Mining increasingly comprehensive chromatin interaction maps for chromosomal domains and complete genomes requires novel computational methods and modelling tools.
Looping interactions between specific genomic elements — for example, gene promoters and regulatory elements — can be identified from chromatin interaction data by detecting interaction frequencies that are significantly higher than empirically estimated background levels. Looping interactions appear to be very abundant: most promoters interact with several other genomic elements.
Statistical analysis of Hi-C data identifies multiple scales of domain organization: larger (1–10 Mb) chromosomal compartments and smaller (<1 Mb) topologically associating domains.
Restraint-based modelling provides experiment-based models of genomes and genomic domains. Such models can be used as a starting point for targeted structure–function analyses.
Polymer simulations provide insights into the global chromatin organization that are consistent with statistical features of the interaction data, suggesting physical principles of chromatin folding.
How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C), the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction data sets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data.
This is a preview of subscription content
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Nègre, N. et al. A cis-regulatory map of the Drosophila genome. Nature 471, 527–531 (2011).
Gerstein, M. B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775–1787 (2010).
Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002).
van Steensel, B. & Dekker, J. Genomics tools for unraveling chromosome architecture. Nature Biotech. 28, 1089–1095 (2010).
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 ONE 5, e11560 (2010).
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).
Cremer, T. & Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Rev. Genet. 2, 292–301 (2001).
Branco, M. R. & Pombo, A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol. 4, e138 (2006).
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).
Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature 447, 413–417 (2007).
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).
Schoenfelder, S. et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nature Genet. 42, 53–61 (2010).
Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948–951 (2008).
Németh, A. et al. Initial genomics of the human nucleolus. PLoS Genet. 6, e1000889 (2010).
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).
Tolhuis, B. et al. Interactions among Polycomb domains are guided by chromosome architecture. PLoS Genet. 7, e1001343 (2011).
Bantignies, F. et al. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144, 214–226 (2011).
Pirrotta, V. & Li, H. B. A view of nuclear Polycomb bodies. Curr. Opin. Genet. Dev. 22, 101–109 (2012).
de Wit, E. & de Laat, W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11–24 (2012).
Hakim, O. & Misteli, T. SnapShot: chromosome conformation capture. Cell 148, 1068–1068.e2 (2012).
Ethier, S. D., Miura, H. & Dostie, J. Discovering genome regulation with 3C and 3C-related technologies. Biochim. Biophys. Acta. 1819, 401–410 (2012).
Felsenfeld, G. & Groudine, M. Controlling the double helix. Nature 421, 448–453 (2003).
Rippe, K. Making contacts on a nucleic acid polymer. Trends Biochem. Sci. 26, 733–740 (2001).
Fudenberg, G. & Mirny, L. A. Higher-order chromatin structure: bridging physics and biology. Curr. Opin. Genet. Dev. 22, 115–124 (2012).
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).
Marshall, W. F. et al. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7, 930–939 (1997).
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.
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).
Miele, A. & Dekker, J. Long-range chromosomal interactions and gene regulation. Mol. BioSyst. 4, 1046–1057 (2008).
Krivega, I. & Dean, A. Enhancer and promoter interactions—long distance calls. Curr. Opin. Genet. Dev. 22, 79–85 (2012).
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. Cell 10, 1453–1465 (2002).
Ott, C. J. et al. Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Proc. Natl Acad. Sci. USA 106, 19934–19939 (2009).
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).
Dekker, J. The 3 C's of chromosome conformation capture: controls, controls, controls. Nature Methods 3, 17–21 (2006).
Palstra, R. J. et al. The β-globin nuclear compartment in development and erythroid differentiation. Nature Genet. 35, 190–194 (2003).
Drissen, R. et al. The active spatial organization of the β-globin locus requires the transcription factor EKLF. Genes Dev. 18, 2485–2490 (2004).
Vakoc, C. R. et al. Proximity among distant regulatory elements at the β-globin locus requires GATA-1 and FOG-1. Mol. Cell 17, 453–462 (2005).
Deng, W. et al. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149, 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.
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).
Spilianakis, C. G. & Flavell, R. A. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nature Immunol. 5, 1017–1027 (2004).
Ahmadiyeh, N. et al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc. Natl Acad. Sci. USA 107, 9742–9746 (2010).
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).
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).
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).
Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 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.
Duan, Z. et al. A three-dimensional model of the yeast genome. Nature 465, 363–367 (2010).
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).
Hakim, O. et al. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 21, 697–706 (2011).
