Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Genome organization in immune cells: unique challenges

Abstract

Each type of cell in the immune system performs critical functions to protect the body and maintain health. In order to fulfil these roles some immune cells rely on unique processes, including antigen receptor loci recombination, clonal expansion or the contortion of their nuclei. In turn, each of these processes relies on, or poses unique challenges to, a genome organized in three dimensions. Here, we explore the current understanding of the importance of 3D genome organization in the function and development of a healthy immune system.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Timeline of key conceptual and technological advances that have shaped our understanding of the structural aspects of gene regulation
Fig. 2: Antigen receptor loci recombination relies on changes in 3D genome organization.

Similar content being viewed by others

References

  1. Bulger, M. & Groudine, M. Looping versus linking: toward a model for long-distance gene activation. Genes Dev. 13, 2465–2477 (1999).

    CAS  PubMed  Google Scholar 

  2. 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). This study shows that DNA loops are important in the regulation of β-globin gene expression.

    CAS  PubMed  Google Scholar 

  3. Song, S.-H., Hou, C. & Dean, A. A positive role for NLI/Ldb1 in long range β-globin locus control region function. Mol. Cell 28, 810–822 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Drissen, R. et al. The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Genes Dev. 18, 2485–2490 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Vakoc, C. R. et al. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol. Cell 17, 453–462 (2005).

    CAS  PubMed  Google Scholar 

  6. Palstra, R. J. et al. The beta-globin nuclear compartment in development and erythroid differentiation. Nat. Genet. 35, 190–194 (2003).

    CAS  PubMed  Google Scholar 

  7. Splinter, E. et al. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev. 20, 2349–2354 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Chien, R. et al. Cohesin mediates chromatin interactions that regulate mammalian beta-globin expression. J. Biol. Chem. 286, 17870–17878 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002). This study reports the development of 3C to detect 3D genome organization.

    CAS  PubMed  Google Scholar 

  10. Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348–1354 (2006).

    CAS  PubMed  Google Scholar 

  11. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455–461 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458–472 (2012). Dixon et al. (2012), Nora et al. and Sexton et al. identify TADs, a common unit of genomic compartmentalization in mammals and Drosophila.

    CAS  PubMed  Google Scholar 

  18. Flavahan, W. A. et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature 529, 110–114 (2016).

    CAS  PubMed  Google Scholar 

  19. Lupianez, D. G. et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161, 1012–1025 (2015). This study demonstrates the importance of TAD boundaries in regulating promoter–enhancer interaction and health.

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Fuxa, M. et al. Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene. Genes Dev. 18, 411–422 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Lin, Y. C. et al. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat. Immunol. 13, 1196–1204 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Sen, R. Access guide to antigen receptor genes. J. Immunol. 199, 3 (2017).

    CAS  PubMed  Google Scholar 

  24. Ebert, A., Hill, L. & Busslinger, M. in Advances in Immunology Vol. 128 (ed. Murre, C.) 93–121 (Academic Press, 2015).

  25. Aiden, E. L. & Casellas, R. Somatic rearrangement in B cells: it’s (mostly) nuclear physics. Cell 162, 708–711 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Chaumeil, J. & Skok, J. A. The role of CTCF in regulating V(D)J recombination. Curr. Opin. Immunol. 24, 153–159 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Proudhon, C., Hao, B., Raviram, R., Chaumeil, J. & Skok, J. A. Long-range regulation of V(D)J recombination. Adv. Immunol. 128, 123–182 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Alt, F. W., Zhang, Y., Meng, F. L., Guo, C. & Schwer, B. Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell 152, 417–429 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Mombaerts, P. et al. RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68, 869–877 (1992).

    CAS  PubMed  Google Scholar 

  30. Shinkai, Y. et al. RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Cell 68, 855–867 (1992).

    CAS  PubMed  Google Scholar 

  31. Spanopoulou, E. et al. Functional immunoglobulin transgenes guide ordered B cell differentiation in Rag-1-deficient mice. Genes Dev. 8, 1030–1042 (1994).

    CAS  PubMed  Google Scholar 

  32. Kim, M.-S., Lapkouski, M., Yang, W. & Gellert, M. Crystal structure of the V(D)J recombinase RAG1–RAG2. Nature 518, 507 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Desiderio, S. Temporal and spatial regulatory functions of the V(D)J recombinase. Semin. Immunol. 22, 362–369 (2010).

