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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ABSTRACT:
ORGANISM(S): Xenopus tropicalis
PROVIDER: GSE222108 | GEO | 2023/04/28
REPOSITORIES: GEO
Similar Datasets
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: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: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:Age-associated DNA methylation changes in Xenopus frogs, and Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs
| PRJNA917774 | ENA
Project description:Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs
| PRJNA917779 | ENA
Project description:Age-associated DNA methylation changes in Xenopus frogs
| PRJNA915337 | ENA
Project description:Current DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets. We report a method to specifically capture an arbitrary subset of genomic targets for single-molecule bisulfite sequencing for digital quantification of DNA methylation at single-nucleotide resolution. A set of ~30,000 padlock probes was designed to assess methylation of ~66,000 CpG sites within 2,020 CpG islands on human chromosome 12, chromosome 20, and 34 selected regions. To investigate epigenetic differences associated with dedifferentiation, we compared methylation in three human fibroblast lines and eight human pluripotent stem cell lines. Chromosome-wide methylation patterns were similar among all lines studied, but cytosine methylation was slightly more prevalent in the pluripotent cells than in the fibroblasts. Induced pluripotent stem (iPS) cells appeared to display more methylation than embryonic stem cells. We found 288 regions methylated differently in fibroblasts and pluripotent cells. This targeted approach should be particularly useful for analyzing DNA methylation in large genomes.
| S-EPMC2715272 | biostudies-literature
Project description:Background: Colorectal cancer (CRC) is a leading cause of cancer death, and early diagnosis of CRC could significantly reduce its mortality rate. Previous studies suggest that the DNA methylation status of zinc finger genes (ZFGs) could be of potential in CRC early diagnosis. However, the comprehensive evaluation of ZFGs in CRC is still lacking. Methods: We first collected 1,426 public samples on genome-wide DNA methylation, including 1,104 cases of CRC tumors, 54 adenomas, and 268 para-tumors. Next, the most differentially methylated ZFGs were identified and validated in two replication cohorts comprising 218 CRC patients. Finally, we compared the prediction capabilities between the ZFGs and the SEPT9 in all CRC patients and the KRAS + and KRAS- subgroup. Results: Five candidate ZFGs were selected: ESR1, ZNF132, ZNF229, ZNF542, and ZNF677. In particular, ESR1 [area under the curve (AUC) = 0.91] and ZNF132 (AUC = 0.93) showed equivalent or better diagnostic capability for CRC than SEPT9 (AUC = 0.91) in the validation dataset, suggesting that these two ZFGs might be of potential for CRC diagnosis in the future. Furthermore, we performed subgroup analysis and found a significantly higher diagnostic capability in KRAS + (AUC ranged from 0.97 to 1) than that in KRAS- patients (AUC ranged from 0.74 to 0.86) for all these five ZFGs, suggesting that these ZFGs could be ideal diagnostic markers for KRAS mutated CRC patients. Conclusion: The methylation profiles of the candidate ZFGs could be potential biomarkers for the early diagnosis of CRC, especially for patients carrying KRAS mutations.
| S-EPMC8581662 | biostudies-literature
Project description:Epigenetic modifications of cytosine residues in the DNA play a critical role for cellular differentiation and potentially also for aging. In mesenchymal stromal cells (MSC) from human bone marrow we have previously demonstrated age-associated methylation changes at specific CpG-sites of developmental genes. In continuation of this work, we have now isolated human dermal fibroblasts from young (<23 years) and elderly donors (>60 years) for comparison of their DNA methylation profiles using the Infinium HumanMethylation27 assay. In contrast to MSC, fibroblasts could not be induced towards adipogenic, osteogenic and chondrogenic lineage and this is reflected by highly significant differences between the two cell types: 766 CpG sites were hyper-methylated and 752 CpG sites were hypo-methylated in fibroblasts in comparison to MSC. Strikingly, global DNA methylation profiles of fibroblasts from the same dermal region clustered closely together indicating that fibroblasts maintain positional memory even after in vitro culture. 75 CpG sites were more than 15% differentially methylated in fibroblasts upon aging. Very high hyper-methylation was observed in the aged group within the INK4A/ARF/INK4b locus and this was validated by pyrosequencing. Age-associated DNA methylation changes were related in fibroblasts and MSC but they were often regulated in opposite directions between the two cell types. In contrast, long-term culture associated changes were very consistent in fibroblasts and MSC. Epigenetic modifications at specific CpG sites support the notion that aging represents a coordinated developmental mechanism that seems to be regulated in a cell type specific manner.
| S-EPMC3035656 | biostudies-literature
Project description:DNA methylation in higher organisms has become an expanding field of study as it often involves the regulation of gene expression. Although Whole Genome Bisulfite Sequencing (WG-BS) based on next-generation sequencing (NGS) is the most versatile method, this is a costly technique that lacks in-depth analytic power. There are no conventional methods based on NGS that enable researchers to easily compare the level of DNA methylation from the practical number of samples handled in the laboratory. Although the targeted BS method based on Sanger sequencing is generally used in this case, it lacks in-depth analytic power. Therefore, we propose a new method that combines the high throughput analytic power of NGS and bioinformatics with the specificity and focus offered by PCR-amplification-based bisulfite sequencing methods. We use in silico size sieving of DNA-fragments and primer matchings instead of whole-fragment alignment in our bioinformatics analyses, and named our method SIMON (Simple Inference for Methylome based On NGS). The results of our targeted BS method based on NGS (SIMON method) show that small variations in DNA methylation patterns can be precisely and efficiently measured at a single nucleotide resolution. SIMON method combines pre-existing techniques to provide a cost-effective technique for in-depth studies that focus on pre-identified loci. It offers significant improvements with regard to workflow and the quality of the acquired DNA methylation information. Because of the high accuracy of the analysis, small variations of DNA methylation levels can be precisely determined even with large numbers of samples and loci.
| S-EPMC6978500 | biostudies-literature