Gibcus, J. H. & Dekker, J. The hierarchy of the 3D genome. Mol. Cell 49, 773–782 (2013).
Phillips, J. E. & Corces, V. G. CTCF: master weaver of the genome. Cell 137, 1194–1211 (2009).
Handoko, L. et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nature Genet. 43, 630–638 (2011).
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).
Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100 (2012).
Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 (2012).
Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116–120 (2012).
Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458–472 (2012).
Nora, E. P. et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 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 genetic cis -elements.
Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012). This paper describes the discovery of TADs and discusses a computational strategy to identify TAD boundaries using Hi-C data sets.
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. Cell 48, 471–484 (2012).
Gaszner, M. & Felsenfeld, G. Insulators: exploiting transcriptional and epigenetic mechanisms. Nature Rev. Genet. 7, 703–713 (2006).
Caron, H. et al. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291, 1289–1292 (2001).
Spellman, P. T. & Rubin, G. M. Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1, 5 (2002).
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 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.
Marti-Renom, M. A. & Mirny, L. A. Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput. Biol. 7, e1002125 (2011).
Baù, D. & Marti-Renom, M. A. Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome Res. 19, 25–35 (2011).
Jhunjhunwala, S. et al. The 3D structure of the immunoglobulin heavy-chain locus: implications for long-range genomic interactions. Cell 133, 265–279 (2008). This worked combined FISH data and polymer modelling to obtained spatial models for the immunoglobulin heavy-chain locus.
Fraser, J. et al. Chromatin conformation signatures of cellular differentiation. Genome Biol. 10, R37 (2009).
Russel, D. et al. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 10, e1001244 (2012).
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).
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.
Umbarger, M. A. et al. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol. Cell 44, 252–264 (2011).
Ebersbach, G., Briegel, A., Jensen, G. J. & Jacobs-Wagner, C. A self-associating protein critical for chromosome attachment, division, and polar organization in caulobacter. Cell 134, 956–968 (2008).
Bowman, G. R. et al. A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole. Cell 134, 945–955 (2008).
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).
Hu, M. et al. Bayesian inference of spatial organizations of chromosomes. PLoS Comput. Biol. 9, e1002893 (2013).
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).
Taddei, A. & Gasser, S. M. Structure and function in the budding yeast nucleus. Genetics 192, 107–129 (2012).
van den Engh, G., Sachs, R. & Trask, B. J. Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. Science 257, 1410 (1992).
McManus, J. et al. Unusual chromosome structure of fission yeast DNA in mouse cells. J. Cell Sci. 107, 469–486 (1994).
Hahnfeldt, P. et al. Polymer models for interphase chromosomes. Proc. Natl Acad. Sci. USA 90, 7854–7858 (1993).
Marko, J. F. & Siggia, E. D. Polymer models of meiotic and mitotic chromosomes. Mol. Biol. Cell 8, 2217–2231 (1997).
Sachs, R. K. et al. A random-walk/giant-loop model for interphase chromosomes. Proc. Natl Acad. Sci. USA 92, 2710–2714 (1995).
Sikorav, J. L. & Jannink, G. Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model. Biophys. J. 66, 827 (1994).
Grosberg, A., Rabin, Y., Havlin, S. & Neer, A. Crumpled globule model of the three-dimensional structure of DNA. Europhys. Lett. 23, 373 (1993).
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).
Bohn, M. & Heermann, D. W. Repulsive forces between looping chromosomes induce entropy-driven segregation. PLoS ONE 6, e14428 (2011).
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).
Vettorel, T., Grosberg, A. Y. & Kremer, K. Statistics of polymer rings in the melt: a numerical simulation study. Phys. Biol. 6, 025013 (2009).
Rosa, A. & Everaers, R. Structure and dynamics of interphase chromosomes. PLoS Comput. Biol. 4, e1000153 (2008).
Cook, P. R. & Marenduzzo, D. Entropic organization of interphase chromosomes. J. Cell Biol. 186, 825–834 (2009).
Jerabek, H. & Heermann, D. W. Expression-dependent folding of interphase chromatin. PLoS ONE 7, e37525 (2012).
Bohn, M. & Heermann, D. W. Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE 5, e12218 (2010).
Mateos-Langerak, J. et al. Spatially confined folding of chromatin in the interphase nucleus. Proc. Natl Acad. Sci. USA 106, 3812–3817 (2009).
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).
