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.

Topology of mammalian developmental enhancers and their regulatory landscapes

Abstract

How a complex animal can arise from a fertilized egg is one of the oldest and most fascinating questions of biology, the answer to which is encoded in the genome. Body shape and organ development, and their integration into a functional organism all depend on the precise expression of genes in space and time. The orchestration of transcription relies mostly on surrounding control sequences such as enhancers, millions of which form complex regulatory landscapes in the non-coding genome. Recent research shows that high-order chromosome structures make an important contribution to enhancer functionality by triggering their physical interactions with target genes.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: Variations in long-range gene regulation.
Figure 2: The mammalian regulatory jungle.
Figure 3: Comparison of instructive and permissive model for three-dimensional controlled gene expression during differentiation.

Similar content being viewed by others

References

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

    Article  CAS  Google Scholar 

  2. Bulger, M. & Groudine, M. Functional and mechanistic diversity of distal transcription enhancers. Cell 144, 327–339 (2011).

    Article  CAS  Google Scholar 

  3. Spitz, F. & Furlong, E. E. Transcription factors: from enhancer binding to developmental control. Nature Rev. Genet. 13, 613–626 (2012).

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  5. Stamatoyannopoulos, J. A. What does our genome encode? Genome Res. 22, 1602–1611 (2012).

    Article  CAS  Google Scholar 

  6. Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012).

    Article  ADS  CAS  Google Scholar 

  7. Kleinjan, D. A. & van Heyningen, V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8–32 (2005).

    Article  CAS  Google Scholar 

  8. Weischenfeldt, J., Symmons, O., Spitz, F. & Korbel, J. O. Phenotypic impact of genomic structural variation: insights from and for human disease. Nature Rev. Genet. 14, 125–138 (2013).

    Article  CAS  Google Scholar 

  9. Montavon, T. & Duboule, D. Landscapes and archipelagos: spatial organization of gene regulation in vertebrates. Trends Cell Biol. 22, 347–354 (2012).

    Article  CAS  Google Scholar 

  10. Lagha, M., Bothma, J. P. & Levine, M. Mechanisms of transcriptional precision in animal development. Trends Genet. 28, 409–416 (2012).

    Article  CAS  Google Scholar 

  11. Maeda, R. K. & Karch, F. Gene expression in time and space: additive vs hierarchical organization of cis-regulatory regions. Curr. Opin. Genet. Dev. 21, 187–193 (2011).

    Article  CAS  Google Scholar 

  12. Levine, M. Transcriptional enhancers in animal development and evolution. Curr. Biol. 20, R754–R763 (2010).

    Article  CAS  Google Scholar 

  13. Duboule, D. & Wilkins, A. S. The evolution of 'bricolage'. Trends Genet. 14, 54–59 (1998).

    Article  CAS  Google Scholar 

  14. Kirschner, M. & Gerhart, J. Evolvability. Proc. Natl Acad. Sci. USA 95, 8420–8427 (1998).

    Article  ADS  CAS  Google Scholar 

  15. Ohno, S. Evolution by Gene Duplication. (Springer, 1970).

    Book  Google Scholar 

  16. Ruf, S. et al. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nature Genet. 43, 379–386 (2011). In this paper, the authors use a transposable reporter gene system in mice to probe for enhancer activity in vivo and show widely varying reporter expression patterns at hundreds of genomic integration sites.

    Article  CAS  Google Scholar 

  17. O'Kane, C. J. & Gehring, W. J. Detection in situ of genomic regulatory elements in Drosophila. Proc. Natl Acad. Sci. USA 84, 9123–9127 (1987).

    Article  ADS  CAS  Google Scholar 

  18. Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499–502 (2006).

    Article  ADS  CAS  Google Scholar 

  19. Odom, D. T. et al. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nature Genet. 39, 730–732 (2007).

    Article  CAS  Google Scholar 

  20. Wilson, M. D. et al. Species-specific transcription in mice carrying human chromosome 21. Science 322, 434–438 (2008).

    Article  ADS  CAS  Google Scholar 

  21. Zinzen, R. P., Girardot, C., Gagneur, J., Braun, M. & Furlong, E. E. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462, 65–70 (2009).

