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Functional implications of genome topology

Abstract

Although genomes are defined by their sequence, the linear arrangement of nucleotides is only their most basic feature. A fundamental property of genomes is their topological organization in three-dimensional space in the intact cell nucleus. The application of imaging methods and genome-wide biochemical approaches, combined with functional data, is revealing the precise nature of genome topology and its regulatory functions in gene expression and genome maintenance. The emerging picture is one of extensive self-enforcing feedback between activity and spatial organization of the genome, suggestive of a self-organizing and self-perpetuating system that uses epigenetic dynamics to regulate genome function in response to regulatory cues and to propagate cell-fate memory.

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Figure 1: A global view of the cell nucleus.

Marina Corral

Figure 2: Four types of transcription regulatory chromatin loops.
Figure 3: A model depicting the interplay of genome structure and function.

Marina Corral

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References

  1. Lanctot, C., Cheutin, T., Cremer, M., Cavalli, G. & Cremer, T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet. 8, 104–115 (2007).

    Article  CAS  PubMed  Google Scholar 

  2. Misteli, T. Beyond the sequence: Cellular organization of genome function. Cell 128, 787–800 (2007).

    Article  CAS  PubMed  Google Scholar 

  3. Rajapakse, I. & Groudine, M. On emerging nuclear order. J. Cell Biol. 192, 711–721 (2011). This comprehensive overview of basic principles of genome organization includes a discussion of the concept of self-organized genome architecture.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Hakim, O. & Misteli, T. SnapShot: chromosome confirmation capture. Cell 148, 1068 e1–e2 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. van Steensel, B. & Dekker, J. Genomics tools for unraveling chromosome architecture. Nat. Biotechnol. 28, 1089–1095 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Branco, M.R. & Pombo, A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol. 4, e138 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Zimmer, C. & Fabre, E. Principles of chromosomal organization: lessons from yeast. J. Cell Biol. 192, 723–733 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sanyal, A., Lajoie, B.R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012). This work comprehensively maps interactions between transcription start sites and distal elements in 1% of the human genome to generate first insights into the spatial arrangements of genes and regulatory elements in their 3D context.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. 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).

    Article  CAS  PubMed  Google Scholar 

  10. Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43–49 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Filion, G.J. et al. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143, 212–224 (2010). This work characterizes five types of chromatin based on combinatorial enrichment of histone modifications and chromatin-binding proteins.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kharchenko, P.V. et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471, 480–485 (2011). Refs. 12 and 15 are two of several reports published from the ModENCODE and the ENCODE projects, respectively. Similar to ref. 11, they highlight the existence of chromosomal domains characterized by distinct epigenomic landscapes in D. melanogaster and humans.

    Article  CAS  PubMed  Google Scholar 

  13. Liu, T. et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res. 21, 227–236 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Schwartz, Y.B. et al. Alternative epigenetic chromatin states of polycomb target genes. PLoS Genet. 6, e1000805 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).

    Article  CAS  Google Scholar 

  16. Caron, H. et al. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291, 1289–1292 (2001).

    Article  CAS  PubMed  Google Scholar 

  17. Gierman, H.J. et al. Domain-wide regulation of gene expression in the human genome. Genome Res. 17, 1286–1295 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Dixon, J.R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012). Results reported in references 18–21 demonstrate the existence of topological domains in the D. melanogaster , mouse and human genomes. This work characterized the chromatin features at boundaries subdividing these domains as well as the nature of the long-distance contacts between different domains.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458–472 (2012).

    Article  CAS  PubMed  Google Scholar 

  21. Nora, E.P. et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381–385 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Boutanaev, A.M., Mikhaylova, L.M. & Nurminsky, D.I. The pattern of chromosome folding in interphase is outlined by the linear gene density profile. Mol. Cell. Biol. 25, 8379–8386 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Simonis, M. et al. High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nat. Methods 6, 837–842 (2009).

    Article  CAS  PubMed  Google Scholar 

  25. Noordermeer, D. et al. The dynamic architecture of Hox gene clusters. Science 334, 222–225 (2011).

    Article  CAS  PubMed  Google Scholar 

  26. Wong, H. et al. A predictive computational model of the dynamic 3D interphase yeast nucleus. Curr. Biol. 22, 1881–1890 (2012). Work reported in refs. 26 and 27 suggests that yeast higher-order nuclear architecture is largely driven by chromosome polymer structure.