    CAS  PubMed  Google Scholar 

  34. Helmink, B. A. & Sleckman, B. P. The response to and repair of RAG-mediated DNA double-strand breaks. Annu. Rev. Immunol. 30, 175–202 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Ji, Y. et al. The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci. Cell 141, 419–431 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Matthews, A. G. & Oettinger, M. A. RAG: a recombinase diversified. Nat. Immunol. 10, 817–821 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Puebla-Osorio, N. & Zhu, C. DNA damage and repair during lymphoid development: antigen receptor diversity, genomic integrity and lymphomagenesis. Immunol. Res. 41, 103–122 (2008).

    CAS  PubMed  Google Scholar 

  38. Jhunjhunwala, S., van Zelm, M. C., Peak, M. M. & Murre, C. Chromatin architecture and the generation of antigen receptor diversity. Cell 138, 435–448 (2009). This study uses imaging to show that the Igh locus forms two megabase domains and provides the first indication of the compartmentalization of antigen receptor loci.

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Montefiori, L. et al. Extremely long-range chromatin loops link topological domains to facilitate a diverse antibody repertoire. Cell Rep. 14, 896–906 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Kumari, G. & Sen, R. Chromatin interactions in the control of immunoglobulin heavy chain gene assembly. Adv. Immunol. 128, 41–92 (2015).

    CAS  PubMed  Google Scholar 

  41. Guo, C. et al. CTCF binding elements mediate control of V(D)J recombination. Nature 477, 424–430 (2011). This study identifies intergenic control region 1 within the Igh locus and its critical role in regulating recombination of the locus and thus antibody repertoire.

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Featherstone, K., Wood, A. L., Bowen, A. J. & Corcoran, A. E. The mouse immunoglobulin heavy chain V-D intergenic sequence contains insulators that may regulate ordered V(D)J recombination. J. Biol. Chem. 285, 9327–9338 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Hu, J. et al. Chromosomal loop domains direct the recombination of antigen receptor genes. Cell 163, 947–959 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Jain, S., Ba, Z., Zhang, Y., Dai, H. Q. & Alt, F. W. CTCF-binding elements mediate accessibility of RAG substrates during chromatin scanning. Cell 174, 102–116 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Narendra, V. et al. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science 347, 1017–1021 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Qiu, X. et al. Sequential enhancer sequestration dysregulates recombination center formation at the IgH locus. Mol. Cell 70, 21–33 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Dekker, J. & Mirny, L. The 3D genome as moderator of chromosomal communication. Cell 164, 1110–1121 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Dixon, J. R., Gorkin, D. U. & Ren, B. Chromatin domains: the unit of chromosome organization. Mol. Cell 62, 668–680 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Choi, N. M. et al. Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies. J. Immunol. 191, 2393–2402 (2013).

    CAS  PubMed  Google Scholar 

  50. Bolland, D. J. et al. Two mutually exclusive local chromatin states drive efficient V(D)J recombination. Cell Rep. 15, 2475–2487 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Zhao, L. et al. Orientation-specific RAG activity in chromosomal loop domains contributes to Tcrd V(D)J recombination during T cell development. J. Exp. Med. 213, 1921–1936 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Kosak, S. T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296, 158–162 (2002). This study provides the first evidence in mammals that gene activity is regulated by nuclear position and that Igh contracts in pro-B cells to facilitate V(D)J recombination.

    CAS  PubMed  Google Scholar 

  53. Roldan, E. et al. Locus ‘decontraction’ and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene. Nat. Immunol. 6, 31–41 (2005).

    CAS  PubMed  Google Scholar 

  54. Sayegh, C. E., Jhunjhunwala, S., Riblet, R. & Murre, C. Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells. Genes Dev. 19, 322–327 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Skok, J. A. et al. Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes. Nat. Immunol. 8, 378–387 (2007).

    CAS  PubMed  Google Scholar 

  56. Nutt, S. L., Urbanek, P., Rolink, A. & Busslinger, M. Essential functions of Pax5 (BSAP) in pro-B cell development: difference between fetal and adult B lymphopoiesis and reduced V-to-DJ recombination at the IgH locus. Genes Dev. 11, 476–491 (1997).

