Project description:ChIP-seq data characterizing the occupancy of TFAM over the mitochondrial and nuclear genomes in HeLa cells. Characterization of mitochondrial and nuclear genome-wide TFAM binding in HeLa cells
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
Project description:Characterization of the complete mitochondrial genome of Rana zhenhaiensis
| PRJNA784715 | ENA
Project description:Characterization of the complete mitochondrial genome of Rana longicrus
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:Spiders are a highly diverse group of arthropods that occur in most habitats on land. Notably, spiders have significant ecological impact as predators because of their extraordinary prey capture adaptations, venom and silk. Spider venom is among the most heterogeneous animal venoms and has pharmacological applications, while spider silk is characterized by great toughness with potential for biomaterial application. We describe the genome sequences of two spiders representing two major taxonomic groups, the social velvet spider Stegodyphus mimosarum (Araneomorphae), and the Brazilian white-knee tarantula Acanthoscurria geniculata (Mygalomorphae). We annotate genes using a combination of transcriptomic and in-depth proteomic analyses. The genomes are large (2.6 Gb and 6 Gb, respectively) with short exons and long introns and approximately 50% repeats, reminiscent of typical mammalian genomes. Phylogenetic analyses show that spiders and ticks are sister groups outgrouped by mites, and phylogenetic dating using a molecular clock dates separation of velvet spider and tarantula at 270 my. Based on the genomes and proteomes, we characterize the genetic basis of venom and silk production of both species in detail. Venom protein composition differs markedly between the two spiders, with lipases as the most abundant protein in the velvet spider and present only at low concentration in tarantula. Venom in both spiders contains proteolytic enzymes, and our analyses suggest that these enzymes target and process precursor peptides that subsequently mediate the toxic effects of venom. Complete analysis of silk genes reveal a diverse suite of silk proteins in the velvet spider including novel types of spidroins, and dynamic evolution of major ampullate spidroin genes, whereas silk protein diversity in tarantula is far less complex. The difference in silk proteins between species is consistent with a more complex silk gland morpholgy and use of three-dimentional capture webs consisting of multiple silk types in aranomorph spiders.