download published datasets please visit our website: http://my5c.umassmed.edu/welcome/welcome.php.

        Job Dekker is a member of the Center for Cancer Systems Biology (CCSB) at the Dana-Farber Cancer Institute. For more information about CCSB see: http://ccsb.dfci.harvard.edu.

        ? ? ? ? ? Link to Dekker Lab website?

         

        Spatial Organization of Genomes

        Photo: Job Dekker, PhDWe study how a genome is organized in three dimensions inside the nucleus.  The spatial organization of a genome plays important roles in regulation of genes and maintenance of genome stability.  Many diseases, including cancer, are characterized by alterations in the spatial organization of the genome.  How genomes are organized in three dimensions, and how this affects gene expression is poorly understood.  To address this issue we study the genomes of human and yeast, using a set of powerful molecular and genomic tools that we developed.

        From linear sequence to three-dimensional organization

        Although the DNA of chromosomes is a linear sequence, the living genome does not function in a linear fashion.  This is most clearly illustrated by the fact that genes are often regulated by elements that can be located far away along the genome sequence. Recent evidence shows that regulatory elements can act over large genomic distances by engaging in direct physical interactions with target genes, resulting in the formation of chromatin loops.  Based on these observations we have proposed that the spatial organization of the genome resembles a three-dimensional network that is driven by physical associations between genes and regulatory elements, both in cis (along the same chromosome) and in trans (between different chromosomes) (Dekker (2006), Nature Methods, 3(1): 17-21).

        How does the spatial organization of a genome relate to its regulation and function?

        In each cell type a distinct set of genes is expressed and therefore the spatial organization of the genome will likely be cell-type specific.  Insights into the mechanisms that modulate the spatial organization of the genome will greatly contribute to a better understanding of tissue-specific gene regulation and may reveal causes of human diseases that are due to defects in these processes.

        In order to understand the spatial organization of a genome we try to answer the following questions.  Which regulatory elements interact with each of the genes in the human genome?  What drives the specificity of these interactions?  Can we identify proteins that mediate these interactions?  How do interactions between regulatory elements and genes result in activation and repression of genes?  How do defects in these interactions result in human disease?  Can we use information about chromatin interactions to generate three-dimensional models of chromosomes?

        Tools we developed for mapping the spatial organization of genomes: 3C, 5C and Hi-C

        We developed Chromosome Conformation Capture (3C), which is used to detect physical interactions between genomic elements (Dekker et al. Science, 2002).  Using 3C we, and others, discovered that gene regulation is mediated by the three-dimensional organization of chromosomes that brings genes and their regulatory elements in close spatial proximity.  3C is now widely used and already has had a major impact on studies of genome regulation.

        Large-scale detection of long-range chromatin interactions will be instrumental in mapping genome-wide networks of communication between genomic elements and the determination of the three-dimensional folding of the genome.  My group was the first to combine 3C with ultra-high-throughput DNA sequencing, thereby dramatically increasing the scale at which interactions between genomic loci can be studied.  Specifically, we have developed 5C, a high-throughput version of 3C for large-scale mapping of chromatin interaction networks (Dostie et al. Genome Res. 2006).  To enable the community to adopt 5C and related technologies we have developed "my5C", a publicly available set of computational tools for design of 5C studies and for visualization and analysis of any large chromatin interaction data sets (my5C.umassmed.edu; Lajoie et al. Nature Methods 2009).

        Ultimately we aim to obtain detailed insights into the three-dimensional arrangements of complete genomes at Kb resolution.  To this end we developed the Hi-C technology: a genome-wide and unbiased method that combines 3C with deep sequencing (Lieberman-Aiden, van Berkum et al. Science 2009).  We have applied Hi-C to generate the first comprehensive and unbiased long-range interaction maps of the human genome.  Hi-C data reveal both known hallmarks of nuclear organization (e.g. formation of chromosome territories, and preferred co-location of particular pairs of chromosomes) as well as novel folding principles of chromosomes.  First, we found that the human genome is divided over two types of spatial compartments, one containing active chromatin, and one containing all inactive segments of the genome.  Second, we discovered a novel higher order chromatin folding motif: at the megabase scale, our data are consistent with a model in which chromatin is described by a polymer state known as the fractal globule: a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.   This conformation is an extremely efficient solution for packing long chromosomes inside the nucleus.  Hi-C data for GM06990 lymphoblastoid cells and for K562 erythroleukemia cells is available in a user friendly format at our website: http://hic.umassmed.edu.

        Topologically Associating Domains

        Using 5C technology, and in collaboration with the laboratory of Dr. Edith Heard, we discovered that mammalian chromosomes are composed of Topologically Associating Domains (TADS; Nora et al. Nature 2012). TADs are hundreds of Kb in size and are characterized by frequent interactions between loci located within the same TAD, but much lower interaction frequencies between loci located in different TADs. We found that TADs are determined by cis-acting boundary regions and spatially separate adjacent TADS. Furthermore, TADs represent functional units as genes located within TADs show related gene expression patterns. We propose that TADs are fundamental structural and functional building blocks of chromosomes.

