Abstract

The HoxA and HoxD gene clusters of jawed vertebrates are organized into bipartite three-dimensional chromatin structures that separate long-range regulatory inputs coming from the anterior and posterior Hox-neighboring regions1. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs2. Almost nothing is known about how these three-dimensional topologies originated. Here we perform extensive 4C-seq profiling of the Hox cluster in embryos of amphioxus, an invertebrate chordate. We find that, in contrast to the architecture in vertebrates, the amphioxus Hox cluster is organized into a single chromatin interaction domain that includes long-range contacts mostly from the anterior side, bringing distant cis-regulatory elements into contact with Hox genes. We infer that the vertebrate Hox bipartite regulatory system is an evolutionary novelty generated by combining ancient long-range regulatory contacts from DNA in the anterior Hox neighborhood with new regulatory inputs from the posterior side.

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Gene Expression Omnibus

Referenced accessions

NCBI Reference Sequence

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Acknowledgements

We specially thank J. Pascual-Anaya for helping with some figures and helpful discussions. We would also like to thank F. Casares, I. Almudí and J.R. Martínez-Morales for fruitful discussions. Work was funded by grants from the Ministerio de Economía y Competitividad (BFU2013-41322-P to J.L.G.-S.; Juan de la Cierva postdoctoral contract to I.M.; BFU2014-58449-JIN to J.J.T.); the Andalusian government (BIO-396 to J.L.G.-S.; C2A (EE: 2013/2506) to D.P.D. and I.I.-A.); the European Research Council (ERC; grant 268513) to P.W.H.H. and F.M.; a European Molecular Biology Organization (EMBO) short fellowship to I.M.; the Universidad Pablo de Olavide to J.J.T.; and Conicyt 'Becas Chile' to D.A.

Author information

Author notes

    • Rafael D Acemel
    • , Juan J Tena
    • , Ibai Irastorza-Azcarate
    •  & Ferdinand Marlétaz

    These authors contributed equally to this work.

Affiliations

  1. Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain.

    • Rafael D Acemel
    • , Juan J Tena
    • , Ibai Irastorza-Azcarate
    • , Carlos Gómez-Marín
    • , Elisa de la Calle-Mustienes
    • , Sergio G Diaz
    • , Damien P Devos
    • , Ignacio Maeso
    •  & José Luis Gómez-Skarmeta
  2. Department of Zoology, University of Oxford, Oxford, UK.

    • Ferdinand Marlétaz
    •  & Peter W H Holland
  3. Université Pierre et Marie Curie Université Paris 6, CNRS, UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Banyuls-sur-Mer, France.

    • Stéphanie Bertrand
    • , Daniel Aldea
    •  & Hector Escrivá
  4. Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.

    • Jean-Marc Aury
    •  & Sophie Mangenot

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Contributions

R.D.A. carried out the 4C-seq experiments with the help of C.G.-M. and S.G.D. J.J.T. performed the bioinformatic analysis of all the 4C-seq and ATAC-seq data sets. I.I.-A. developed and applied the three-dimensional modeling and virtual Hi-C procedures. F.M. generated the assembly and annotation of the Hox locus in the European amphioxus. J.-M.A. and S.M. ensured sequencing project management at Genoscope. E.d.l.C.-M., R.D.A., J.J.T. and I.M. carried out the zebrafish reporter assays. S.B. and D.A. collected and processed the amphioxus embryonic material and performed in situ hybridizations. I.M. completed the amphioxus ATAC-seq experiments and the evolution of synteny analyses. J.L.G.-S., H.E., I.M. and D.P.D. conceived, designed and coordinated the project. J.L.G.-S. and I.M. wrote the manuscript with the help of P.W.H.H. All authors revised and contributed to the final version of the text.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Damien P Devos or Ignacio Maeso or Hector Escrivá or José Luis Gómez-Skarmeta.

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DOI

https://doi.org/10.1038/ng.3497

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