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.

  • Perspective
  • Published:

Engineering three-dimensional genome folding

Nature Genetics volume 53, pages 602–611 (2021)Cite this article

Subjects

Abstract

Animal genomes are partitioned and folded at various scales that contribute distinctly to nuclear processes. While structural features have been disrupted either globally or at select loci in loss-of-function studies, gain-of-function studies that probe the role of genome architecture have lagged behind. Here we examine recent advances in experimentally creating chromatin loops, contact domains, boundaries and compartments. Furthermore, we explore parallels between this emerging theme and natural evolution of mammalian genomes with increasing architectural complexity. Finally, we provide a perspective on how insights arising from recent gain-of-function studies may inform future endeavors toward engineering the three-dimensional genome.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Fig. 1: Hi-C maps reveal features of 3D genome organization.
Fig. 2: Engineering enhancer–promoter loops.
Fig. 3: Engineering contact domains and compartments.
Fig. 4: Future scalability of gain-of-function studies.

Similar content being viewed by others

References

  1. 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 

  2. Casolari, J. M. et al. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117, 427–439 (2004).

    Article  CAS  PubMed  Google Scholar 

  3. Németh, A. et al. Initial genomics of the human nucleolus. PLoS Genet. 6, e1000889 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Wijchers, P. J. et al. Characterization and dynamics of pericentromere-associated domains in mice. Genome Res. 25, 958–969 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. 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 

  6. 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  Google Scholar 

  7. 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 

  8. 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 

  9. Andrulis, E. D., Neiman, A. M., Zappulla, D. C. & Sternglanz, R. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394, 592–595 (1998).

    Article  CAS  PubMed  Google Scholar 

  10. Therizols, P. et al. Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells. Science 346, 1238–1242 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Clowney, E. J. et al. Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 151, 724–737 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Jachowicz, J. W., Santenard, A., Bender, A., Muller, J. & Torres-Padilla, M. Heterochromatin establishment at pericentromeres depends on nuclear position. Genes Dev. 27, 2427–2432 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Rao, S. S. P. 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 

  16. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002).

    Article  CAS  PubMed  Google Scholar 

  17. Kempfer, R. & Pombo, A. Methods for mapping 3D chromosome architecture. Nat. Rev. Genet. 21, 207–226 (2020).

    Article  CAS  PubMed  Google Scholar 

  18. Tjalsma, S. J. & de Laat, W. Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture. Curr. Opin. Genet. Dev. 67, 10–17 (2020).

    Article  PubMed  Google Scholar 

  19. 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 

  20. 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 

  21. Bonev, B. & Cavalli, G. Organization and function of the 3D genome. Nat. Rev. Genet. 17, 661–678 (2016).

    Article  CAS  PubMed  Google Scholar 

  22. Sanborn, A. L. et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc. Natl Acad. Sci. USA 112, E6456–E6465 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Fudenberg, G. et al. Formation of chromosomal domains by loop extrusion. Cell Rep. 15, 2038–2049 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. de Wit, E. et al. CTCF binding polarity determines chromatin looping. Mol. Cell 60, 676–684 (2015).

    Article  PubMed  Google Scholar 

  25. Guo, Y. et al. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell 162, 900–910 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Rowley, M. J. & Corces, V. G. Organizational principles of 3D genome architecture. Nat. Rev. Genet. 19, 789–800 (2018).

    Article  CAS  PubMed  Google Scholar 

  27. Vermunt, M. W., Zhang, D. & Blobel, G. A. The interdependence of gene-regulatory elements and the 3D genome. J. Cell Biol. 218, 12–26 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Beagan, J. A. & Phillips-Cremins, J. E. On the existence and functionality of topologically associating domains. Nat. Genet. 52, 8–16 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Lupiáñez, D. et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene–enhancer interactions. Cell 161, 1012–1025 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  30. 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 

  31. Hnisz, D. et al. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science 351, 1454–1458 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  33. Symmons, O. et al. The Shh topological domain facilitates the action of remote enhancers by reducing the effects of genomic distances. Dev. Cell 39, 529–543 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. van Bemmel, J. G. et al. The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist. Nat. Genet. 51, 1024–1034 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Despang, A. et al. Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture. Nat. Genet. 51, 1263–1271 (2019).