    CAS  PubMed  Google Scholar 

  57. Ebert, A. et al. The distal V(H) gene cluster of the Igh locus contains distinct regulatory elements with Pax5 transcription factor-dependent activity in pro-B cells. Immunity 34, 175–187 (2011).

    CAS  PubMed  Google Scholar 

  58. Medvedovic, J. et al. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire. Immunity 39, 229–244 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Verma-Gaur, J. et al. Noncoding transcription within the Igh distal V(H) region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells. Proc. Natl Acad. Sci. USA 109, 17004–17009 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Liu, H. et al. Yin Yang 1 is a critical regulator of B cell development. Genes Dev. 21, 1179–1189 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Pan, X. et al. YY1 controls Igκ repertoire and B cell development, and localizes with condensin on the Igκ locus. EMBO J. 32, 1168–1182 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Degner, S. C. et al. CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells. Proc. Natl Acad. Sci. USA 108, 9566–9571 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Barajas-Mora, E. M. et al. A B-cell-specific enhancer orchestrates nuclear architecture to generate a diverse antigen receptor repertoire. Mol. Cell 73, 48–60 (2019).

    CAS  PubMed  Google Scholar 

  64. Lin, S. G. et al. Highly sensitive and unbiased approach for elucidating antibody repertoires. Proc. Natl Acad. Sci. USA 113, 7846–7851 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Geyer, P. K., Vitalini, M. W. & Wallrath, L. L. Nuclear organization: taking a position on gene expression. Curr. Opin. Cell Biol. 23, 354–359 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Corcoran, L. et al. The lymphoid past of mouse plasmacytoid cells and thymic dendritic cells. J. Immunol. 170, 4926–4932 (2003).

    CAS  PubMed  Google Scholar 

  67. Kurosawa, Y. et al. Identification of D segments of immunoglobulin heavy-chain genes and their rearrangement in T lymphocytes. Nature 290, 565–570 (1981).

    CAS  PubMed  Google Scholar 

  68. Chaumeil, J. et al. The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage. Nat. Commun. 4, 2231 (2013).

    PubMed  Google Scholar 

  69. Vettermann, C. & Schlissel, M. S. Allelic exclusion of immunoglobulin genes: models and mechanisms. Immunol. Rev. 237, 22–42 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Corcoran, A. E. Immunoglobulin locus silencing and allelic exclusion. Semin. Immunol. 17, 141–154 (2005).

    CAS  PubMed  Google Scholar 

  71. Brady, B. L., Steinel, N. C. & Bassing, C. H. Antigen receptor allelic exclusion: an update and reappraisal. J. Immunol. 185, 3801–3808 (2010).

    CAS  PubMed  Google Scholar 

  72. Bergman, Y. & Cedar, H. A stepwise epigenetic process controls immunoglobulin allelic exclusion. Nat. Rev. Immunol. 4, 753–761 (2004).

    CAS  PubMed  Google Scholar 

  73. Levin-Klein, R. et al. Clonally stable Vkappa allelic choice instructs Igkappa repertoire. Nat. Commun. 8, 15575 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Chaumeil, J. et al. Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers. Cell Rep. 3, 359–370 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Hewitt, S. L. et al. Association between the Igk and Igh immunoglobulin loci mediated by the 3’ Igk enhancer induces ‘decontraction’ of the Igh locus in pre-B cells. Nat. Immunol. 9, 396–404 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Johanson, T. M. et al. Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development. PLOS Genet. 14, e1007431 (2018).

    PubMed  PubMed Central  Google Scholar 

  77. Belmont, A. S. Large-scale chromatin organization: the good, the surprising, and the still perplexing. Curr. Opin. Cell Biol. 26, 69–78 (2014).

    CAS  PubMed  Google Scholar 

  78. Fudenberg, G. & Imakaev, M. FISH-ing for captured contacts: towards reconciling FISH and 3C. Nat. Methods 14, 673–678 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Giorgetti, L. & Heard, E. Closing the loop: 3C versus DNA FISH. Genome Biol. 17, 215 (2016).

