DNA methylation clocks for clawed frogs reveal evolutionary conservation of epigenetic ageing

Abstract

DNA methylation-based biomarkers of ageing (epigenetic clocks) have been developed for many mammals, but not yet for amphibian species. We generated DNA methylation data from African clawed frogs (Xenopus laevis) and Western clawed frogs (Xenopus tropicalis), from adult tissues, whole embryos, and tadpoles. We used an array platform designed for CpGs that are highly conserved in mammals to build multiple DNA methylation-based estimators of age for Xenopus. We found that dual species clock could be developed that apply to both humans and frogs (human-clawed frog clocks), and whose high accuracy supports that epigenetic ageing processes are evolutionary conserved outside mammals. Crossing vast evolutionary distances, we characterize age-related CpGs in Xenopus and mammalian species. Highly conserved positively age-related CpGs are located in neural-developmental genes such as uncx, tfap2d as well as nr4a2 implicated in age-associated disease. As in human clocks, positively age-related CpGs are associated with Polycomb repressive complex 2 (PRC2) target sites. Negative age-related CpGs are associated with genes involved in synaptic transmission. We conclude that signatures of epigenetic ageing are evolutionary conserved between frogs and mammals and that the associated genes relate to neural-developmental processes, altogether opening opportunities to employ Xenopus as a model organism to study development and ageing.

Epigenetic drift underlies epigenetic clock signals, but displays distinct responses to lifespan interventions, development, and cellular dedifferentiation

“…Consistent with the hypothesis that disorder in DNA methylation patterns underlies signals in conventional CpG clocks (i.e., those based on mean CpG methylation levels), we find that loci comprising clocks constructed using RD, RM, RE, and CpG contexts are all enriched for regions in which disorder changes with age, and loci which are shared across clocks are involved biological processes such as cell cycle, tumor suppression, and development. Interestingly, Evx2 is shared across all clock contexts, and is frequently reported as being ageassociated across a variety of vertebrate species [38][39][40][41]. However, we identify notable distinctions and minimal overlap across clock contexts.…”

DNA methylation markers of age(ing) in non‐model animals

“…The most widely used methylation array, HorvathMammalMethylChip40 has been developed to leverage epigenetic age clocks in all mammal species, regardless of the existence of a reference genome and to ensure that biological insights gained in one species can apply to others (Arneson et al, 2022). Surprisingly, this array was recently used to infer an epigenetic clock in non‐mammalian species, namely, African clawed frogs and Western clawed frogs (Zoller et al, 2022). The success in developing usable epigenetic clocks for many species using this chip suggests there can be great benefits in developing chips in taxonomic groups other than mammals, or taxonomic sub‐groups of mammals, for example, primates or rodents.…”

“…For example, in the frog study, only 4635 of the ~36,000 CpG sites on the chip mapped to the frog genomes (in contrast to for example, 29,846 CpG sites on the chip mapping to the roe deer genome, Lemaître et al, 2021). While this amount of sites may be sufficient to develop an epigenetic clock ( R 2 = 0.64, MAD = 2.05 years, Zoller et al, 2022), it is but a small fraction of all CpG sites in the genome. We take the lower R 2 value of this clock (when compared with mammal clocks that were based on the HorvathMammalMethylChip40, Table S3) as a preliminary indication that the chip is less suitable to predict chronological age in non‐mammalian taxons.…”

Biological clocks as age estimation markers in animals: a systematic review and meta‐analysis

“…A total of 331 age‐correlated CpGs were identified, from which an age clock was established that was able to classify individuals into young, middle, or old age classes with high accuracy; the largest errors occurred in very young or very old individuals. A study published in parallel (Zoller et al ., 2022), on both Western clawed frog and African clawed frogs [ Xenopus laevis (Daudin)], used the same methylation array chip previously developed in mammals, found thousands of conserved CpGs and constructed both individual as well as combined clocks for age. In the Western clawed frog, the mean error of prediction for age was less than a year, while the error for African clawed frog was ~3 years.…”