An epigenetic clock for Xenopus tropicalis

DNA methylation clocks have been widely used for accurate age prediction, but most studies have been carried out on mammals. Here we present an epigenetic clock for the aquatic frog Xenopus tropicalis, a widely used model organism in developmental biology and genomics. To construct the clock, we collected DNA methylation data from 192 frogs using targeted bisulfite sequencing at genomic regions containing CpG sites previously shown to have age-associated methylation in Xenopus. We found highly positively and negatively age-correlated CpGs are enriched in heterochromatic regions marked with H4K20me3 and H3K9me3. Positively age-correlated CpGs are enriched in bivalent chromatin and gene bodies with H3K36me3, and tend to be proximal to lowly expressed genes. These epigenetic features of aging are similar to those found in mammals, suggesting evolutionary conservation of epigenetic aging mechanisms. Our clock enables future aging biology experiments that leverage the unique properties of amphibians. Targeted bisulfite sequencing of 187 adult Xenopus tropicalis frogs (hindlimb webbing skin punch tissue), and 5 whole tadpole Xenopus tropicalis. The animals were raised in aquatic tanks from birth, allowing measurement of the relationship between DNA methylation and age.

DNA甲基化时钟（DNA methylation clocks）已被广泛应用于精准年龄预测，但现有多数相关研究均以哺乳动物为研究对象。本文针对发育生物学与基因组学领域广泛使用的水生模式生物热带爪蟾（Xenopus tropicalis），构建了一款表观遗传时钟（epigenetic clock）。
为构建该时钟，研究人员针对此前已被证实与爪蟾年龄相关的CpG位点（CpG sites）所在基因组区域，采用靶向亚硫酸氢盐测序（targeted bisulfite sequencing）技术，从192只爪蟾中采集了DNA甲基化数据。
研究发现，与年龄呈强正相关与强负相关的CpG位点，均富集于以H4K20me3和H3K9me3标记的异染色质区域。与年龄呈正相关的CpG位点则富集于二价染色质（bivalent chromatin）以及带有H3K36me3标记的基因本体（gene bodies）区域，且倾向于靠近低表达基因。
上述衰老相关的表观遗传特征与哺乳动物中观测到的特征高度相似，提示表观遗传衰老机制存在进化保守性。本时钟可为未来利用两栖类独特特性开展的衰老生物学实验提供有力支撑。
本研究对187只成年热带爪蟾的后肢蹼皮肤穿刺组织，以及5只完整的热带爪蟾蝌蚪样本开展了靶向亚硫酸氢盐测序。所有受试动物均从出生起即在水生饲养箱中培育，从而得以精准量化DNA甲基化水平与年龄之间的关联。