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Identifying active cis-regulatory elements during the development of the limbs and external genitalia in the mouse and lizard.

ABSTRACT: The morphologies of the amniote phallus and limbs differ dramatically, but these structures share signaling pathways and patterns of gene expression in early development. Thus far, the extent to which genital and limb transcriptional networks share cis-regulatory elements has remained unexplored. Using chromatin immunoprecipitation with an antibody against the histone modification mark H3K27ac followed by Illumina high-throughput sequencing, we identify thousands of active enhancers in developing limbs, genital tubercle, and additional embryonic tissues of the mouse and green anole lizard (Anolis carolinensis). We show in global analyses of cis-regulatory activity that embryonic limbs and genitalia display overlapping patterns of enhancer activity, and that many H3K27ac-marked regions are shared between mouse and green anole. Our findings support the hypothesis that the amniote phallus evolved through co-option of a preexisting appendage developmental program.

ORGANISM(S): Mus musculus Anolis carolinensis

PROVIDER: GSE64055 | GEO | 2015/10/01

SECONDARY ACCESSION(S): PRJNA269973

REPOSITORIES: GEO

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Project description:Protemics of anolis carolinensis tails undergoing regeneration. As amniote vertebrates, lizards are the most closely related organisms to humans capable of appendage regeneration. Lizards can autotomize, or release their tails as a means of predator evasion, and subsequently regenerate a functional replacement. Green anoles (Anolis carolinensis) can regenerate their tails through a process that involves differential expression of hundreds of genes, which has previously been analyzed by transcriptomic and microRNA analysis. To investigate protein expression in regenerating tissue, we performed whole proteomic analysis of regenerating tail tip and base. This is the first proteomic data set available for the green anole lizard. We identified 976 proteins only in the regenerating tail base, 796 only in the tail tip, and 874 in both tip and base. For 90% of these proteins in these tissues, we were able to assign a clear orthology to gene models in either the Ensembl or NCBI databases. For 20 proteins in the tail base (2.5%), 7 proteins in the tail tip (0.9%), and 7 proteins in both regions (0.8%), the gene model in Ensembl and NCBI matched an uncharacterized protein, confirming that these predictions are present in the proteome. Ontology and pathways analysis of proteins expressed in the regenerating tail base identified categories including actin filament-based process, ncRNA metabolism, regulation of phosphatase activity, small GTPase mediated signal transduction, and cellular component organization or biogenesis. Analysis of proteins expressed in the tail tip identified categories including regulation of organelle organization, regulation of protein localization, ubiquitin-dependent protein catabolism, small GTPase mediated signal transduction, morphogenesis of epithelium, and regulation of biological quality. These proteomic findings confirm pathways and gene families activated in tail regeneration in the green anole as well as identify uncharacterized proteins whose role in regrowth remains to be revealed.

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Identifying active cis-regulatory elements during the development of the limbs and external genitalia in the mouse and lizard.

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