Gerstein, M. B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science330, 1775–1787 (2010). ArticleCASPubMed CentralPubMed Google Scholar
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science295, 1306–1311 (2002). ArticleCASPubMed Google Scholar
van Steensel, B. & Dekker, J. Genomics tools for unraveling chromosome architecture. Nature Biotech.28, 1089–1095 (2010). ArticleCAS Google Scholar
Müller, I., Boyle, S., Singer, R. H., Bickmore, W. A. & Chubb, J. R. Stable morphology, but dynamic internal reorganisation, of interphase human chromosomes in living cells. PLoS ONE5, e11560 (2010). ArticlePubMed CentralPubMedCAS Google Scholar
Boyle, S., Rodesch, M. J., Halvensleben, H. A., Jeddeloh, J. A. & Bickmore, W. A. Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Chromosome Res.19, 901–909 (2011). ArticleCASPubMed CentralPubMed Google Scholar
Cremer, T. & Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Rev. Genet.2, 292–301 (2001). ArticleCASPubMed Google Scholar
Branco, M. R. & Pombo, A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol.4, e138 (2006). ArticlePubMed CentralPubMedCAS Google Scholar
Iborra, F. J., Pombo, A., Jackson, D. A. & Cook, P. R. Active RNA polymerases are localized within discrete transcription “factories' in human nuclei. J. Cell Sci.109, 1427–1436 (1996). ArticleCASPubMed Google Scholar
Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature447, 413–417 (2007). ArticleCASPubMed Google Scholar
Brown, J. M. et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J. Cell Biol.182, 1083–1097 (2008). ArticleCASPubMed CentralPubMed Google Scholar
Schoenfelder, S. et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nature Genet.42, 53–61 (2010). ArticleCASPubMed Google Scholar
Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature453, 948–951 (2008). ArticleCASPubMed Google Scholar
van Koningsbruggen, S. et al. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol. Biol. Cell.21, 3735–3748 (2010). ArticleCASPubMed CentralPubMed Google Scholar
Bantignies, F. et al. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell144, 214–226 (2011). ArticleCASPubMed Google Scholar
Pirrotta, V. & Li, H. B. A view of nuclear Polycomb bodies. Curr. Opin. Genet. Dev.22, 101–109 (2012). ArticleCASPubMed Google Scholar
Ethier, S. D., Miura, H. & Dostie, J. Discovering genome regulation with 3C and 3C-related technologies. Biochim. Biophys. Acta.1819, 401–410 (2012). ArticleCASPubMed Google Scholar
Rippe, K. Making contacts on a nucleic acid polymer. Trends Biochem. Sci.26, 733–740 (2001). ArticleCASPubMed Google Scholar
Fudenberg, G. & Mirny, L. A. Higher-order chromatin structure: bridging physics and biology. Curr. Opin. Genet. Dev.22, 115–124 (2012). ArticleCASPubMed CentralPubMed Google Scholar
Chubb, J. R., Boyle, S., Perry, P. & Bickmore, W. A. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr. Biol.12, 439–445 (2002). ArticleCASPubMed Google Scholar
Marshall, W. F. et al. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol.7, 930–939 (1997). ArticleCASPubMed Google Scholar
Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F. & Chen, L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nature Biotech.30, 90–98 (2011). These authors apply simulations to analyse genome-wide chromatin interaction data to generate spatial models of nuclear organization that also capture the cell-to-cell variability in chromosome organization. ArticleCAS Google Scholar
Tjong, H., Gong, K., Chen, L. & Alber, F. Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome Res.22, 1295–1305 (2012). ArticleCASPubMed CentralPubMed Google Scholar
Krivega, I. & Dean, A. Enhancer and promoter interactions—long distance calls. Curr. Opin. Genet. Dev.22, 79–85 (2012). ArticleCASPubMed Google Scholar
Tolhuis, B., Palstra, R. J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol. Cell10, 1453–1465 (2002). ArticleCASPubMed Google Scholar
Ott, C. J. et al. Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc. Natl Acad. Sci. USA106, 19934–19939 (2009). ArticleCASPubMed CentralPubMed Google Scholar
Gheldof, N. et al. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res.38, 4235–4336 (2010). ArticleCAS Google Scholar
Dekker, J. The 3 C's of chromosome conformation capture: controls, controls, controls. Nature Methods3, 17–21 (2006). ArticleCASPubMed Google Scholar
Palstra, R. J. et al. The β-globin nuclear compartment in development and erythroid differentiation. Nature Genet.35, 190–194 (2003). ArticleCASPubMed Google Scholar
Drissen, R. et al. The active spatial organization of the β-globin locus requires the transcription factor EKLF. Genes Dev.18, 2485–2490 (2004). ArticleCASPubMed CentralPubMed Google Scholar
Vakoc, C. R. et al. Proximity among distant regulatory elements at the β-globin locus requires GATA-1 and FOG-1. Mol. Cell17, 453–462 (2005). ArticleCASPubMed Google Scholar