    Article  CAS  PubMed  Google Scholar 

  27. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948–951 (2008).

    Article  CAS  PubMed  Google Scholar 

  29. Kind, J. & van Steensel, B. Genome-nuclear lamina interactions and gene regulation. Curr. Opin. Cell Biol. 22, 320–325 (2010).

    Article  CAS  PubMed  Google Scholar 

  30. Wang, J. et al. Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions. J. Cell Biol. 164, 515–526 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Shopland, L.S. et al. Replication-dependent histone gene expression is related to Cajal body (CB) association but does not require sustained CB contact. Mol. Biol. Cell 12, 565–576 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Bantignies, F. et al. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144, 214–226 (2011).

    Article  CAS  PubMed  Google Scholar 

  33. Cheutin, T. & Cavalli, G. Progressive polycomb assembly on H3K27me3 compartments generates polycomb bodies with developmentally regulated motion. PLoS Genet. 8, e1002465 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Eskiw, C.H. et al. Transcription factories and nuclear organization of the genome. Cold Spring Harb. Symp. Quant. Biol. 75, 501–506 (2010).

    Article  CAS  PubMed  Google Scholar 

  35. Meaburn, K.J., Gudla, P.R., Khan, S., Lockett, S.J. & Misteli, T. Disease-specific gene repositioning in breast cancer. J. Cell Biol. 187, 801–812 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Kalhor, R., Tjong, H., Jayahilaka, N., Alber, F. & Chen, L. Solid-phase chromosome conformation capture for structural characterization of genome architectures. Nat. Biotechnol. 30, 90–98 (2012).

    Article  CAS  Google Scholar 

  37. Cvackova, Z., Masata, M., Stanek, D., Fidlerova, H. & Raska, I. Chromatin position in human HepG2 cells: although being non-random, significantly changed in daughter cells. J. Struct. Biol. 165, 107–117 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Hou, C. & Corces, V.G. Throwing transcription for a loop: expression of the genome in the 3D nucleus. Chromosoma 121, 107–116 (2012).

    Article  CAS  PubMed  Google Scholar 

  39. O'Sullivan, J.M. et al. Gene loops juxtapose promoters and terminators in yeast. Nat. Genet. 36, 1014–1018 (2004).

    Article  CAS  PubMed  Google Scholar 

  40. Tan-Wong, S.M., French, J.D., Proudfoot, N.J. & Brown, M.A. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc. Natl. Acad. Sci. USA 105, 5160–5165 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Tan-Wong, S.M., Wijayatilake, H.D. & Proudfoot, N.J. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev. 23, 2610–2624 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Tan-Wong, S.M. et al. Gene loops enhance transcriptional directionality. Science 338, 671–675 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell 10, 1453–1465 (2002).

    Article  CAS  PubMed  Google Scholar 

  44. Orom, U.A. & Shiekhattar, R. Noncoding RNAs and enhancers: complications of a long-distance relationship. Trends Genet. 27, 433–439 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wang, K.C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120–124 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. 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). This work demonstrates that chromatin looping causally underlies gene regulation, as determined by experimentally manipulating the formation of chromatin loops.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Vernimmen, D. et al. Polycomb eviction as a new distant enhancer function. Genes Dev. 25, 1583–1588 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Tiwari, V.K., Cope, L., McGarvey, K.M., Ohm, J.E. & Baylin, S.B. A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Res. 18, 1171–1179 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Tiwari, V.K. et al. PcG proteins, DNA methylation, and gene repression by chromatin looping. PLoS Biol. 6, 2911–2927 (2008).

    Article  CAS  PubMed  Google Scholar 

  51. 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. 9, 1167–1174 (2007).

    Article  CAS  PubMed  Google Scholar 

  52. Breiling, A., Turner, B.M., Bianchi, M.E. & Orlando, V. General transcription factors bind promoters repressed by Polycomb group proteins. Nature 412, 651–655 (2001).

    Article  CAS  PubMed  Google Scholar 

  53. Lanzuolo, C. & Orlando, V. The function of the epigenome in cell reprogramming. Cell. Mol. Life Sci. 64, 1043–1062 (2007).