    Article  ADS  CAS  Google Scholar 

  22. Lee, D., Karchin, R. & Beer, M. A. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 21, 2167–2180 (2011).

    Article  CAS  Google Scholar 

  23. Gorkin, D. U. et al. Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res. 22, 2290–2301 (2012).

    Article  CAS  Google Scholar 

  24. Crawford, G. E. et al. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nature Methods 3, 503–509 (2006).

    Article  CAS  Google Scholar 

  25. Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 1 (2012).

    Article  ADS  CAS  Google Scholar 

  26. Hardison, R. C. & Taylor, J. Genomic approaches towards finding cis-regulatory modules in animals. Nature Rev. Genet. 13, 469–483 (2012).

    Article  CAS  Google Scholar 

  27. Arnold, C. D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074–1077 (2013). In this paper, the authors report a genome-wide screening method that quantifies the self-transcription of random DNA segments to identify sequence modules with enhancer activity.

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  29. de Wit, E. & de Laat, W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11–24 (2012).

    Article  CAS  Google Scholar 

  30. Carter, D., Chakalova, L., Osborne, C. S., Dai, Y. F. & Fraser, P. Long-range chromatin regulatory interactions in vivo. Nature Genet. 32, 623–626 (2002).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  32. Palstra, R. J. et al. Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PloS ONE 3, e1661 (2008).

    Article  ADS  Google Scholar 

  33. Deng, W. et al. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149, 1233–1244 (2012). In this study, it is shown that the artificial physical tethering of a distant enhancer to a gene promoter leads to highly activated transcription, illustrating that enhancer contacts causally underlie transcriptional output.

    Article  CAS  Google Scholar 

  34. Noordermeer, D. et al. Variegated gene expression caused by cell-specific long-range DNA interactions. Nature Cell Biol. 13, 944–951 (2011). This article shows that inter-chromosomal gene activation by an ectopic enhancer leads to variegated gene expression in subsets of mouse cells.

    Article  CAS  Google Scholar 

  35. Andrey, G. et al. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science 340, 1234167 (2013). In this paper, the authors show that different regulatory landscapes are recruited during development by the same genes, which switch contacts from one to the other.

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  37. Vernimmen, D., De Gobbi, M., Sloane-Stanley, J. A., Wood, W. G. & Higgs, D. R. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J. 26, 2041–2051 (2007).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  39. Vakoc, C. R. et al. Proximity among distant regulatory elements at the β-globin locus requires GATA-1 and FOG-1. Mol. Cell 17, 453–462 (2004.12.028 (2005).

    Article  CAS  Google Scholar 

  40. van de Werken, H. J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 9, 969–972 (2012).

    Article  CAS  Google Scholar 

  41. Riddle, R. D., Johnson, R. L., Laufer, E. & Tabin, C. Sonic hedgehog mediates the polarizing activity of the ZPA. Cell 75, 1401–1416 (1993).

    Article  CAS  Google Scholar 

  42. Lettice, L. A. et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12, 1725–1735 (2003).

    Article  CAS  Google Scholar 

  43. Sagai, T., Hosoya, M., Mizushina, Y., Tamura, M. & Shiroishi, T. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development 132, 797–803 (2005).

    Article  CAS  Google Scholar 

  44. Amano, T. et al. Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription. Dev. Cell 16, 47–57 (2009).

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  46. Lettice, L. A. et al. Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly. Dev. Cell 22, 459–467 (2012).

    Article  CAS  Google Scholar 

  47. Eijkelenboom, A. et al. Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II profiling. Mol. Syst. Biol. 9, 638 (2013).

    Article  Google Scholar 

  48. Melo, C. A. et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol. Cell 49, 524–535 (2012).

    Article  Google Scholar 

  49. Nora, E. P., Dekker, J. & Heard, E. Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? BioEssays 5, 201300040 (2013).

    Google Scholar 

  50. Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012). This report is the first systematic analysis, based on 5C, of promoter-centred DNA contacts, revealing complex and dynamic contact networks, which change during development.

    Article  ADS  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  52. 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  Google Scholar 

  53. Montavon, T. et al. A regulatory archipelago controls Hox genes transcription in digits. Cell 147, 1132–1145 (2011). In this paper, the authors report the existence of a regulatory archipelago that controls transcription in developing digits and contains several islands with various quantitative and qualitative contributions.

    Article  CAS  Google Scholar 

  54. Bender, M. A. et al. Flanking HS-62.5 and 3-HS1, and regions upstream of the LCR, are not required for β-globin transcription. Blood 108, 1395–1401 (2006).