Deng, W. et al. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell149, 1233–1244 (2012). In this work, the authors show that physical tethering of an enhancer to its target promoter can activate the gene, providing one of the first direct mechanistic insights into the role of chromatin looping in gene control. ArticleCASPubMed CentralPubMed Google Scholar
Vernimmen, D., De Gobbi, M., Sloane-Stanley, J. A., Wood, W. G. & Higgs, D. R. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J.26, 2041–2051 (2007). ArticleCASPubMed CentralPubMed Google Scholar
Spilianakis, C. G. & Flavell, R. A. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nature Immunol.5, 1017–1027 (2004). ArticleCAS Google Scholar
Ahmadiyeh, N. et al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc. Natl Acad. Sci. USA107, 9742–9746 (2010). ArticleCASPubMedPubMed Central Google Scholar
Wright, J. B., Brown, S. J. & Cole, M. D. Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol. Cell. Biol.30, 1411–1420 (2010). ArticleCASPubMed CentralPubMed Google Scholar
Majumder, P., Gomez, J. A., Chadwick, B. P. & Boss, J. M. The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions. J. Exp. Med.205, 785–798 (2008). ArticleCASPubMed CentralPubMed Google Scholar
Miele, A., Bystricky, K. & Dekker, J. Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS Genet.5, e1000478 (2009). ArticlePubMed CentralPubMedCAS Google Scholar
Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature489, 109–113 (2012). In this paper, thousands of long-range interactions across 30 Mb in the human genome are discovered. This paper describes some of the statistical approaches that can be used to identify significant locus–locus interactions in comprehensive chromatin interaction data sets. ArticleCASPubMed CentralPubMed Google Scholar
Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genet.38, 1348–1354 (2006). ArticleCASPubMed Google Scholar
Hakim, O. et al. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res.21, 697–706 (2011). ArticleCASPubMed CentralPubMed Google Scholar
Handoko, L. et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nature Genet.43, 630–638 (2011). ArticleCASPubMed Google Scholar
Kleinjan, D. A. & van Heyningen, V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet.76, 8–32 (2005). ArticleCASPubMed Google Scholar
Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell148, 458–472 (2012). ArticleCASPubMed Google Scholar
Nora, E. P. et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature485, 381–385 (2012). This paper describes the discovery of TADs using 5C and shows that TAD boundaries are independent of chromatin modification but are defined by geneticcis-elements. ArticleCASPubMed CentralPubMed Google Scholar
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature485, 376–380 (2012). This paper describes the discovery of TADs and discusses a computational strategy to identify TAD boundaries using Hi-C data sets. ArticleCASPubMed CentralPubMed Google Scholar
Hou, C., Li, L., Qin, Z. S. & Corces, V. G. Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol. Cell48, 471–484 (2012). ArticleCASPubMed CentralPubMed Google Scholar
Gaszner, M. & Felsenfeld, G. Insulators: exploiting transcriptional and epigenetic mechanisms. Nature Rev. Genet.7, 703–713 (2006). ArticleCASPubMed Google Scholar
Caron, H. et al. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science291, 1289–1292 (2001). ArticleCASPubMed Google Scholar
Spellman, P. T. & Rubin, G. M. Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol.1, 5 (2002). ArticlePubMed CentralPubMed Google Scholar
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science326, 289–293 (2009). This work describes development of the Hi-C method and how polymer simulations can be used to analyse chromatin interaction data. This work also described the fractal globule state of chromatin at the 1–10 Mb scale. ArticleCASPubMed CentralPubMed Google Scholar
Marti-Renom, M. A. & Mirny, L. A. Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput. Biol.7, e1002125 (2011). ArticleCASPubMed CentralPubMed Google Scholar
Baù, D. & Marti-Renom, M. A. Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome Res.19, 25–35 (2011). ArticleCASPubMed Google Scholar
Jhunjhunwala, S. et al. The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions. Cell133, 265–279 (2008). This worked combined FISH data and polymer modelling to obtained spatial models for the immunoglobulin heavy-chain locus. ArticleCASPubMed CentralPubMed Google Scholar
Russel, D. et al. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol.10, e1001244 (2012). ArticleCASPubMed CentralPubMed Google Scholar
Sanyal, A., Baù, D., Martí-Renom, M. A. & Dekker, J. Chromatin globules: a common motif of higher order chromosome structure? Curr. Opin. Cell Biol.23, 325–331 (2011). ArticleCASPubMed CentralPubMed Google Scholar