    Article  CAS  PubMed  Google Scholar 

  54. Saurin, A.J., Shao, Z., Erdjument-Bromage, H., Tempst, P. & Kingston, R.E. A Drosophila Polycomb group complex includes Zeste and dTAFII proteins. Nature 412, 655–660 (2001).

    Article  CAS  PubMed  Google Scholar 

  55. Cleard, F., Moshkin, Y., Karch, F. & Maeda, R.K. Probing long-distance regulatory interactions in the Drosophila melanogaster bithorax complex using Dam identification. Nat. Genet. 38, 931–935 (2006).

    Article  CAS  PubMed  Google Scholar 

  56. Li, B., Carey, M. & Workman, J.L. The role of chromatin during transcription. Cell 128, 707–719 (2007).

    Article  CAS  PubMed  Google Scholar 

  57. Wicks, K. & Knight, J.C. Transcriptional repression and DNA looping associated with a novel regulatory element in the final exon of the lymphotoxin-beta gene. Genes Immun. 12, 126–135 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Hsu, P.Y. et al. Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping. Genome Res. 20, 733–744 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Hewetson, A. & Chilton, B.S. Progesterone-dependent deoxyribonucleic acid looping between RUSH/SMARCA3 and Egr-1 mediates repression by c-Rel. Mol. Endocrinol. 22, 813–822 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Yang, J. & Corces, V.G. Insulators, long-range interactions, and genome function. Curr. Opin. Genet. Dev. 22, 86–92 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Thurman, R.E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Van Bortle, K. et al. Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains. Genome Res. 22, 2176–2187 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Schwartz, Y.B. et al. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 22, 2188–2198 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Masui, O. et al. Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell 145, 447–458 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Augui, S. et al. Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic. Science 318, 1632–1636 (2007).

    Article  CAS  PubMed  Google Scholar 

  66. Zhang, Y. et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148, 908–921 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38, 1341–1347 (2006).

    Article  CAS  PubMed  Google Scholar 

  68. Sandhu, K.S. et al. Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development. Genes Dev. 23, 2598–2603 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Ling, J.Q. et al. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312, 269–272 (2006).

    Article  CAS  PubMed  Google Scholar 

  70. Schoenfelder, S. et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 42, 53–61 (2010).

    Article  CAS  PubMed  Google Scholar 

  71. Dundr, M. & Misteli, T. Biogenesis of nuclear bodies. Cold Spring Harb. Perspect. Biol. 2, a000711 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Noordermeer, D. et al. Variegated gene expression caused by cell-specific long-range DNA interactions. Nat. Cell Biol. 13, 944–951 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Spilianakis, C.G., Lalioti, M.D., Town, T., Lee, G.R. & Flavell, R.A. Interchromosomal associations between alternatively expressed loci. Nature 435, 637–645 (2005).

    Article  CAS  PubMed  Google Scholar 

  74. Lomvardas, S. et al. Interchromosomal interactions and olfactory receptor choice. Cell 126, 403–413 (2006).

    Article  CAS  PubMed  Google Scholar 

  75. Clowney, E.J. et al. Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 151, 724–737 (2012). This work reveals that, in mouse olfactory neurons, silent olfactory receptor genes from different chromosomes converge in a small number of heterochromatic foci, suggesting that monogenic and monoallelic expression of olfactory receptors may be dependent on nuclear organization.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Apostolou, E. & Thanos, D. Virus infection induces NF-κB-dependent interchromosomal associations mediating monoallelic IFN-β gene expression. Cell 134, 85–96 (2008).

    Article  CAS  PubMed  Google Scholar 

  77. Kumaran, R.I. & Spector, D.L. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J. Cell Biol. 180, 51–65 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Finlan, L.E. et al. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet. 4, e1000039 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  79. Reddy, K.L., Zullo, J.M., Bertolino, E. & Singh, H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452, 243–247 (2008).

    Article  CAS  PubMed  Google Scholar 

  80. Zullo, J.M. et al. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell 149, 1474–1487 (2012).

    Article  CAS  PubMed  Google Scholar 

  81. Egecioglu, D. & Brickner, J.H. Gene positioning and expression. Curr. Opin. Cell Biol. 23, 338–345 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Towbin, B.D. et al. Step-wise methylation of Histone H3K9 positions heterochromatin at the nuclear periphery. Cell 150, 934–947 (2012).