    Article  CAS  Google Scholar 

  55. Noordermeer, D. et al. Transcription and chromatin organization of a housekeeping gene cluster containing an integrated β-globin locus control region. PLoS Genet. 4, e1000016 (2008).

    Article  Google Scholar 

  56. Marinić, M., Aktas, T., Ruf, S. & Spitz, F. An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Dev. Cell 24, 530–542 (2013).

    Article  Google Scholar 

  57. 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  Google Scholar 

  58. Spitz, F., Gonzalez, F. & Duboule, D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113, 405–417 (2003).

    Article  CAS  Google Scholar 

  59. Zuniga, A. et al. Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev. 18, 1553–1564 (2004).

    Article  CAS  Google Scholar 

  60. Lower, K. M. et al. Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition. Proc. Natl Acad. Sci. USA 106, 21771–21776 (2009).

    Article  ADS  CAS  Google Scholar 

  61. Tschopp, P., Fraudeau, N., Bena, F. & Duboule, D. Reshuffling genomic landscapes to study the regulatory evolution of Hox gene clusters. Proc. Natl Acad. Sci. USA 108, 10632–10637 (2011).

    Article  ADS  CAS  Google Scholar 

  62. De Gobbi, M. et al. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science 312, 1215–1217 (2006).

    Article  ADS  CAS  Google Scholar 

  63. Bender, M. A. et al. Targeted deletion of 5-HS1 and 5-HS4 of the β-globin locus control region reveals additive activity of the DNaseI hypersensitive sites. Blood 98, 2022–2027 (2001).

    Article  CAS  Google Scholar 

  64. Wijgerde, M., Grosveld, F. & Fraser, P. Transcription complex stability and chromatin dynamics in vivo. Nature 377, 209–213 (1995).

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  66. Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458–472 (2012). Refs 45, 65 and 66 report that mammalian and fly chromosomes are structurally subdivided into topological domains with flanking boundaries that hamper DNA contacts across.

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  68. Phillips-Cremins, J. E. et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153, 1281–1295 (2013).

    Article  CAS  Google Scholar 

  69. Williams, A., Spilianakis, C. G. & Flavell, R. A. Interchromosomal association and gene regulation in trans. Trends Genet. 26, 188–197 (2010).

    Article  CAS  Google Scholar 

  70. Fuss, S. H., Omura, M. & Mombaerts, P. Local and cis effects of the H element on expression of odorant receptor genes in mouse. Cell 130, 373–384 (2007).

    Article  CAS  Google Scholar 

  71. Gaetz, J. et al. Evidence for a critical role of gene occlusion in cell fate restriction. Cell Res. 22, 848–858 (2012).

    Article  CAS  Google Scholar 

  72. Miller, J. C. et al. A TALE nuclease architecture for efficient genome editing. Nature Biotechnol. 29, 143–148 (2011).

    Article  CAS  Google Scholar 

  73. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    Article  ADS  CAS  Google Scholar 

  74. Kleinjan, D. J. & Coutinho, P. Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease. Brief. Funct. Genomic Proteomic 8, 317–332 (2009).

    Article  CAS  Google Scholar 

  75. Ovcharenko, I. et al. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15, 137–145 (2005).

    Article  CAS  Google Scholar 

  76. Ahituv, N. et al. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 5, e234 (2007).

    Article  Google Scholar 

Download references

Acknowledgements

The authors thank Y. Oz for preparing the figures, and G. Geeven, M. Janssen, G. Andrey, L. Beccari, T. Montavon and M. Leleu for their help. The authors' laboratories are supported by funds from the Dutch Scientific Organization (NWO) (714012002 and 724012003 (VICI)), EU grant 2010-259743 (MODHEP), a KWF Dutch Cancer Foundation grant (2009-4459) and a NanoNextNL grant (to W.dL) and the Ecole Polytechnique Fédérale de Lausanne, the University of Geneva, the Swiss National Research Foundation, the ERC grant SystemsHox.ch and the FP7 program IDEAL (to D.D.).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Wouter de Laat or Denis Duboule.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Reprints and permissions information is available at www.nature.com/reprint.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

de Laat, W., Duboule, D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502, 499–506 (2013). https://doi.org/10.1038/nature12753

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature12753

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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