A clockwork fish: Age prediction using DNA methylation‐based biomarkers in the European seabass

Abstract

Age‐related changes in DNA methylation do occur. Taking advantage of this, mammalian and avian epigenetic clocks have been constructed to predict age. In fish, studies on age‐related DNA methylation changes are scarce and no epigenetic clocks have been constructed. However, in fisheries and population dynamics studies there is a need for accurate estimation of age, something that is often impossible for some economically important species with the currently available methods. Here, we used the European sea bass, a marine fish the age of which can be determined with accuracy, to construct a piscine epigenetic clock, the first one in a cold‐blooded vertebrate. We used targeted bisulfite sequencing to amplify 48 CpGs from four genes in muscle samples and applied penalized regressions to predict age. We thus developed an age predictor in fish that is highly accurate (0.824) and precise (2.149 years). In juvenile fish, accelerated growth due to elevated temperatures had no effect on age prediction, indicating that the clock is able to predict the chronological age independently of environmentally‐driven perturbations. An epigenetic clock developed using muscle samples accurately predicted age in samples of testis but not ovaries, possibly reflecting the reproductive biology of fish. In conclusion, we report the development of the first piscine epigenetic clock, paving the way for similar studies in other species. Piscine epigenetic clocks should be of great utility for fisheries management and conservation purposes, where age determination is of crucial importance.

Genome-Wide Epigenomic Stress Response in the European Sea Bass (Dicentrarchus Labrax, L.)

“…The European sea bass has become one of the most studied species in sh epigenetics [77][78][79][80][81][82][83][84]. Because of the availability of its genome and the development of selection programs, efforts should be dedicated to further explore its epigenomic landscape regarding the stress response, especially in an aquaculture context.…”

“…This suggests that methylation patterns observed in sea bass could also potentially rely on the ontogenetic regulation of a particular phenotype between pre-and post-stress sh, rather than being directly related to the stress challenge. Variation in gene expression or methylation accompanying ontogeny are reported in sh [45,185] and, as for other organisms, cytosine methylation is known to vary with age in sea bass [84].…”

“…It has been extensively studied over the last three decades, for both natural and farmed populations (reviewed in [75]). This includes the sequencing of its genome [76] and an increasing number of epigenetic studies [77][78][79][80][81][82][83][84]. The stress response of European sea bass remains evaluated using blood parameters that have been shown to re ect multiple components of its stress response [16,85], despite authors have proposed alternatives [86,87].…”

Genome-wide epigenomic stress response in the European sea bass (Dicentrarchus labrax, L.)

“…The European sea bass has become one of the most studied species in fish epigenetics [77–84]. Because of the availability of its genome and the development of selection programs, efforts should be dedicated to further explore its epigenomic landscape regarding the stress response, especially in an aquaculture context.…”

“…It has been extensively studied over the last three decades, for both natural and farmed populations (reviewed in [75]). This includes the sequencing of its genome [76] and an increasing number of epigenetic studies [77–84]. The stress response of European sea bass remains evaluated using blood parameters that have been shown to reflect multiple components of its stress response [16,85], despite authors have proposed alternatives [86,87].…”