        Gene regulation by long-range looping interactions

        The most direct way in which chromosome folding affects gene regulation is through the formation of long-range looping interactions between gene promoters and distal gene regulatory elements such as enhancers. As part of the ENCODE project, we recently completed a comprehensive analysis of looping interactions between genes and distal elements throughout 1% of the human genome (Sanyal, Lajoie et al. Nature 2012). We discovered >1,000 long-range interactions between promoters and distal sites that include elements resembling enhancers, promoters and CTCF-bound sites. We observed significant correlations between gene expression, promoter-enhancer interactions and the presence of enhancer RNAs. Long-range interactions display striking asymmetry with a bias for interactions with elements located ~120 Kb upstream of the TSS. Long-range interactions are often not blocked by sites bound by CTCF and cohesin implying that many of these sites do not demarcate physically insulated gene domains. Further, only ~7% of looping interactions are with the nearest gene, suggesting that genomic proximity is not a simple predictor for long-range interactions. Finally, promoters and distal elements are engaged in multiple long-range interactions to form complex networks. Our results start to place genes and regulatory elements in three-dimensional context, revealing their functional relationships.

        Building three-dimensional models of chromosomes

        As a first step towards studying the spatial organization of entire chromosomes we have used 3C to determine the three-dimensional structure of yeast chromosome III (Dekker et al. (2002), Science, 295: 1306-1311).  We generated a matrix of interaction frequencies and developed mathematical tools to determine a population-average three-dimensional model of this ~320 kb chromosome based on the pattern of chromatin interactions (Figure 3).  Chromosome III emerged as a contorted ring, due to prominent interactions between the sub-telomeric regions. 

        More recently, we worked with the laboratory of Dr. Marc A. Marti-Renom to use chromatin interaction data to build spatial models of chromosomal domains and even complete genomes. For instance, using 5C data for the human alpha-globin domain, we discovered that chromatin folds in globular domains of several hundreds of Kb (Baù, Sanyal, A. et al. Nat. Struct. Mol. Biol.) 2011 . These are probably equivalent to TADs (see above). In collaboration with Mark Umbarger and George Church we were able to generate a three-dimensional model of the complete genome of the bacterium Caulobacter crescentus, which led to the identification of cis-elements that determine the folding of the entire genome (Umbarger, Toro et al. Mol. Cell 2011.

        For more information on the work in my laboratory, please see our lab website at http://my5c.umassmed.edu/welcome/welcome.php

        Figures

        Chromosome Conformation Capture

        Figure 1.   (a) Genes (blue rectangles) and regulatory elements (red circles) are linearly organized along chromosomes (top), but as a result of specific interactions between elements (indicated by arrows, both in cis and in trans) a complex three-dimensional network is formed inside the cell (bottom).  (b) Schematic representation of the 3C assay.  Chromatin is cross-linked, digested with a restriction enzyme and then ligated.  Specific ligation products can be detected by PCR.  [Figure from Dekker (2006), Nature Methods, 3(1): 17-21].

         

         

        The human beta-globin locus

        Figure 2.   Schematic representation of the human beta-globin locus.  Activation of the g-globin genes in K562 cells involves interactions between the LCR and the activated genes resulting in a large (~40 kb) chromatin loop.  The LCR also interacts with an element located downstream of the locus (3’HS1).

         

         

        Spatial organization of yeast chromosome III

        Figure 3. Spatial organization of yeast chromosome III (~ 320 kb) as determined by Chromosome Conformation Capture (3C). 3C was applied to determine the frequency with which several loci along the chromosome interact.  Interaction frequencies were then used to model the average spatial organization of the chromosome.  Interactions between the telomeres result in the formation of a ring-like structure with a diameter of around 300 nm.

         

        Laboratory Personnel

        Sharon Briggs, Financial Assistant, Grant & Contract Specialist
        Houda Belaghzal, Graduate Student
        Jon-Matthew Belton, Graduate Student
        Johan Gibcus, Postdoctoral Fellow
        Gaurav Jain, Bioinformatician Level I
        Bryan Lajoie, Bioinformatician Level II
        Noam Kaplan, Postdoctoral Fellow
        Rachel McCord, Postdoctoral Fellow
        Natalia Naumova, Postdoctoral Fellow
        Amartya Sanyal, Postdoctoral Fellow
        Emily Smith, Graduate Student
        Ye Zhan, Research Associate



        Rotation Projects
        ?

