Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
The James Hutton Institute, Craigiebuckler, Aberdeen, UK.
Epigenetics Chromatin. 2021 Jan 6;14(1):4. doi: 10.1186/s13072-020-00379-z.
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.
甲基化模式会影响寿命，但甲基化和寿命也可能取决于饮食，或者在不同基因型之间存在差异。在这项研究之前，饮食和基因型之间的相互作用尚未一起进行探讨，以确定它们对甲基化的影响。无脊椎动物大型溞是测试环境对表观遗传反应的绝佳选择：孤雌生殖的后代与它们的兄弟姐妹完全相同（进行强有力的遗传比较），它们的寿命相对较短，并且具有特征鲜明的种间生活史特征差异。我们进行了一项生存分析，以响应热量限制，然后进行了一项 47 次重复实验，以测试两种大型溞的衰老和热量限制对 DNA 甲基化的反应。
甲基化的胞嘧啶（CpG）在基因体的外显子 2 到 5 中最为普遍。一种菌株在响应热量限制时表现出显著延长的寿命，但食物水平的 CpG 甲基化状态没有影响。种间差异主导了甲基化实验，有超过 15000 个不同甲基化的 CpG。一个基因，Me31b，在一个菌株中广泛超甲基化，是胚胎表达的关键调节剂。61 个 CpG 在年轻和年老个体之间存在差异甲基化，包括组蛋白 H3 基因内的多个 CpG，在年老个体中这些 CpG 被高度甲基化。在所有与年龄相关的 CpG 中，我们鉴定了一组与实际年龄高度相关的 CpG。
尽管在这个物种中总 DNA 甲基化百分比较低，但甲基化的胞嘧啶集中在基因序列的早期外显子中，表明这是一个有指导的、非随机的过程。与我们之前的结果相反，我们没有发现热量限制对 DNA 甲基化的影响，并确定了热量限制对表型和基因表达的影响。我们提出，鉴于基因组范围内的 CpG 分布，我们在这里采用的方法在无脊椎动物中更稳健。对于两种菌株和衰老，一个基因作为差异甲基化基因出现，对于每个因素都可能具有广泛的表型影响。我们的数据显示，在一部分年龄位置存在表观遗传钟的潜力，这令人兴奋，但需要进一步确认。
