Shaping Up the Embryo: The Role of Genome 3D Organization

  • Karina Jácome-López
  • Mayra Furlan-Magaril
Part of the Methods in Molecular Biology book series (MIMB, volume 1752)


The spatial organization of the chromatinized genome inside the cell nucleus impacts genomic function. In transcription, the hierarchical genome structure creates spatial regulatory landscapes, in which modulating elements like enhancers can contact their target genes and activate their expression, as a result of restricting their exploration to a specific topological neighbourhood. Here we describe exciting recent findings obtained through “C” technologies in pluripotent cells and early embryogenesis and emphasize some of the key unanswered questions arising from them.

Key words

Genome 3D organization Topologically associated domains Boundary Enhancer Chromatin Chromosome conformation capture Embryonic stem cells 



This work was funded by the Technology Innovation and Research Support Programme (PAPIIT) num. IA201817.


  1. 1.
    Jost KL, Bertulat B, Cardoso MC (2012) Heterochromatin and gene positioning: Inside, outside, any side? Chromosoma 121:555–563. CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Denker A, De Laat W (2016) The second decade of 3C technologies: detailed insights into nuclear organization. Genes Dev 30:1357–1382. CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Bolzer A, Kreth G, Solovei I et al (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3:0826–0842. CrossRefGoogle Scholar
  4. 4.
    Fraser J, Ferrai C, Chiariello AM et al (2015) Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Mol Syst Biol 11:1–14. CrossRefGoogle Scholar
  5. 5.
    Dekker J (2006) The three “C” s of chromosome conformation capture: controls, controls, controls. Nat Methods 3:17–21. CrossRefPubMedGoogle Scholar
  6. 6.
    Brant L, Georgomanolis T, Nikolic M et al (2016) Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Mol Syst Biol 561:1–23. Google Scholar
  7. 7.
    Simonis M, Klous P, Splinter E et al (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348–1354. CrossRefPubMedGoogle Scholar
  8. 8.
    Schwartzman O, Mukamel Z, Oded-Elkayam N et al (2016) UMI-4C for quantitative and targeted chromosomal contact profiling. Nat Methods 13:685–691. CrossRefPubMedGoogle Scholar
  9. 9.
    Ghavi-Helm Y, Klein FA, Pakozdi T et al (2014) Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512:96–100. CrossRefPubMedGoogle Scholar
  10. 10.
    Nora EP, Lajoie BR, Schulz EG et al (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485:381–385. CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Dostie J, Richmond TA, Arnaout RA et al (2006) Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16:1299–1309. CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Lieberman-Aiden E, vand Berkum N (2009) Comprehensive mapping of long range interactions reveals folding principles of the human genome. Science 326:289–293. CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Hughes JR, Roberts N, McGowan S et al (2014) Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 46:205–212. CrossRefPubMedGoogle Scholar
  14. 14.
    Schoenfelder S, Sugar R, Dimond A et al (2015) Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome. Nat Genet 47:1179–1186. CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Mifsud B, Tavares-Cadete F, Young AN et al (2015) Sup mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet 47:598–606. CrossRefPubMedGoogle Scholar
  16. 16.
    Nagano T, Lubling Y, Stevens TJ et al (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502:59–64. CrossRefPubMedGoogle Scholar
  17. 17.
    Nagano T, Lubling Y, Varnai C et al (2017) Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547: 61–67.
  18. 18.
    Stevens TJ, Lando D, Basu S et al (2017) 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature 544:59–64. CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Flyamer IM, Gassler J, Imakaev M et al (2017) Single-cell Hi-C reveals unique chromatin reorganization at oocyte-tozygote transition. Nat Publ Gr 544:1–17. Google Scholar
  20. 20.
    Fullwood MJ, Liu MH, Pan YF et al (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58–64. CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Mumbach MR, Rubin AJ, Flynn RA et al (2016) HiChIP: efficient and sensitive analysis of protein-directed genome architecture. bioRxiv:73619.
  22. 22.
    Dixon JR, Selvaraj S, Yue F et al (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376–380. CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Nora EP, Lajoie BR, Schulz EG et al (2013) Spatial partitioning of the regulatory landscape of the X- inactivation center. Nature 485:381–385. CrossRefGoogle Scholar
  24. 24.
