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SCetMax

ABSTRACT: Cetorhinus maximus (basking shark), genomic and transcriptomic data

PROVIDER: PRJEB75717 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13132926_1.fastq.gz	Fastqsanger.gz
	ERR13132926_2.fastq.gz	Fastqsanger.gz
	ERR13132927_1.fastq.gz	Fastqsanger.gz
	ERR13132927_2.fastq.gz	Fastqsanger.gz
	ERR13132928_1.fastq.gz	Fastqsanger.gz

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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [ATAC-seq]

Project description:We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

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A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [RNA-seq]

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The methylome of a cartilaginous fish, Callorhinchus milii, reveals conservation of epigenetic regulation across jawed vertebrates

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.

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RNA-seq of scallop mantle tissue

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