    Article  CAS  PubMed  Google Scholar 

  83. Peric-Hupkes, D. et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol. Cell 38, 603–613 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Kubben, N. et al. Mapping of lamin A- and progerin-interacting genome regions. Chromosoma 121, 447–464 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Yokochi, T. et al. G9a selectively represses a class of late-replicating genes at the nuclear periphery. Proc. Natl. Acad. Sci. USA 106, 19363–19368 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Mechali, M. Eukaryotic DNA replication origins: many choices for appropriate answers. Nat. Rev. Mol. Cell Biol. 11, 728–738 (2010).

    Article  CAS  PubMed  Google Scholar 

  87. Schwaiger, M. et al. Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. Genes Dev. 23, 589–601 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Cadoret, J.C. et al. Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc. Natl. Acad. Sci. USA 105, 15837–15842 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Cayrou, C., Gregoire, D., Coulombe, P., Danis, E. & Mechali, M. Genome-scale identification of active DNA replication origins. Methods 57, 158–164 (2012).

    Article  CAS  PubMed  Google Scholar 

  90. Danis, E. et al. Specification of a DNA replication origin by a transcription complex. Nat. Cell Biol. 6, 721–730 (2004).

    Article  CAS  PubMed  Google Scholar 

  91. Schubeler, D. et al. Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat. Genet. 32, 438–442 (2002).

    Article  PubMed  CAS  Google Scholar 

  92. Hiratani, I., Takebayashi, S., Lu, J. & Gilbert, D.M. Replication timing and transcriptional control: beyond cause and effect–part II. Curr. Opin. Genet. Dev. 19, 142–149 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Gilbert, D.M. Replication timing and transcriptional control: beyond cause and effect. Curr. Opin. Cell Biol. 14, 377–383 (2002).

    Article  CAS  PubMed  Google Scholar 

  94. Hiratani, I. et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 6, e245 (2008). Work described in refs. 94 and 95 reveals a tight correlation between the timing of replication in large chromosomal domains and their spatial organization as assessed by 3C technologies.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  95. Ryba, T. et al. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 20, 761–770 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Moindrot, B. et al. 3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Res. 40, 9470–9481 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Takebayashi, S., Dileep, V., Ryba, T., Dennis, J.H. & Gilbert, D.M. Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding. Proc. Natl. Acad. Sci. USA 109, 12574–12579 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Gilbert, D.M. Cell fate transitions and the replication timing decision point. J. Cell Biol. 191, 899–903 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Goodarzi, A.A. et al. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol. Cell 31, 167–177 (2008).

    Article  CAS  PubMed  Google Scholar 

  100. Cowell, I.G. et al. gammaH2AX foci form preferentially in euchromatin after ionising-radiation. PLoS ONE 2, e1057 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Kruhlak, M.J. et al. Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J. Cell Biol. 172, 823–834 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Ayoub, N., Jeyasekharan, A.D., Bernal, J.A. & Venkitaraman, A.R. HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response. Nature 453, 682–686 (2008).

    Article  CAS  PubMed  Google Scholar 

  103. Ziv, Y. et al. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway. Nat. Cell Biol. 8, 870–876 (2006).

    Article  CAS  PubMed  Google Scholar 

  104. Chiolo, I. et al. Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell 144, 732–744 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Soutoglou, E. et al. Positional stability of single double-strand breaks in mammalian cells. Nat. Cell Biol. 9, 675–682 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Roix, J.J., McQueen, P.G., Munson, P.J., Parada, L.A. & Misteli, T. Spatial proximity of translocation-prone gene loci in human lymphomas. Nat. Genet. 34, 287–291 (2003). This work provides extensive evidence for a key role of spatial genome organization in determining chromosome translocations.

    Article  CAS  PubMed  Google Scholar 

  107. Hakim, O. et al. DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature 484, 69–74 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Klein, I.A. et al. Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell 147, 95–106 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Chiarle, R. et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 147, 107–119 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Dion, V., Kalck, V., Horigome, C., Towbin, B.D. & Gasser, S.M. Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery. Nat. Cell Biol. 14, 502–509 (2012).