    PubMed  PubMed Central  Google Scholar 

  80. Williamson, I. et al. Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev. 28, 2778–2791 (2014).

    PubMed  PubMed Central  Google Scholar 

  81. Fraser, J., Williamson, I., Bickmore, W. A. & Dostie, J. An overview of genome organization and how we got there: from FISH to Hi-C. Microbiol. Mol. Biol. Rev. 79, 347–372 (2015).

    PubMed  PubMed Central  Google Scholar 

  82. Kaech, S. M., Wherry, E. J. & Ahmed, R. Effector and memory T cell differentiation: implications for vaccine development. Nat. Rev. Immunol. 2, 251 (2002).

    CAS  PubMed  Google Scholar 

  83. Brown, K. E., Baxter, J., Graf, D., Merkenschlager, M. & Fisher, A. G. Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol. Cell 3, 207–217 (1999). This study shows for the first time that resting lymphocytes reorganize loci nuclear position upon activation.

    CAS  PubMed  Google Scholar 

  84. Grogan, J. L. et al. Early transcription and silencing of cytokine genes underlie polarization of T helper cell subsets. Immunity 14, 205–215 (2001).

    CAS  PubMed  Google Scholar 

  85. Araki, Y. et al. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Immunity 30, 912–925 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Russ, Brendan,E. et al. Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8+ T cell differentiation. Immunity 41, 853–865 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Johanson, T. M. et al. Transcription-factor-mediated supervision of global genome architecture maintains B cell identity. Nat. Immunol. 19, 1257–1264 (2018).

    CAS  PubMed  Google Scholar 

  88. Kieffer-Kwon, K.-R. et al. Myc regulates chromatin decompaction and nuclear architecture during B cell activation. Mol. Cell 67, 566–578 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Hawkins, E. D., Markham, J. F., McGuinness, L. P. & Hodgkin, P. D. A single-cell pedigree analysis of alternative stochastic lymphocyte fates. Proc. Natl Acad. Sci. USA 106, 13457 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Kaech, S. M. & Ahmed, R. Memory CD8+ T cell differentiation: initial antigen encounter triggers a developmental program in naïve cells. Nat. Immunol. 2, 415 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Mercado, R. et al. Early programming of T cell populations responding to bacterial infection. J. Immunol. 165, 6833–6839 (2000).

    CAS  PubMed  Google Scholar 

  92. van Stipdonk, M. J. B., Lemmens, E. E. & Schoenberger, S. P. Naïve CTLs require a single brief period of antigenic stimulation for clonal expansion and differentiation. Nat. Immunol. 2, 423 (2001).

    PubMed  Google Scholar 

  93. Bevan, M. J. & Fink, P. J. The CD8 response on autopilot. Nat. Immunol. 2, 381 (2001).

    CAS  PubMed  Google Scholar 

  94. Veiga-Fernandes, H., Walter, U., Bourgeois, C., McLean, A. & Rocha, B. Response of naïve and memory CD8+ T cells to antigen stimulation in vivo. Nat. Immunol. 1, 47 (2000).

    CAS  PubMed  Google Scholar 

  95. Weisel, F. & Shlomchik, M. Memory B cells of mice and humans. Annu. Rev. Immunol. 35, 255–284 (2017).

    CAS  PubMed  Google Scholar 

  96. Hoffmann, K., Sperling, K., Olins, A. L. & Olins, D. E. The granulocyte nucleus and lamin B receptor: avoiding the ovoid. Chromosoma 116, 227–235 (2007).

    CAS  PubMed  Google Scholar 

  97. Skinner, B. M. & Johnson, E. E. Nuclear morphologies: their diversity and functional relevance. Chromosoma 126, 195–212 (2017).

    PubMed  Google Scholar 

  98. Gaines, P. et al. Mouse neutrophils lacking lamin B-receptor expression exhibit aberrant development and lack critical functional responses. Exp. Hematol. 36, 965–976 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Rowat, A. C. et al. Nuclear envelope composition determines the ability of neutrophil-type cells to passage through micron-scale constrictions. J. Biol. Chem. 288, 8610–8618 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. McGregor, A. L., Hsia, C. R. & Lammerding, J. Squish and squeeze-the nucleus as a physical barrier during migration in confined environments. Curr. Opin. Cell Biol. 40, 32–40 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Lamborot-Manzur, M. & Tishler, P. V. Fluorescent drumsticks in male polymorphs. Lancet 1, 973–974 (1971).