Rosa, A., Becker, N. B. & Everaers, R. Looping probabilities in model. Interphase chromosomes. Biophys. J. 98, 2410–2419 (2010).
Grosberg, A. Y., Nechaev, S. K. & Shakhnovich, E. I. The role of topological constraints in the kinetics of collapse of macromolecules. J. Physique 49, 2095–2100 (1988).
Mirny, L. A. The fractal globule as a model of chromatin architecture in the cell. Chromosome Res. 19, 37–51 (2011).
Rapkin, L. M., Anchel, D. R. P., Li, R. & Bazett-Jones, D. P. A view of the chromatin landscape. Micron 43, 150–158 (2012).
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).
Towbin, B. D. et al. Step-wise methylation of histone h3k9 positions heterochromatin at the nuclear periphery. Cell 150, 934–947 (2012).
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).
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).
Rubinstein, M. & Colby, R. H. Polymer Physics (Oxford Univ. Press, 2003).
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).
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).
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).
Lajoie, B. R., van Berkum, N. L., Sanyal, A. & Dekker, J. My5C: web tools for chromosome conformation capture studies. Nature Methods 6, 690–691 (2009).
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).
Fullwood, M. J. et al. An oestrogen-receptor-α-bound human chromatin interactome. Nature 462, 58–64 (2009).
Zhang, Y. et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148, 908–921 (2012).
Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature Methods 9, 999–1003 (2012).
Mouse ENCODE Consortium. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 13, 418 (2012).
We are grateful to all the members of our groups for many discussions about three-dimensional genomics. Supported by grants from the US National Institutes of Health (NIH), US National Human Genome Research Institute (HG003143 and HG003143-06S1) and a W.M. Keck Foundation distinguished young scholar in medical research grant to J.D.; financial support from the Spanish Ministerio de Ciencia e Innovación (BFU2010-19310/BMC), the Human Frontiers Science Program (RGP0044/2011) and the BLUEPRINT project (EU FP7 grant agreement 282510) to M.A.M.-R.; and a grant from the NIH National Cancer Institute (Physical Sciences–Oncology Center at Massachusetts Institutes of Technology Grant U54CA143874) to L.A.M.
The authors declare no competing financial interests.
- Restraint-based modelling
A computational method to model the three-dimensional structure of an object represented by points and restraints between them.
- Chromosome territories
Each territory is the domain of a nucleus occupied by a chromosome.
- Polycomb bodies
Discrete nuclear foci containing Polycomb proteins and their silenced target genes. Polycomb bodies have been observed in Drosophila melanogaster and human cells by imaging and in situ hybridization.
- Nuclear lamina
A scaffold of lamin proteins predominantly found in the nuclear periphery associated with the inner surface of the nuclear membrane.
- Transcription factory
A nuclear compartments in which active transcription takes place; it has a high concentration of RNA polymerase II.
Forces (or scoring functions) that restrict the movement of objects (or points) that they apply to. Often used synonymously with 'restraint'.
- Locus control region
(LCR). A cis-acting element that organizes a gene cluster into an active chromatin domain and enhances transcription in a tissue-specific manner.
A highly conserved zinc finger protein that influences chromatin organization and architecture and is implicated in diverse regulatory functions, including transcriptional activation, repression and insulation.
- X-chromosome inactivation centre
A genetically defined locus of several megabases on the X chromosome of mammals that is required to initiate transcriptional repression along a single X chromosome in female cells.
- Boundary elements
DNA elements that lie between two gene-controlling elements, such as a promoter and an enhancer, or between two large chromosomal domains, preventing their communication or interaction. The function of boundary elements is usually mediated by the binding of specific factors.
Forces (or scoring functions) that maintain the objects (or points) to which they apply at their position of equilibrium.
- Rabl configuration
A pattern of nuclear organization in which centromeres of all chromosomes are spatially clustered and their arms run in parallel. This organization has been proposed to be a passive consequence of chromosome segregation but can also be actively maintained by mechanisms that cluster centromeres.
- Fractal globule
A dense, non-equilibrium polymer state, which emerges as a result of a polymer condensation. In this state, the polymer is unknotted and each region of the chain is locally compact, allowing easy opening and closing of chromosomal regions.
About this article
Cite this article
Dekker, J., Marti-Renom, M. & Mirny, L. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 14, 390–403 (2013). https://doi.org/10.1038/nrg3454
BMC Biology (2021)
Genome Biology (2021)
Cell & Bioscience (2021)
ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function
Nature Communications (2021)
Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states
Nature Communications (2021)