    Article  CAS  PubMed  Google Scholar 

  111. Mine-Hattab, J. & Rothstein, R. Increased chromosome mobility facilitates homology search during recombination. Nat. Cell Biol. 14, 510–517 (2012).

    Article  CAS  PubMed  Google Scholar 

  112. Mekhail, K., Seebacher, J., Gygi, S.P. & Moazed, D. Role for perinuclear chromosome tethering in maintenance of genome stability. Nature 456, 667–670 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Bressan, D.A., Vazquez, J. & Haber, J.E. Mating type-dependent constraints on the mobility of the left arm of yeast chromosome III. J. Cell Biol. 164, 361–371 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Parada, L., McQueen, P. & Misteli, T. Tissue-specific spatial organization of genomes. Genome Biol. 5, R44 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  115. Mathas, S. et al. Gene deregulation and spatial genome reorganization near breakpoints prior to formation of translocations in anaplastic large cell lymphoma. Proc. Natl. Acad. Sci. USA 106, 5831–5836 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Lin, C. et al. Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer. Cell 139, 1069–1083 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Meshorer, E. et al. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev. Cell 10, 105–116 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Efroni, S. et al. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2, 437–447 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Fussner, E. et al. Constitutive heterochromatin reorganization during somatic cell reprogramming. EMBO J. 30, 1778–1789 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Gaspar-Maia, A. et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 460, 863–868 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Ho, L. et al. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nat. Cell Biol. 13, 903–913 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Biran, A. & Meshorer, E. Concise review: chromatin and genome organization in reprogramming. Stem Cells 30, 1793–1799 (2012).

    Article  CAS  PubMed  Google Scholar 

  124. Puschendorf, M. et al. PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Nat. Genet. 40, 411–420 (2008).

    Article  CAS  PubMed  Google Scholar 

  125. Meister, P., Towbin, B.D., Pike, B.L., Ponti, A. & Gasser, S.M. The spatial dynamics of tissue-specific promoters during C. elegans development. Genes Dev. 24, 766–782 (2010). This study reveals a developmental stage–specific and cell differentiation–specific regulation of gene positioning in the 3D space of the nucleus in C. elegans , opening the way to genetic dissection of developmental determinants of nuclear organization and function.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Ishimi, Y. et al. Changes in chromatin structure during aging of human skin fibroblasts. Exp. Cell Res. 169, 458–467 (1987).

    Article  CAS  PubMed  Google Scholar 

  127. O'Sullivan, R.J., Kubicek, S., Schreiber, S.L. & Karlseder, J. Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat. Struct. Mol. Biol. 17, 1218–1225 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Scaffidi, P. & Misteli, T. Lamin A-dependent nuclear defects in human aging. Science 312, 1059–1063 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. O'Sullivan, R.J. & Karlseder, J. The great unravelling: chromatin as a modulator of the aging process. Trends Biochem. Sci. 37, 466–476 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Pegoraro, G. et al. Aging-related chromatin defects via loss of the NURD complex. Nat. Cell Biol. 11, 1261–1267 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Feser, J. et al. Elevated histone expression promotes life span extension. Mol. Cell 39, 724–735 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Sutton, A., Bucaria, J., Osley, M.A. & Sternglanz, R. Yeast ASF1 protein is required for cell cycle regulation of histone gene transcription. Genetics 158, 587–596 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Lesur, I. & Campbell, J.L. The transcriptome of prematurely aging yeast cells is similar to that of telomerase-deficient cells. Mol. Biol. Cell 15, 1297–1312 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Burgess, R.C., Misteli, T. & Oberdoerffer, P. DNA damage, chromatin, and transcription: the trinity of aging. Curr. Opin. Cell Biol. 24, 724–730 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Oberdoerffer, P. et al. SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging. Cell 135, 907–918 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

G.C. was supported by the European Research Council (ERC-2008-AdG No 232947), the Centre National de la Recherche Scientifique, the European Network of Excellence EpiGeneSys and the Agence Nationale de la Recherche. T.M. was supported by the Intramural Research Program of the US National Institutes of Health, the National Cancer Institute, the Center for Cancer Research.

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Cavalli, G., Misteli, T. Functional implications of genome topology. Nat Struct Mol Biol 20, 290–299 (2013). https://doi.org/10.1038/nsmb.2474

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