    Article  CAS  PubMed  Google Scholar 

  36. Choudhary, M. N. et al. Co-opted transposons help perpetuate conserved higher-order chromosomal structures. Genome Biol. 21, 16 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Rao, S. S. P. et al. Cohesin loss eliminates all loop domains. Cell 171, 305–320 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Schwarzer, W. et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature 551, 51–56 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Rowley, M. J. et al. Evolutionarily conserved principles predict 3D chromatin organization. Mol. Cell 67, 837–852 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Nora, E. P. et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169, 930–944 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Wutz, G. et al. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 36, 3573–3599 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Thiecke, M. J. et al. Cohesin-dependent and -independent mechanisms mediate chromosomal contacts between promoters and enhancers. Cell Rep. 32, 107929 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Gassler, J. et al. A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. EMBO J. 36, 3600–3618 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Haarhuis, J. H. I. et al. The cohesin release factor WAPL restricts chromatin loop extension. Cell 169, 693–707 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Anderson, E. C. & Nora, E. P. Setting new boundaries with transcription and CTCF. Nat. Genet. 52, 1003–1004 (2020).

    Article  PubMed  Google Scholar 

  46. Hug, C. B., Grimaldi, A. G., Kruse, K. & Vaquerizas, J. M. Chromatin architecture emerges during zygotic genome activation independent of transcription. Cell 169, 216–228 (2017).

    Article  CAS  PubMed  Google Scholar 

  47. Li, L. et al. Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing. Mol. Cell 58, 216–231 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Barutcu, A. R., Blencowe, B. J. & Rinn, J. L. Differential contribution of steady‐state RNA and active transcription in chromatin organization. EMBO Rep. 20, e48068 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Ke, Y. et al. 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Cell 170, 367–381 (2017).

    Article  CAS  PubMed  Google Scholar 

  50. Jiang, Y. et al. Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III. Genome Biol. 21, 158 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Rowley, M. J. & Corces, V. G. Organizational principles of 3D genome architecture. Nat. Rev. Genet. 19, 789–800 (2018).

    Article  CAS  PubMed  Google Scholar 

  52. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Saldaña-Meyer, R. et al. RNA interactions are essential for CTCF-mediated genome organization. Mol. Cell 76, 412–422 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  54. Mayer, A. et al. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell 161, 541–554 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Luan, J. et al. Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Cell Rep. 34, 108783 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Busslinger, G. A. et al. Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl. Nature 544, 503–507 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Heinz, S. et al. Transcription elongation can affect genome 3D structure. Cell 174, 1522–1536 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Leidescher, S. et al. Spatial organization of transcribed eukaryotic genes. Preprint at bioRxiv https://doi.org/10.1101/2020.05.20.106591 (2020).

  59. van Steensel, B. & Furlong, E. E. M. The role of transcription in shaping the spatial organisation of the genome. Nat. Rev. Mol. Cell Biol. 20, 327–337 (2019).

    PubMed  PubMed Central  Google Scholar 

  60. Schoenfelder, S. & Fraser, P. Long-range enhancer–promoter contacts in gene expression control. Nat. Rev. Genet. 20, 437–455 (2019).

    Article  CAS  PubMed  Google Scholar 

  61. Vernimmen, D., Gobbi, M. D., 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Deng, W. & Blobel, G. A. Manipulating nuclear architecture. Curr. Opin. Genet. Dev. 25, 1–7 (2014).

    Article  CAS  PubMed  Google Scholar 

  64. Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290–294 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Spilianakis, C. G. & Flavell, R. A. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat. Immunol. 5, 1017–1027 (2004).