    Sexton T, Yaffe E, Kenigsberg E et al (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148:458–472. CrossRefPubMedGoogle Scholar
  25. 25.
    Mizuguchi T, Fudenberg G, Mehta S et al (2014) Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature 516:432–435. CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Crane E, Bian Q, Mccord RP et al (2015) Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature.
  27. 27.
    Le TBK, Imakaev MV, Mirny LA, Laub MT (2013) High-resolution mapping of the spatial organization of a bacterial chromosome. Science 342:731–735CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Rao SSP, Huntley MH, Durand NC et al (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665–1680. CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Nora EP, Goloborodko A, Valton AL et al (2017) Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization. Cell 169:930-944e.22. Google Scholar
  30. 30.
    Eagen K, Lieberman Aiden E, Kornberg DR (2017) Polycomb-mediated chromatin loops revealed by a sub-kilobase resolution chromatin interaction map. bioRxiv.
  31. 31.
    Melcer S, Meshorer E (2010) Chromatin plasticity and genome organization in pluripotent embryonic stem cells. Curr Opin Cell Biol 22:334–341. CrossRefGoogle Scholar
  32. 32.
    Meshorer E, Yellajoshula D, George E et al (2006) Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev Cell 10:105–116. CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Gaspar-Maia A, Alajem A, Meshorer E, Ramalho-Santos M (2011) Open chromatin in pluripotency and reprogramming. Nat Rev Mol Cell Biol 12:36–47. CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Zhu J, Adli M, Zou JY et al (2013) Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152:642–654. CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Ficz G, Heintzmann R, Arndt-Jovin DJ (2005) Polycomb group protein complexes exchange rapidly in living Drosophila. Development 132:3963–3976. CrossRefPubMedGoogle Scholar
  36. 36.
    Ren X, Vincenz C, Kerppola TK (2008) Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation. Mol Cell Biol 28:2884–2895. CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Denholtz M, Bonora G, Chronis C et al (2013) Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell 13:602–616. CrossRefPubMedGoogle Scholar
  38. 38.
    Kundu S, Ji F, Sunwoo H et al (2017) Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Mol Cell 65:432–445.e6.
  39. 39.
    Richly H, Aloia L, Di Croce L (2011) Roles of the polycomb group proteins in stem cells and cancer. Cell Death Dis 2:e204. CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Wang W, Quin J-J, Voruganti S et al (2015) Polycomb Group (PcG) proteins and human cancers: multifaceted functions and therapeutic implications. Med Res Rev 22:134–139. Google Scholar
  41. 41.
    Yamanaka S, Blau HM (2010) Nuclear reprogramming to a pluripotent state by three approaches. Nature 465:704–712. CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Whyte WA, Orlando DA, Hnisz D et al (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153:307–319. CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Li Y, Rivera CM, Ishii H et al (2014) CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. PLoS One 9:1–17. Google Scholar
  44. 44.
    de Wit E, Bouwman BA, Zhu Y et al (2013) The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature 501:227–231. CrossRefPubMedGoogle Scholar
  45. 45.
    Wei Z, Gao F, Kim S et al (2013) Klf4 organizes long-range chromosomal interactions with the OCT4 locus inreprogramming andpluripotency. Cell Stem Cell 13:36–47. CrossRefPubMedGoogle Scholar
  46. 46.
    Monahan K, Rudnick ND, Kehayova PD et al (2012) Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-α gene expression. Proc Natl Acad Sci U S A 109:9125–9130. CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Zuin J, Dixon JR, van der Reijden MIJA et al (2014) Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci U S A 111:996–1001. CrossRefPubMedGoogle Scholar
  48. 48.
    Merkenschlager M, Nora EP (2016) CTCF and cohesin in genome folding and transcriptional gene regulation. Annu Rev Genomics Hum Genet 17:17–43. CrossRefPubMedGoogle Scholar
  49. 49.
    Nitzsche A, Paszkowski-Rogacz M, Matarese F et al (2011) RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PLoS One.
  50. 50.
    Dowen JM, Fan ZP, Hnisz D et al (2014) Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159:374–387. CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Kubo N, Ishii H, Gorkin D et al (2017) Preservation of chromatin organization after acute loss of CTCF in mouse embryonic stem cells 2 3. bioRxiv.
  52. 52.
    Dixon JR, Jung I, Selvaraj S et al (2015) Chromatin architecture reorganization during stem cell differentiation. Nature 518:331–336. CrossRefPubMedPubMedCentralGoogle Scholar
