Patterns of methylation influence lifespan, but methylation and lifespan may also depend on diet, or differ between genotypes. Prior to this study, interactions between diet and genotype have not been explored together to determine their influence on methylation. The invertebrate Daphnia magna is an excellent choice for testing the epigenetic response to the environment: parthenogenetic offspring are identical to their siblings (making for powerful genetic comparisons), they are relatively short lived and have well-characterised inter-strain life-history trait differences. We performed a survival analysis in response to caloric restriction and then undertook a 47-replicate experiment testing the DNA methylation response to ageing and caloric restriction of two strains of D. magna. Methylated cytosines (CpGs) were most prevalent in exons two to five of gene bodies. One strain exhibited a significantly increased lifespan in response to caloric restriction, but there was no effect of food-level CpG methylation status. Inter-strain differences dominated the methylation experiment with over 15,000 differently methylated CpGs. One gene, Me31b, was hypermethylated extensively in one strain and is a key regulator of embryonic expression. Sixty-one CpGs were differentially methylated between young and old individuals, including multiple CpGs within the histone H3 gene, which were hypermethylated in old individuals. Across all age-related CpGs, we identified a set that are highly correlated with chronological age. Methylated cytosines are concentrated in early exons of gene sequences indicative of a directed, non-random, process despite the low overall DNA methylation percentage in this species. We identify no effect of caloric restriction on DNA methylation, contrary to our previous results, and established impacts of caloric restriction on phenotype and gene expression. We propose our approach here is more robust in invertebrates given genome-wide CpG distributions. For both strain and ageing, a single gene emerges as differentially methylated that for each factor could have widespread phenotypic effects. Our data showed the potential for an epigenetic clock at a subset of age positions, which is exciting but requires confirmation.

中文翻译：

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大型溞中，同一地理起源的菌株之间的 DNA 甲基化存在很大差异，并且随着年龄的变化而变化

甲基化模式影响寿命，但甲基化和寿命也可能取决于饮食，或因基因型而异。在这项研究之前，尚未一起探索饮食和基因型之间的相互作用以确定它们对甲基化的影响。无脊椎动物大型水蚤是测试对环境的表观遗传反应的绝佳选择：孤雌生殖后代与其兄弟姐妹相同（进行强有力的遗传比较），它们的寿命相对较短，并且具有明确的品系间生活史特征差异。我们针对热量限制进行了生存分析，然后进行了 47 次重复实验，测试了两种 D. magna 菌株对衰老和热量限制的 DNA 甲基化反应。甲基化胞嘧啶 (CpG) 在基因体的第二至五个外显子中最为普遍。一种菌株在热量限制下表现出显着延长的寿命，但食物水平的 CpG 甲基化状态没有影响。菌株间差异主导了超过 15,000 个不同甲基化 CpG 的甲基化实验。Me31b 基因在一种菌株中广泛甲基化，是胚胎表达的关键调节因子。61 个 CpG 在年轻个体和老年个体之间存在差异甲基化，其中组蛋白 H3 基因内的多个 CpG 在老年个体中高度甲基化。在所有与年龄相关的 CpG 中，我们确定了一组与实际年龄高度相关的 CpG。尽管该物种的总体 DNA 甲基化百分比较低，但甲基化胞嘧啶集中在基因序列的早期外显子中，表明这是一个定向的、非随机的过程。与我们之前的结果相反，我们发现热量限制对 DNA 甲基化没有影响，并确定了热量限制对表型和基因表达的影响。我们认为，考虑到全基因组 CpG 分布，我们的方法在无脊椎动物中更加稳健。对于应变和衰老，单个基因出现差异甲基化，对于每个因素都可能产生广泛的表型效应。我们的数据显示了表观遗传时钟在年龄位置子集上的潜力，这是令人兴奋的，但需要确认。