    Article  CAS  PubMed  Google Scholar 

  66. Stik, G. et al. CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response. Nat. Genet. 52, 655–661 (2020).

    Article  CAS  PubMed  Google Scholar 

  67. Kubo, N. et al. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat. Struct. Mol. Biol. 28, 152–161 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Zhang, H. et al. Chromatin structure dynamics during the mitosis-to-G1 phase transition. Nature 576, 158–162 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Benabdallah, N. S. et al. Decreased enhancer–promoter proximity accompanying enhancer activation. Mol. Cell 76, 473–484 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Alexander, J. M. et al. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 8, e41769 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  71. Hay, D. et al. Genetic dissection of the α-globin super-enhancer in vivo. Nat. Genet. 48, 895–903 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Bender, M. A. et al. The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation. Blood 119, 3820–3827 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Allahyar, A. et al. Enhancer hubs and loop collisions identified from single-allele topologies. Nat. Genet. 50, 1151–1160 (2018).

    Article  CAS  PubMed  Google Scholar 

  74. Oudelaar, A. M. et al. A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus. Nat. Commun. 10, 5412 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  75. Bartman, C. R., Hsu, S. C., Hsiung, C. C.-, Raj, A. & Blobel, G. A. Enhancer regulation of transcriptional bursting parameters revealed by forced chromatin looping. Mol. Cell 62, 237–247 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Cho, S. W. et al. Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element. Cell 173, 1398–1412 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Foley, K. P. & Engel, J. D. Individual stage selector element mutations lead to reciprocal changes in β- vs. ε-globin gene transcription: genetic confirmation of promoter competition during globin gene switching. Genes Dev. 6, 730–744 (1992).

    Article  CAS  PubMed  Google Scholar 

  78. Nolis, I. K. et al. Transcription factors mediate long-range enhancer–promoter interactions. Proc. Natl Acad. Sci. USA 106, 20222–20227 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Song, S., 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Deng, W. et al. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell 158, 849–860 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Cajiao, I., Zhang, A., Yoo, E. J., Cooke, N. E. & Liebhaber, S. A. Bystander gene activation by a locus control region. EMBO J. 23, 3854–3863 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Chen, H. et al. Dynamic interplay between enhancer–promoter topology and gene activity. Nat. Genet. 50, 1296–1303 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Williamson, I., Lettice, L. A., Hill, R. E. & Bickmore, W. A. Shh and ZRS enhancer colocalisation is specific to the zone of polarising activity. Development 143, 2994–3001 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Finn, E. H. & Misteli, T. Molecular basis and biological function of variability in spatial genome organization. Science 365, eaaw9498 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Bartolomei, M. S. Genomic imprinting: employing and avoiding epigenetic processes. Genes Dev. 23, 2124–2133 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Hou, C., Zhao, H., Tanimoto, K. & Dean, A. CTCF-dependent enhancer-blocking by alternative chromatin loop formation. Proc. Natl Acad. Sci. USA 105, 20398–20403 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Melamed, A. et al. The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis. eLife 7, e36245 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  89. Redolfi, J. et al. DamC reveals principles of chromatin folding in vivo without crosslinking and ligation. Nat. Struct. Mol. Biol. 26, 471–480 (2019).

