Project description:Background Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates. Methods We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data. Results Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates. Conclusions Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.
Project description:Gene expression profiling of pooled late stage embryos from Leucoraja erinacea, Scyliorhinus canicula and Callorhinchus milii show that HOXC cluster genes are not expressed in the two elasmobranch fishes, L. erinacea and S. canicula. This finding supports the observations that these genes are not found in whole genome shotgun sequencing of L. erinacea or genomic clones from S. canicula. Profile gene expression in pooled late stage embryos from three species (L. erinacea, S. canicula and C. milii)
Project description:Gene expression profiling of pooled late stage embryos from Leucoraja erinacea, Scyliorhinus canicula and Callorhinchus milii show that HOXC cluster genes are not expressed in the two elasmobranch fishes, L. erinacea and S. canicula. This finding supports the observations that these genes are not found in whole genome shotgun sequencing of L. erinacea or genomic clones from S. canicula.