Baù, D. et al. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nature Struct. Mol. Biol.18, 107–114 (2011). These authors describe a restraint-based modelling approach to use chromatin interaction data to derive spatial models of chromatin domains. ArticleCAS Google Scholar
Umbarger, M. A. et al. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol. Cell44, 252–264 (2011). ArticleCASPubMed Google Scholar
Ebersbach, G., Briegel, A., Jensen, G. J. & Jacobs-Wagner, C. A self-associating protein critical for chromosome attachment, division, and polar organization in caulobacter. Cell134, 956–968 (2008). ArticleCASPubMed CentralPubMed Google Scholar
Bowman, G. R. et al. A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole. Cell134, 945–955 (2008). ArticleCASPubMed CentralPubMed Google Scholar
Tanizawa, H. et al. Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res.38, 8164–8177 (2010). ArticleCASPubMed CentralPubMed Google Scholar
Jin, Q. W., Fuchs, J. & Loidl, J. Centromere clustering is a major determinant of yeast interphase nuclear organization. J. Cell Sci.113, 1903–1912 (2000). ArticleCASPubMed Google Scholar
van den Engh, G., Sachs, R. & Trask, B. J. Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. Science257, 1410 (1992). ArticleCASPubMed Google Scholar
McManus, J. et al. Unusual chromosome structure of fission yeast DNA in mouse cells. J. Cell Sci.107, 469–486 (1994). ArticleCASPubMed Google Scholar
Sikorav, J. L. & Jannink, G. Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model. Biophys. J.66, 827 (1994). ArticleCASPubMed CentralPubMed Google Scholar
Grosberg, A., Rabin, Y., Havlin, S. & Neer, A. Crumpled globule model of the three-dimensional structure of DNA. Europhys. Lett.23, 373 (1993). ArticleCAS Google Scholar
Vologodskii, A. V., Levene, S. D., Klenin, K. V., Frank-Kamenetskii, M. & Cozzarelli, N. R. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol.227, 1224–1243 (1992). ArticleCASPubMed Google Scholar
Dorier, J. & Stasiak, A. The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture. Nucleic Acids Res.38, 7410–7421 (2010). ArticleCASPubMed CentralPubMed Google Scholar
Vettorel, T., Grosberg, A. Y. & Kremer, K. Statistics of polymer rings in the melt: a numerical simulation study. Phys. Biol.6, 025013 (2009). ArticleCASPubMed Google Scholar
Bohn, M. & Heermann, D. W. Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE5, e12218 (2010). ArticlePubMed CentralPubMedCAS Google Scholar
Mateos-Langerak, J. et al. Spatially confined folding of chromatin in the interphase nucleus. Proc. Natl Acad. Sci. USA106, 3812–3817 (2009). ArticleCASPubMedPubMed Central Google Scholar
Barbieri, M. et al. Complexity of chromatin folding is captured by the strings and binders switch model. Proc. Natl Acad. Sci.109, 16173–16178 (2012). ArticleCASPubMedPubMed Central Google Scholar
Grosberg, A. Y., Nechaev, S. K. & Shakhnovich, E. I. The role of topological constraints in the kinetics of collapse of macromolecules. J. Physique49, 2095–2100 (1988). ArticleCAS Google Scholar
Rapkin, L. M., Anchel, D. R. P., Li, R. & Bazett-Jones, D. P. A view of the chromatin landscape. Micron43, 150–158 (2012). ArticleCASPubMed Google Scholar
Belmont, A. S. et al. Insights into interphase large-scale chromatin structure from analysis of engineered chromosome regions. Cold Spring Harbor Symp. Quant. Biol.75, 453–460 (2011). Article Google Scholar
Towbin, B. D. et al. Step-wise methylation of histone h3k9 positions heterochromatin at the nuclear periphery. Cell150, 934–947 (2012). ArticleCASPubMed Google Scholar
Emanuel, M., Radja, N. H., Henriksson, A. & Schiessel, H. The physics behind the larger scale organization of DNA in eukaryotes. Phys. Biol.6, 025008 (2009). ArticleCASPubMed Google Scholar
Shopland, L. S. et al. Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J. Cell Biol.174, 27–38 (2006). ArticleCASPubMed CentralPubMed Google Scholar
Rubinstein, M. & Colby, R. H. Polymer Physics (Oxford Univ. Press, 2003). Google Scholar
Würtele, H. & Chartrand, P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended chromosome conformation capture methodology. Chromosome Res.14, 477–495 (2006). ArticleCASPubMed Google Scholar
Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genet.38, 1341–1347 (2006). ArticleCASPubMed Google Scholar
Dostie, J. et al. Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res.16, 1299–1309 (2006). ArticleCASPubMed CentralPubMed Google Scholar
Lajoie, B. R., van Berkum, N. L., Sanyal, A. & Dekker, J. My5C: web tools for chromosome conformation capture studies. Nature Methods6, 690–691 (2009). ArticleCASPubMed CentralPubMed Google Scholar
Horike, S., Cai, S., Miyano, M., Cheng, J. F. & Kohwi-Shigematsu, T. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nature Genet.37, 31–40 (2005). ArticleCASPubMed Google Scholar
Zhang, Y. et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell148, 908–921 (2012). ArticleCASPubMed CentralPubMed Google Scholar