  90. Zhang, D. et al. Alteration of genome folding via contact domain boundary insertion. Nat. Genet. 52, 1076–1087 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Froberg, J. E., Pinter, S. F., Kriz, A. J., Jégu, T. & Lee, J. T. Megadomains and superloops form dynamically but are dispensable for X-chromosome inactivation and gene escape. Nat. Commun. 9, 5004 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  92. Rawat, P., Jalan, M., Sadhu, A., Kanaujia, A. & Srivastava, M. Chromatin domain organization of the TCRb locus and its perturbation by ectopic CTCF binding. Mol. Cell. Biol. 37, e00557-16 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  93. Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR–Cas system. Nucleic Acids Res. 41, 7429–7437 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Hao, N., Shearwin, K. E. & Dodd, I. B. Programmable DNA looping using engineered bivalent dCas9 complexes. Nat. Commun. 8, 1628 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  96. Kim, J. H. et al. LADL: light-activated dynamic looping for endogenous gene expression control. Nat. Methods 16, 633–639 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  97. Hao, N., Shearwin, K. E. & Dodd, I. B. Positive and negative control of enhancer–promoter interactions by other DNA loops generates specificity and tunability. Cell Rep. 26, 2419–2433 (2019).

    Article  CAS  PubMed  Google Scholar 

  98. Geyer, P. K. The role of insulator elements in defining domains of gene expression. Curr. Opin. Genet. Dev. 7, 242–248 (1997).

    Article  CAS  PubMed  Google Scholar 

  99. Choi, O. R. & Engel, J. D. Developmental regulation of β-globin gene switching. Cell 55, 17–26 (1988).

    Article  CAS  PubMed  Google Scholar 

  100. Fukaya, T., Lim, B. & Levine, M. Enhancer control of transcriptional bursting. Cell 166, 358–368 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Franke, M. et al. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature 538, 265–269 (2016).

    Article  CAS  PubMed  Google Scholar 

  102. Dekker, J. et al. The 4D nucleome project. Nature 549, 219–226 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Barutcu, A. R., Maass, P. G., Lewandowski, J. P., Weiner, C. L. & Rinn, J. L. A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nat. Commun. 9, 1444 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  104. Anderson, E. C. et al. X chromosome domain architecture regulates Caenorhabditis elegans lifespan but not dosage compensation. Dev. Cell 51, 192–207 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Zhang, Y. et al. Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat. Genet. 51, 1380–1388 (2019).

  106. Kruse, K. et al. Transposable elements drive reorganisation of 3D chromatin during early embryogenesis. Preprint at bioRxiv, https://doi.org/10.1101/523712 (2019).

  107. Vian, L. et al. The energetics and physiological impact of cohesin extrusion. Cell 173, 1165–1178 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Krietenstein, N. et al. Ultrastructural details of mammalian chromosome architecture. Mol. Cell 78, 554–565 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Hsieh, T. S. et al. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Mol. Cell 78, 539–553 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Diehl, A. G., Ouyang, N. & Boyle, A. P. Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nat. Commun. 11, 1796 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Schmidt, D. et al. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148, 335–348 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Sundaram, V. et al. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 24, 1963–1976 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Kentepozidou, E. et al. Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. Genome Biol. 21, 5 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  115. Kaaij, L. J. T., Mohn, F., van der Weide, R. H., de Wit, E. & Bühler, M. The ChAHP complex counteracts chromatin looping at CTCF sites that emerged from SINE expansions in mouse. Cell 178, 1437–1451 (2019).

    Article  CAS  PubMed  Google Scholar 

  116. Smith, C. J. et al. Enabling large-scale genome editing at repetitive elements by reducing DNA nicking. Nucleic Acids Res. 48, 5183–5195 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Ivics, Z., Hackett, P. B., Plasterk, R. H. & Izsvák, Z. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91, 501–510 (1997).

    Article  CAS  PubMed  Google Scholar 

  118. Cary, L. C. et al. Transposon mutagenesis of baculoviruses: analysis of Trichoplusia ni transposon IFP2 insertions within the FP-locus of nuclear polyhedrosis viruses. Virology 172, 156–169 (1989).

    Article  CAS  PubMed  Google Scholar 

  119. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Ruf, S. et al. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat. Genet. 43, 379–386 (2011).

    Article  CAS  PubMed  Google Scholar 

  122. Fanucchi, S., Shibayama, Y., Burd, S., Weinberg, M. S. & Mhlanga, M. M. Chromosomal contact permits transcription between coregulated genes. Cell 155, 606–620 (2013).

