Genomics

Dataset Information

38

Reorganization of HoxD regulatory landscapes during the evolution of a snake-like body plan (4C-seq)


ABSTRACT: While the vertebrate body plan is highly conserved amongst all species of this taxon, extreme variations thereof can be documented in snakes, which display both an absence of limbs and an unusually elongated trunk. As Hox genes are strong candidates both for the making and the evolution of this body plan, their comparative study in such a morphologically diverged group is informative regarding their potential causative importance in these processes. In this work we use an interspecies comparative approach where different aspects of regulation at the HoxD locus are investigated. We find that although spatial collinearity and associated epigenetic mark dynamics are conserved in the corn snake, other regulatory modalities have been largely restructured. A BAC transgenic approach indeed revealed that, while the majority of mesodermal enhancers in vertebrates appear to be mostly located outside of the cluster, the corn snake contains most mesodermal trunk enhancers within the HoxD cluster. We also find that, despite the absence of limbs and an altered Hoxd gene regulation in external genitalia, the bimodal chromatin structure at the corn snake HoxD locus is maintained. The analysis of particular enhancer sequences initially defined in the mouse and further isolated at the snake orthologous locus showed differences in their specificities for the limb and genital bud expression. Of particular interest, a snake counterpart of a mouse limb-only enhancer sequence evolved into a genital-only enhancer. Such a regulatory exaptation suggests that enhancer versatility may have been an important factor to accompany the transition towards the snake body plan. These results show that vertebrate morphological evolution is likely to have been associated with extensive reorganization at the HoxD regulatory landscapes while respecting a very conserved general regulatory framework. Overall design: 4C-seq analysis of mouse and snake whole embryo and genital bud tissue using viewpoints contained within the cluster

INSTRUMENT(S): Illumina HiSeq 2500 (Mus musculus)

SUBMITTER: Isabel Guerreiro  

PROVIDER: GSE79045 | GEO | 2016-11-05

SECONDARY ACCESSION(S): PRJNA314793

REPOSITORIES: GEO

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Publications

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan.

Guerreiro Isabel I   Gitto Sandra S   Novoa Ana A   Codourey Julien J   Nguyen Huynh Thi Hanh TH   Gonzalez Federico F   Milinkovitch Michel C MC   Mallo Moises M   Duboule Denis D  

eLife 20160801


Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific e  ...[more]

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