Age-associated DNA methylation changes in Xenopus frogs, and Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs
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PROVIDER: PRJNA917774 | ENA |
REPOSITORIES: ENA
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Project description:Age-associated DNA methylation changes in Xenopus frogs
| PRJNA915337 | ENA
Project description:Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vertebrate species Xenopus tropicalis. We selected approximately 3500 sites highly correlated with age from WGBS data from 9 frogs of 3 different age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old - GSE221656) and designed probes for the development of cost effective targeted bisulfite sequencing (TBSeq) assay. Here, we present the TBSeq assay in sixteen different frogs as a pilot experiment to validate our previous findings.
2023-04-28 | GSE222107 | GEO
Project description:Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vetebrate species Xenopus tropicalis. We generated nine whole-genome bisulfite sequencing (WGBS) datasets from three distinct age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old) to characterize the gene- and chromosome-scale changes.
2023-04-28 | GSE221656 | GEO
Project description:Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs
| PRJNA917779 | ENA
Project description:Age-associated changes in DNA methylation have been characterized across various animals, but not yet in amphibians, which are of particular interest because they include widely studied model organisms. In this study, we present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays patterns of age-associated changes in DNA methylation. We have generated whole-genome bisulfite sequencing (WGBS) profiles from skin samples of nine frogs representing young, mature, and old adults and characterized the gene- and chromosome-scale DNA methylation changes with age. Many of the methylation features and changes we observe are consistent with what is known in mammalian species, suggesting that the mechanism of age-related changes is conserved. Moreover, we selected a few thousand age-associated CpG sites to build an assay based on targeted DNA methylation analysis (TBSseq) to expand our findings in future studies involving larger cohorts of individuals. Preliminary results of a pilot TBSeq experiment recapitulate the findings obtained with WGBS setting the basis for the development of an epigenetic clock assay. The results of this study will allow us to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of ageing.
| S-EPMC10128463 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-04-28 | GSE222108 | GEO
Project description:Xenopus borealis, Xenopus laevis Raw sequence reads
| PRJNA616217 | ENA
Project description:Pregnane X receptor (PXR) is generally considered the most important sensor of natural and anthropogenic xenobiotics in vertebrates. In Xenopus, however, PXR plays a role in neural development and it is irresponsive to xenobiotics. We report a first broad-spectrum amphibian xenobiotic receptor, which is an ortholog of the mammalian constitutive androstane receptor (CAR). The low basal activity and pronounced responsiveness to activators such as drugs and steroids displayed by the Xenopus CAR resemble PXR, which both trace back to a common ancestor early in the divergence of land vertebrates. The constitutive activity of CAR emerged first in Sauropsida (reptiles and birds) and it is common to all fully terrestrial land vertebrates (Amniota). This activity can be mimicked by humanizing just two amino acids of the Xenopus CAR. These results demonstrate a remarkable plasticity of CAR which enabled its employment as Xenopus xenosensors. They open way to toxicogenomic and bioaugmentation studies in amphibians, a critically endangered taxon of land vertebrates. Taken together, we provide evidence for a much earlier origin of CAR, for its conservation in tetrapods which exceeds that of PXR, and for its remarkable functional plasticity which enabled its role as a PXR-like xenosensor in Amphibia. We used microarrays to detect global transcriptional changes in Xenopus laevis livers following pregnenolone and artemisinin treatment in order to identify target genes of xlCAR. Arteminisin or pregnenolone were injected intraperitoneally into three frogs on two consecutive days. The control group received in parallel two DMSO injections. All frogs were sacrificed 24 h after the second injection by decapitation, and livers were immediately frozen in liquid nitrogen. After RNA isolation, specimens within the same experimental group were pooled.
2011-10-10 | E-GEOD-28510 | biostudies-arrayexpress
Project description:Comprehensive RNA-seq experiments to measure the expression of homoeologs across different tissues, as a part of the Xenopus laevis genome project. This work is funded by Agency Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT; "Genome Science" Grant ID 221S0002). Collect mRNA from whole tissue; two female frogs were used as donors for most tissues (Taira dataset for one frog, Ueno dataset for the other frog); testis samples were collected from two male frogs (sibling of two female donors)
2016-10-24 | E-GEOD-73419 | biostudies-arrayexpress
Project description:Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
2022-03-30 | GSE199671 | GEO