    Article  CAS  PubMed  Google Scholar 

  123. Feng, Y. et al. Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. Genome Biol. 21, 296 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Nagano, T. et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59–64 (2013).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Nagano, T. et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547, 61–67 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Flyamer, I. M. et al. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature 544, 110–114 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Ramani, V. et al. Massively multiplex single-cell Hi-C. Nat. Methods 14, 263–266 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Wang, S. et al. Spatial organization of chromatin domains and compartments in single chromosomes. Science 353, 598–602 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Nguyen, H. Q. et al. 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. Nat. Methods 17, 822–832 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Su, J., Zheng, P., Kinrot, S. S., Bintu, B. & Zhuang, X. Genome-scale imaging of the 3D organization and transcriptional activity of chromatin. Cell 182, 1641–1659 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Levo, M. & Segal, E. In pursuit of design principles of regulatory sequences. Nat. Rev. Genet. 15, 453–468 (2014).

    Article  CAS  PubMed  Google Scholar 

  134. Akhtar, W. et al. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 154, 914–927 (2013).

    Article  CAS  PubMed  Google Scholar 

  135. Senior, A. W. et al. Improved protein structure prediction using potentials from deep learning. Nature 577, 706–710 (2020).

    Article  CAS  PubMed  Google Scholar 

  136. Fudenberg, G., Kelley, D. R. & Pollard, K. S. Predicting 3D genome folding from DNA sequence with Akita. Nat. Methods 17, 1111–1117 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  137. Schwessinger, R. et al. DeepC: predicting 3D genome folding using megabase-scale transfer learning. Nat. Methods 17, 1118–1124 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Mercy, G. et al. 3D organization of synthetic and scrambled chromosomes. Science 355, eaaf4597 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  139. Ghavi-Helm, Y. et al. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nat. Genet. 51, 1272–1282 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Boeke, J. D. et al. The Genome Project-Write. Science 353, 126–127 (2016).

    Article  CAS  PubMed  Google Scholar 

  141. Ganji, M. et al. Real-time imaging of DNA loop extrusion by condensin. Science 360, 102–105 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Kim, Y., Shi, Z., Zhang, H., Finkelstein, I. J. & Yu, H. Human cohesin compacts DNA by loop extrusion. Science 366, 1345–1349 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Davidson, I. F. et al. DNA loop extrusion by human cohesin. Science 366, 1338–1345 (2019).

    Article  CAS  PubMed  Google Scholar 

  144. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article  CAS  PubMed  Google Scholar 

  145. Huang, P. et al. Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. Genes Dev. 31, 1704–1713 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Luo, H. et al. CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia. Blood 132, 837–848 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Wienert, B. et al. Editing the genome to introduce a beneficial naturally occurring mutation associated with increased fetal globin. Nat. Commun. 6, 7085 (2015).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank members of the Blobel laboratory for helpful discussions. This research was supported by grants R01DK054937 and U01HL129998A to G.A.B. and by the Spatial and Functional Genomics program at the Children’s Hospital of Philadelphia.

Author information

Authors and Affiliations

  1. Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Di Zhang, Jessica Lam & Gerd A. Blobel

  2. Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Di Zhang, Jessica Lam & Gerd A. Blobel

Authors
  1. Di Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jessica Lam
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gerd A. Blobel
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

D.Z., J.L. and G.A.B. wrote the paper.

Corresponding author

Correspondence to Gerd A. Blobel.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Genetics thanks Elphège Nora, Stefan Mundlos and Bing Ren for their contribution to the peer review of this work.

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

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhang, D., Lam, J. & Blobel, G.A. Engineering three-dimensional genome folding. Nat Genet 53, 602–611 (2021). https://doi.org/10.1038/s41588-021-00860-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41588-021-00860-9

This article is cited by

Search

Advanced 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