        Rotation Projects

        Multiple rotation projects are available in several areas related to long-range gene regulation and higher order chromosome organization.  Projects include thorough analyses of the biochemical mechanisms of long-range gene regulation of specific disease-related genes, as well as large-scale analyses of chromosome organization using high-throughput genomics technologies (5C and Hi-C).  The lab employs a wide range of experimental approaches, including cell culture, protein biochemistry, microscopy, genomics as well computational approaches such as bioinformatics and modeling.  Specific rotation projects are determined dependent on the interest of the student.



        Bibliographic 
        selected publications
        List All   |   Timeline
        1. Kaplan N, Dekker J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol. 2013 Dec; 31(12):1143-7.
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        2. Kumar S, Wuerffel R, Achour I, Lajoie B, Sen R, Dekker J, Feeney AJ, Kenter AL. Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny. Genes Dev. 2013 Nov 15; 27(22):2439-44.
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        3. Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science. 2013 Nov 22; 342(6161):948-53.
          View in: PubMed
        4. Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one. Nature. 2013 Oct 3; 502(7469):45-46.
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        5. Nora EP, Dekker J, Heard E. Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods? Bioessays. 2013 Sep; 35(9):818-28.
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        6. Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG. Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment. Cell. 2013 Jun 6; 153(6):1281-95.
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        7. Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013 Jun; 14(6):390-403.
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        8. Dekker J, Wysocka J, Mattaj I, Lieberman Aiden E, Pikaard C. Nuclear biology: what's been most surprising? Cell. 2013 Mar 14; 152(6):1207-8.
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        9. Gibcus JH, Dekker J. The Hierarchy of the 3D Genome. Mol Cell. 2013 Mar 7; 49(5):773-82.
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        10. McCord RP, Nazario-Toole A, Zhang H, Chines PS, Zhan Y, Erdos MR, Collins FS, Dekker J, Cao K. Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome. Genome Res. 2013 Feb; 23(2):260-9.
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        11. Ferraiuolo MA, Sanyal A, Naumova N, Dekker J, Dostie J. From cells to chromatin: Capturing snapshots of genome organization with 5C technology. Methods. 2012 Nov; 58(3):255-67.
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        12. de Laat W, Dekker J. 3C-based technologies to study the shape of the genome. Methods. 2012 Nov; 58(3):189-91.
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        13. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6; 489(7414):57-74.
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        14. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6; 489(7414):75-82.
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        15. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012 Sep 6; 489(7414):109-13.
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        16. Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012 Oct; 9(10):999-1003.
          View in: PubMed
        17. Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen CJ, Heard E, Dekker J, Barillot E. HiTC: exploration of high-throughput 'C' experiments. Bioinformatics. 2012 Nov 1; 28(21):2843-4.
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        18. Naumova N, Smith EM, Zhan Y, Dekker J. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. Methods. 2012 Nov; 58(3):192-203.
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        19. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13; 13(8):418.
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        20. Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: A comprehensive technique to capture the conformation of genomes. Methods. 2012 Nov; 58(3):268-76.
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        21. Dekker J. CTCF and cohesin help neurons raise their self-awareness. Proc Natl Acad Sci U S A. 2012 Jun 5; 109(23):8799-800.
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        22. Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, Dekker J, Kim JK, Jacobsen SE. MORC family ATPases required for heterochromatin condensation and gene silencing. Science. 2012 Jun 15; 336(6087):1448-51.
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        23. Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J, Heard E. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012; 485(7398):381-5.
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        24. Felsenfeld G, Dekker J. Genome architecture and expression. Curr Opin Genet Dev. 2012 Apr; 22(2):59-61.
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        25. Gibcus JH, Dekker J. The context of gene expression regulation. F1000 Biol Rep. 2012; 4:8.
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        26. Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, Becker MS, Alt FW, Dekker J. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell. 2012 Mar 2; 148(5):908-21.
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        27. Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR. Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells. PLoS One. 2012; 7(1):e28213.
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        28. Noble WS, Blau CA, Dekker J, Duan ZJ, Mao Y. The structure and function of chromatin and chromosomes. Pac Symp Biocomput. 2012; 434-40.
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        29. Reece-Hoyes JS, Barutcu AR, McCord RP, Jeong JS, Jiang L, Macwilliams A, Yang X, Salehi-Ashtiani K, Hill DE, Blackshaw S, Zhu H, Dekker J, Walhout AJ. Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods. 2011; 8(12):1050-2.
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        30. Reece-Hoyes JS, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S, Pesyna C, Dekker J, Myers CL, Walhout AJ. Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat Methods. 2011; 8(12):1059-64.
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        31. Umbarger MA, Toro E, Wright MA, Porreca GJ, Baù D, Hong SH, Fero MJ, Zhu LJ, Marti-Renom MA, McAdams HH, Shapiro L, Dekker J, Church GM. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell. 2011 Oct 21; 44(2):252-64.