  53. 53.
    Freire-pritchett P, Schoenfelder S, Várnai C, Steven W (2017) Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. elife 6:pii:e21926. CrossRefGoogle Scholar
  54. 54.
    de Laat W, Duboule D (2013) Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502:499–506. CrossRefPubMedGoogle Scholar
  55. 55.
    Mallo M, Alonso CR (2013) The regulation of Hox gene expression during animal development. Development 140:3951–3963. CrossRefPubMedGoogle Scholar
  56. 56.
    Montavon T, Duboule D (2013) Chromatin organization and global regulation of Hox gene clusters. Philos Trans R Soc Lond Ser B Biol Sci 368:20120367. CrossRefGoogle Scholar
  57. 57.
    Montavon T, Duboule D (2012) Landscapes and archipelagos: spatial organization of gene regulation in vertebrates. Trends Cell Biol 22:347–354. CrossRefPubMedGoogle Scholar
  58. 58.
    Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM (2017) Chromatin architecture emerges during zygotic genome activation independent of transcription. Cell 169:216–228.e19. CrossRefPubMedGoogle Scholar
  59. 59.
    Ma Z, Li M, Roy S et al (2016) Chromatin boundary elements organize genomic architecture and developmental gene regulation in Drosophila Hox clusters. World J Biol Chem 7:223–230. CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Cannavò E, Khoueiry P, Garfield DA et al (2016) Shadow enhancers are pervasive features of developmental regulatory networks. Curr Biol 26:38–51. CrossRefPubMedPubMedCentralGoogle Scholar
  61. 61.
    Perry MW, Boettiger AN, Levine M (2011) Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. PNAS 108:1–12. CrossRefGoogle Scholar
  62. 62.
    Hong J-W, Hendrix DA, Levine MS (2008) Shadow enhancers as a source of evolutionary novelty. Science 321:1314. CrossRefPubMedPubMedCentralGoogle Scholar
  63. 63.
    Jin F, Li Y, Dixon JR et al (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503:290–294. CrossRefPubMedPubMedCentralGoogle Scholar
  64. 64.
    Li M, Ma Z, Liu JK et al (2015) An organizational hub of developmentally regulated chromatin loops in the drosophila antennapedia complex. Mol Cell Biol 35:MCB.00663-15. Google Scholar
  65. 65.
    Pindyurin AV, van Steensel B (2012) Hox in space. Nucleus 3:118–122. CrossRefPubMedPubMedCentralGoogle Scholar
  66. 66.
    Montavon T, Soshnikova N (2014) Hox gene regulation and timing in embryogenesis. Semin Cell Dev Biol 34:76–84. CrossRefPubMedGoogle Scholar
  67. 67.
    Andrey G, Montavon T, Mascrez B et al (2012) A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Nat Rev Genet 13:613–626. CrossRefGoogle Scholar
  68. 68.
    Beccari L, Yakushiji-Kaminatsui N, Woltering JM et al (2016) A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus. Genes Dev 30:1172–1186. PubMedPubMedCentralGoogle Scholar
  69. 69.
    Soshnikova N, Montavon T, Leleu M et al (2010) Functional analysis of CTCF during mammalian limb development. Dev Cell 19:819–830. CrossRefPubMedGoogle Scholar
  70. 70.
    Narendra V, Rocha PP, An D et al (2015) Transcription. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science 347:1017–1021. CrossRefPubMedPubMedCentralGoogle Scholar
  71. 71.
    Lupiáñez DG, Kraft K, Heinrich V et al (2015) Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161:1012–1025. CrossRefPubMedPubMedCentralGoogle Scholar
  72. 72.
    Spielmann M, Brancati F, Krawitz PM et al (2012) Homeotic arm-to-leg transformation associated with genomic rearrangements at the PITX1 locus. Am J Hum Genet 91:629–635. CrossRefPubMedPubMedCentralGoogle Scholar
  73. 73.
    Lupiáñez DG, Spielmann M, Mundlos S (2016) Breaking TADs: how alterations of chromatin domains result in disease. Trends Genet 32:225–237. CrossRefPubMedGoogle Scholar
  74. 74.
    Flottmann R, Wagner J, Kobus K et al (2015) Microdeletions on 6p22.3 are associated with mesomelic dysplasia Savarirayan type. J Med Genet 52:476–483. CrossRefPubMedGoogle Scholar
  75. 75.
    Giorgio E, Robyr D, Spielmann M et al (2014) A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD). Hum Mol Genet 24:3143–3154. CrossRefGoogle Scholar
  76. 76.
    Chakraborty PB, Marjit B, Dutta S, De A (2007) Polydactyly: a case study. J Anat Soc India 56:35–38Google Scholar
  77. 77.
    Flatt AE (2005) Webbed fingers. Proc (Bayl Univ Med Cent) 18:26–37CrossRefGoogle Scholar
  78. 78.
    Temtamy SA, Aglan MS (2008) Brachydactyly. Orphanet J Rare Dis 3:15. CrossRefPubMedPubMedCentralGoogle Scholar
  79. 79.
    Mennen U, Mundlos S, Spielmann M (2014) The Liebenberg syndrome: in depth analysis of the original family. J Hand Surg 39:919–925. CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Departamento de Genética Molecular, Instituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMexico CityMexico

Personalised recommendations