    CAS  PubMed  Google Scholar 

  102. Karni, R. J., Wangh, L. J. & Sanchez, J. A. Nonrandom location and orientation of the inactive X chromosome in human neutrophil nuclei. Chromosoma 110, 267–274 (2001).

    CAS  PubMed  Google Scholar 

  103. Hochstenbach, P. F., Scheres, J. M., Hustinx, T. W. & Wieringa, B. Demonstration of X chromatin in drumstick-like nuclear appendages of leukocytes by in situ hybridization on blood smears. Histochemistry 84, 383–386 (1986).

    CAS  PubMed  Google Scholar 

  104. Aquiles Sanchez, J., Karni, R. J. & Wangh, L. J. Fluorescent in situ hybridization (FISH) analysis of the relationship between chromosome location and nuclear morphology in human neutrophils. Chromosoma 106, 168–177 (1997).

    CAS  PubMed  Google Scholar 

  105. Zhu, Y. et al. Comprehensive characterization of neutrophil genome topology. Genes Dev. 31, 141–153 (2017). This study provides the first genome-wide examination of the impact of nuclear lobing on genome organization.

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F. & Chen, L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat. Biotechnol. 30, 90 (2011).

    PubMed  PubMed Central  Google Scholar 

  107. Javierre, B. M. et al. Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell 167, 1369–1384 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. Cusanovich, D. A. et al. A single-cell atlas of in vivo mammalian chromatin accessibility. Cell 174, 1309–1324 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Hedlund, E. & Deng, Q. Single-cell RNA sequencing: technical advancements and biological applications. Mol. Aspects Med. 59, 36–46 (2018).

    CAS  PubMed  Google Scholar 

  110. Stevens, T. J. et al. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature 544, 59–64 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. Klein, J. C., Chen, W., Gasperini, M. & Shendure, J. Identifying novel enhancer elements with CRISPR-based screens. ACS Chem. Biol. 13, 326–332 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Fulco, C. P. et al. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science 354, 769–773 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. Isoda, T. et al. Non-coding transcription instructs chromatin folding and compartmentalization to dictate enhancer-promoter communication and T cell fate. Cell 171, 103–119 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. Morgan, S. L. et al. Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping. Nat. Commun. 8, 15993 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. Wang, H. et al. CRISPR-mediated programmable 3D genome positioning and nuclear organization. Cell 175, 1405–1417 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. Pflueger, C. et al. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Res. 28, 1193–1206 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Vian, L. et al. The energetics and physiological impact of cohesin extrusion. Cell 173, 1165–1178 (2018). This study describes the model of asymmetric loop extrusion, explaining how cohesin complexes efficiently scan vast genomic distances.

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Ciosk, R. et al. Cohesin’s binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins. Mol. Cell 5, 243–254 (2000).

    CAS  PubMed  Google Scholar 

  119. Vietri Rudan, M. et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep. 10, 1297–1309 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. Hu, G. et al. Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells. Immunity 48, 227–242 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  121. Beagan, J. A. et al. YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Genome Res. 27, 1139–1152 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Donohoe, M. E., Zhang, L. F., Xu, N., Shi, Y. & Lee, J. T. Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. Mol. Cell 25, 43–56 (2007).

    CAS  PubMed  Google Scholar 

  123. Mehra, P. et al. YY1 controls Emu-3’RR DNA loop formation and immunoglobulin heavy chain class switch recombination. Blood Adv. 1, 15–20 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Bronstein, I. et al. Transient anomalous diffusion of telomeres in the nucleus of mammalian cells. Phys. Rev. Lett. 103, 018102 (2009).

    CAS  PubMed  Google Scholar 

  125. Lucas, J. S., Zhang, Y., Dudko, O. K. & Murre, C. 3D trajectories adopted by coding and regulatory DNA elements: first-passage times for genomic interactions. Cell 158, 339–352 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. Hajjoul, H. et al. High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome. Genome Res. 23, 1829–1838 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  127. Lutz, E. Fractional Langevin equation. Phys. Rev. E 64, 051106 (2001).

