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Science 319 (5871): 1793-1794

Copyright © 2008 by the American Association for the Advancement of Science

Gene Regulation in the Third Dimension

Job Dekker*

Abstract: Analysis of the spatial organization of chromosomes reveals complex three-dimensional networks of chromosomal interactions. These interactions affect gene expression at multiple levels, including long-range control by distant enhancers and repressors, coordinated expression of genes, and modification of epigenetic states. Major challenges now include deciphering the mechanisms by which loci come together and understanding the functional consequences of these often transient associations.

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.

* To whom correspondence should be addressed. E-mail: Job.Dekker{at}

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Mol Syst Biol 6, 395
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Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data.
T. Trieu and J. Cheng (2014)
Nucleic Acids Res. 42, e52
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rSNPBase: a database for curated regulatory SNPs.
L. Guo, Y. Du, S. Chang, K. Zhang, and J. Wang (2014)
Nucleic Acids Res. 42, D1033-D1039
   Abstract »    Full Text »    PDF »
Organization of the Mitotic Chromosome.
N. Naumova, M. Imakaev, G. Fudenberg, Y. Zhan, B. R. Lajoie, L. A. Mirny, and J. Dekker (2013)
Science 342, 948-953
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Unifying model for molecular determinants of the preselection V{beta} repertoire.
S. Gopalakrishnan, K. Majumder, A. Predeus, Y. Huang, O. I. Koues, J. Verma-Gaur, S. Loguercio, A. I. Su, A. J. Feeney, M. N. Artyomov, et al. (2013)
PNAS 110, E3206-E3215
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From remote enhancers to gene regulation: charting the genome's regulatory landscapes.
O. Symmons and F. Spitz (2013)
Phil Trans R Soc B 368, 20120358
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Functional Analysis of Predisposition Loci.
M. A. Buckley, A. Gjyshi, and A. Monteiro (2013)
Am. Assoc. Cancer Res. Educ. Book 2013, 85-90
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DNA Looping in Prokaryotes: Experimental and Theoretical Approaches.
A. Cournac and J. Plumbridge (2013)
J. Bacteriol. 195, 1109-1119
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Transvection Is Common Throughout the Drosophila Genome.
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Genetics 191, 1129-1141
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Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth.
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EMBO J. 30, 2405-2419
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On emerging nuclear order.
I. Rajapakse and M. Groudine (2011)
J. Cell Biol. 192, 711-721
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ChIPing the cistrome of PXR in mouse liver.
J. Y. Cui, S. S. Gunewardena, C. E. Rockwell, and C. D. Klaassen (2010)
Nucleic Acids Res. 38, 7943-7963
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Diffusion-based DNA target colocalization by thermodynamic mechanisms.
A. Scialdone and M. Nicodemi (2010)
Development 137, 3877-3885
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Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.
N. Gheldof, E. M. Smith, T. M. Tabuchi, C. M. Koch, I. Dunham, J. A. Stamatoyannopoulos, and J. Dekker (2010)
Nucleic Acids Res. 38, 4325-4336
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Integrating one-dimensional and three-dimensional maps of genomes.
N. Naumova and J. Dekker (2010)
J. Cell Sci. 123, 1979-1988
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Setdb1 Histone Methyltransferase Regulates Mood-Related Behaviors and Expression of the NMDA Receptor Subunit NR2B.
Y. Jiang, M. Jakovcevski, R. Bharadwaj, C. Connor, F. A. Schroeder, C. L. Lin, J. Straubhaar, G. Martin, and S. Akbarian (2010)
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CD8 Locus Nuclear Dynamics during Thymocyte Development.
E. Ktistaki, A. Garefalaki, A. Williams, S. R. Andrews, D. M. Bell, K. E. Foster, C. G. Spilianakis, R. A. Flavell, N. Kosyakova, V. Trifonov, et al. (2010)
J. Immunol. 184, 5686-5695
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Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament.
P. A. Wiggins, K. C. Cheveralls, J. S. Martin, R. Lintner, and J. Kondev (2010)
PNAS 107, 4991-4995
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Chromosome Territories.
T. Cremer and M. Cremer (2010)
Cold Spring Harb Perspect Biol 2, a003889
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Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres.
P. Therizols, T. Duong, B. Dujon, C. Zimmer, and E. Fabre (2010)
PNAS 107, 2025-2030
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Defining specificity of transcription factor regulatory activities.
J. Eeckhoute, R. Metivier, and G. Salbert (2009)
J. Cell Sci. 122, 4027-4034
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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome.
E. Lieberman-Aiden, N. L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B. R. Lajoie, P. J. Sabo, M. O. Dorschner, et al. (2009)
Science 326, 289-293
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Gene dates, parties and galas: Symposium on Chromatin Dynamics and Higher Order Organization.
H. Y. Chang, O. Cuvier, and J. Dekker (2009)
EMBO Rep. 10, 689-693
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Cistromics of hormone-dependent cancer.
M. Lupien and M. Brown (2009)
Endocr. Relat. Cancer 16, 381-389
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A Genome-Wide Screen for {beta}-Catenin Binding Sites Identifies a Downstream Enhancer Element That Controls c-Myc Gene Expression.
G. S. Yochum, R. Cleland, and R. H. Goodman (2008)
Mol. Cell. Biol. 28, 7368-7379
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GATA transcription factors directly regulate the Parkinson's disease-linked gene {alpha}-synuclein.
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PNAS 105, 10907-10912
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