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Elasmobranchii

ABSTRACT: Elasmobranch shark genome evolution

PROVIDER: PRJDB6260 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	DRR111712_1.fastq.gz	Fastqsanger.gz
	DRR111712_2.fastq.gz	Fastqsanger.gz
	DRR111713_1.fastq.gz	Fastqsanger.gz
	DRR111713_2.fastq.gz	Fastqsanger.gz

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Rhincodon typus

Project description:Elasmobranch shark transcriptome sequencing

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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.

2017-03-24 | GSE96683 | GEO

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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Project description:Elasmobranch Isolates

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Late-stage embryonic gene expression in three cartilaginous fishes

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.

2011-12-15 | GSE26235 | GEO

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Project description:Elasmobranch Targeted loci

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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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Late-stage embryonic gene expression in three cartilaginous fishes

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Shark Cartilage in Treating Patients With Advanced Colorectal or Breast Cancer

Project description:RATIONALE: Shark cartilage extract may help shrink or slow the growth of colorectal cancer or breast cancer cells. PURPOSE: Randomized phase III trial to determine the effectiveness of shark cartilage in treating patients who have advanced colorectal cancer or advanced breast cancer.

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Exploration of the nurse shark (Ginglymostoma cirratum) plasma immunoproteome using high-throughput LC-MS/MS

Project description:LC-MS/MS proteomics was used to identify immune proteins in the plasma of the nurse shark (Ginglymostoma cirratum), using a de novo multi-tissue transcriptome generated for this species. LC-MS/MS was then used to assess the host response to immunization with human serum albumin (HSA) and Complete Freund’s Adjuvant (CFA).

2022-08-12 | PXD032158 | Pride

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