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        32. McCord RP, Dekker J. Translocation mapping exposes the risky lifestyle of B cells. Cell. 2011 Sep 30; 147(1):20-2.
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        33. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046.
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        34. Sanyal A, Baù D, Martí-Renom MA, Dekker J. Chromatin globules: a common motif of higher order chromosome structure? Curr Opin Cell Biol. 2011 Jun; 23(3):325-31.
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        35. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011 Apr 7; 472(7341):120-4.
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        36. Kim KP, Weiner BM, Zhang L, Jordan A, Dekker J, Kleckner N. Sister cohesion and structural axis components mediate homolog bias of meiotic recombination. Cell. 2010 Dec 10; 143(6):924-37.
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        37. Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol. 2011 Jan; 18(1):107-14.
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        38. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, Young RA. Mediator and cohesin connect gene expression and chromatin architecture. Nature. 2010 Sep 23; 467(7314):430-5.
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        39. Bradner JE, Mak R, Tanguturi SK, Mazitschek R, Haggarty SJ, Ross K, Chang CY, Bosco J, West N, Morse E, Lin K, Shen JP, Kwiatkowski NP, Gheldof N, Dekker J, DeAngelo DJ, Carr SA, Schreiber SL, Golub TR, Ebert BL. Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12617-22.
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        40. Naumova N, Dekker J. Integrating one-dimensional and three-dimensional maps of genomes. J Cell Sci. 2010 Jun 15; 123(Pt 12):1979-88.
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        41. van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES. Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp. 2010; (39).
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        42. Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res. 2010 Jul; 38(13):4325-36.
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        43. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 9; 326(5950):289-93.
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        44. Lajoie BR, van Berkum NL, Sanyal A, Dekker J. My5C: web tools for chromosome conformation capture studies. Nat Methods. 2009 Oct; 6(10):690-1.
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        45. D'haene B, Attanasio C, Beysen D, Dostie J, Lemire E, Bouchard P, Field M, Jones K, Lorenz B, Menten B, Buysse K, Pattyn F, Friedli M, Ucla C, Rossier C, Wyss C, Speleman F, De Paepe A, Dekker J, Antonarakis SE, De Baere E. 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 Genet. 2009 Jun; 5(6):e1000522.
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        46. Chang HY, Cuvier O, Dekker J. Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization. EMBO Rep. 2009 Jul; 10(7):689-93.
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        47. Miele A, Bystricky K, Dekker J. Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS Genet. 2009 May; 5(5):e1000478.
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        48. Oza P, Jaspersen SL, Miele A, Dekker J, Peterson CL. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev. 2009 Apr 15; 23(8):912-27.
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        49. Miele A, Dekker J. Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C). Methods Mol Biol. 2009; 464:105-21.
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        50. van Berkum NL, Dekker J. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol. 2009; 567:189-213.
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        51. Dekker J. Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. J Biol Chem. 2008 Dec 12; 283(50):34532-40.
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        52. Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Mol Biosyst. 2008 Nov; 4(11):1046-57.
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        53. Dekker J. Gene regulation in the third dimension. Science. 2008 Mar 28; 319(5871):1793-4.
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        54. Keys JR, Tallack MR, Zhan Y, Papathanasiou P, Goodnow CC, Gaensler KM, Crossley M, Dekker J, Perkins AC. A mechanism for Ikaros regulation of human globin gene switching. Br J Haematol. 2008 May; 141(3):398-406.
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        55. Dostie J, Zhan Y, Dekker J. Chromosome conformation capture carbon copy technology. Curr Protoc Mol Biol. 2007 Oct; Chapter 21:Unit 21.14.
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        56. Lanzuolo C, Roure V, Dekker J, Bantignies F, Orlando V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol. 2007 Oct; 9(10):1167-74.
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        57. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816.
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        58. Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc. 2007; 2(4):988-1002.
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        59. Dekker J. GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p. Genome Biol. 2007; 8(6):R116.
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        60. Hagège H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, de Laat W, Forné T. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc. 2007; 2(7):1722-33.
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        61. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct; 16(10):1299-309.
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        62. Gheldof N, Tabuchi TM, Dekker J. The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc Natl Acad Sci U S A. 2006 Aug 15; 103(33):12463-8.
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        63. Miele A, Gheldof N, Tabuchi TM, Dostie J, Dekker J. Mapping chromatin interactions by chromosome conformation capture. Curr Protoc Mol Biol. 2006 May; Chapter 21:Unit 21.11.
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        64. Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006 Jan; 3(1):17-21.
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        65. Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, Weiss MJ, Dekker J, Blobel GA. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell. 2005 Feb 4; 17(3):453-62.
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        66. Kleckner N, Zickler D, Jones GH, Dekker J, Padmore R, Henle J, Hutchinson J. A mechanical basis for chromosome function. Proc Natl Acad Sci U S A. 2004 Aug 24; 101(34):12592-7.
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