    CAS  Google Scholar 

  128. Miescher, F. Ueber die chemische Zusammensetzung der Eiterzellen. Hoppe Seyler Med. Chem. Unters. 4, 441–460 (1871).

    Google Scholar 

  129. Flemming, W. Zellsubstanz, Kern und Zelltheilung (F.C.W. Vogel, Leipzig, 1882).

  130. Waldeyer, W. Über Karyokinese und ihre Beziehung zu den Befruchtungsvorgängen. Arch. Mikrosk. Anat. 32, 1–122 (1888).

    Google Scholar 

  131. Boveri, T. Die Blastomerenkerne von Ascaris megalocephala und die Theorie der Chromosomenindividualität. Arch. Zellforsch. 3, 181–268 (1909).

    Google Scholar 

  132. Franklin, R. E. & Gosling, R. G. Molecular configuration in sodium thymonucleate. Nature 171, 740–741 (1953).

    CAS  PubMed  Google Scholar 

  133. Watson, J. D. & Crick, F. H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953).

    CAS  PubMed  Google Scholar 

  134. Wilkins, M. H., Stokes, A. R. & Wilson, H. R. Molecular structure of deoxypentose nucleic acids. Nature 171, 738–740 (1953).

    CAS  PubMed  Google Scholar 

  135. Gall, J. G. & Pardue, M. L. Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc. Natl Acad. Sci. USA 63, 378–383 (1969).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. John, H. A., Birnstiel, M. L. & Jones, K. W. RNA-DNA hybrids at the cytological level. Nature 223, 582–587 (1969).

    CAS  PubMed  Google Scholar 

  137. Kornberg, R. D. Chromatin structure: a repeating unit of histones and DNA. Science 184, 868–871 (1974).

    CAS  PubMed  Google Scholar 

  138. Kornberg, R. D. & Thomas, J. O. Chromatin structure: oligomers of the histones. Science 184, 865–868 (1974).

    CAS  PubMed  Google Scholar 

  139. Olins, A. L. & Olins, D. E. Spheroid chromatin units (v bodies). Science 183, 330–332 (1974).

    CAS  PubMed  Google Scholar 

  140. Stack, S. M., Brown, D. B. & Dewey, W. C. Visualization of interphase chromosomes. J. Cell Sci. 26, 281–299 (1977).

    CAS  PubMed  Google Scholar 

  141. Banerji, J., Rusconi, S. & Schaffner, W. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell 27, 299–308 (1981).

    CAS  PubMed  Google Scholar 

  142. Moreau, P. et al. The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. Nucleic Acids Res. 9, 6047–6068 (1981).

    CAS  PubMed  PubMed Central  Google Scholar 

  143. Langer-Safer, P. R., Levine, M. & Ward, D. C. Immunological method for mapping genes on Drosophila polytene chromosomes. Proc. Natl Acad. Sci. USA 79, 4381–4385 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  144. Mukherjee, S., Erickson, H. & Bastia, D. Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. Cell 52, 375–383 (1988).

    CAS  PubMed  Google Scholar 

  145. Cullen, K. E., Kladde, M. P. & Seyfred, M. A. Interaction between transcription regulatory regions of prolactin chromatin. Science 261, 203–206 (1993).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors thank S. Nutt, A. Johanson, N. Alpern and H. Batterham for constructive discussion. This work was supported by grants and fellowships from the National Health and Medical Research Council (NHMRC) of Australia (R.S.A.: #1049307 and #1100451; T.M.J.: #1124081; and C.R.K.: #1125436) and the Australian Research Council (R.S.A.: #130100541). This study was made possible through the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institute Infrastructure Support scheme.

Author information

Authors and Affiliations

Authors

Contributions

The authors contributed equally to all aspects of the article.

Corresponding authors

Correspondence to Timothy M. Johanson or Rhys S. Allan.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Glossary

Recombination centre

A complex containing recombination activating gene 1 (RAG1) and RAG2 that binds to, digests and facilitates repair of antigen receptor loci DNA during recombination.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Johanson, T.M., Chan, W.F., Keenan, C.R. et al. Genome organization in immune cells: unique challenges. Nat Rev Immunol 19, 448–456 (2019). https://doi.org/10.1038/s41577-019-0155-2

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41577-019-0155-2

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing