Section: Publications

Job Dekker, Ph.D.

Academic Role: Associate Professor

Faculty Appointment(s) In:
   Biochemistry and Molecular Pharmacology
   Program in Gene Function and Expression

Other Affiliation(s):
   Interdisciplinary Graduate Program
   Program in Bioinformatics & Integrative Biology



Representative Publications

2009

Lieberman-Aiden, E.*, van Berkum, N.L.*, Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., Sandstrom, R., Bernstein, B., Bender, M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J.A., Mirny, L., Lander, E.S.# and Dekker, J.# (2009) [* denotes co-first authors, # denotes co-corresponding authors] Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326(5950): 289-293.

Lajoie, B.R., van Berkum, N.L., Sanyal, A. and Dekker, J. (2009) My5C: web tools for chromosome conformation capture studies. Nat. Methods, 6(10): 690-691.

van Berkum, N.L. and Dekker, J. (2009) Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol. Biol., 567: 189-213.

Chang, H.Y., Cuvier, O. and Dekker, J.  (2009)  Gene dates, parties and galas:  chromatin dynamics and higher order oganization.  EMBO Rep., 10(7): 689-693. 

D'haene, B., Attanasio, C., Beysen, D., Dostie, J., Lemire, E., Bouchard, Ph., 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, S.E. and De Baere, E.  (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 Genet., 5 (6): e1000522.

Miele, A., Bystricky, K. and Dekker, J. (2009) Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions.  PLoS Genet., 5: e1000478.

Oza, P., Jaspersen, S.L., Miele, A., Dekker, J. and Peterson, C.L. (2009) Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev., 23: 912-927. 

Miele, A. and Dekker, J. (2009) Mapping cis- and trans-chromatin interaction networks using Chromosome Conformation Capture (3C). Methods Mol. Biol., 464: 105-121.

2008

Dekker, J. (2008) Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction.  J. Biol. Chem., 283(50): 34532-34540.

Miele, A. and Dekker, J. (2008) Long-range looping interactions and gene regulation.  Mol. BioSyst., 4(11): 1046-1057.

Keys, J.R., Tallack, M.R., Zhan, Y., Papathanasiou, P., Goodnow, C.C., Gaensler, K.M., Crossley, M., Dekker, J. and Perkins, A.C. (2008) A mechanism for Ikaros regulation of human globin gene switching. Br. J. Haematol., 141(3): 398-406.

Dekker, J. (2008) Gene regulation in the third dimension.  Science, 319(5871): 1793-1794.

2007

Dostie, J., Zhan, Y. and Dekker, J. (2007) Chromosome Conformation Capture Carbon Copy Technology. In: Current Protocols in Molecular Biology, (F.M. Ausubel, et al., eds.). Chapter 21.14.1-21.14.13. John Wiley & Sons, Hoboken, N.J.

Lanzuolo, C., Roure, V., Dekker, J., Bantignies, F. and Orlando, V. (2007) Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nature Cell Biology, 9(10): 1167-1174.

Hagège, H., Klous, P., Braem, C., Splinter, E., Dekker, J., Cathala, G., de Laat, W. and Forné, T. (2007) Quantitative analysis of Chromosome Conformation Capture assays (3C-qPCR). Nature Protocols, 2(7): 1722-1733.

Dekker, J. (2007). GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p.  Genome Biol. 8(6): R116.

The Encode Project Consortium (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447(7146): 799-816.

Dostie, J. and Dekker, J. (2007). Mapping networks of physical interactions between genomic elements using 5C technology. Nature Protocols, 2(4): 988-1002.

2006

Dostie, J., Richmond, T.A., Arnaout, R.A., Selzer, R.R., Lee, W.L., Honan, T.A., Rubio, E.D., Krumm, A., Lamb, J., Nusbaum, C., Green, R.D. and Dekker, J. (2006). Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Research, 16(10): 1299-1309. [Highlighted in Kiermer, V. (2006) The Story of C's. Nature Methods, 3(11): 872-873]

Gheldof, N., Tabuchi, T.M. and Dekker, J. (2006). The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc. Natl. Acad. Sci. USA, 103(33): 12463-12468.

Miele, A., Gheldof, N., Tabuchi, T.M., Dostie, J. and Dekker, J. (2006). Mapping chromatin interactions by Chromosome Conformation Capture (3C). In: Current Protocols in Molecular Biology, (F.M. Ausubel, et al., eds.). Chapter 21.11.1-21.11.20. John Wiley & Sons, Hoboken, N.J.

Dekker, J. (2006). The three C's of chromosome conformation capture: controls, controls, controls. Nat. Methods, 3(1): 17-21.

2005

Vakoc, C., Letting, D.L., Gheldof, N., Sawado, T., Bender, M.A., Groudine, M., Weiss, M.J., Dekker, J., and Blobel, G.A. (2005). Proximity among distant regulatory elements at the ß-globin locus requires GATA-1 and FOG-1. Mol. Cell, 17(3): 453-462.

2004

ENCODE Project Consortium (2004).  The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306(5696), 636-640.

Kleckner, N., Zickler, D., Jones, G.H., Dekker, J., Padmore, R., Henle, J., and Hutchinson, J. (2004). A mechanical basis for chromosome function. Proc. Natl. Acad. Sci. USA, 101(34), 12592-15297.

Gheldof, N. and Dekker, J. (2004). Spatial organization of genomes. Current Genomics, 5(2), 157-168.

2003

Dekker, J. (2003).  A closer look at long-range chromosomal interactions.  Trends Biochem. Sci., 28(6), 277-280.

2002

Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002). Capturing Chromosome Conformation.  Science, 295, 1306-1311.

2000

Cha, R.S., Weiner, B.M., Keeney, S., Dekker, J., and Kleckner, N. (2000). Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p. Genes & Dev., 14, 493-503.

Office: LRB 519
Phone: 508-856-4371
E-mail: Job.Dekker@umassmed.edu
Keywords: Cell Biology, DNA Replication, Gene Expression

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