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Nat Genet. 2016 Mar;48(3):336-41. doi: 10.1038/ng.3497. Epub 2016 Feb 1.

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation.

Author information

1
Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain.
2
Department of Zoology, University of Oxford, Oxford, UK.
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.
4
Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.

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 regions. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs. 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.

PMID:
26829752
DOI:
10.1038/ng.3497
[Indexed for MEDLINE]

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