Genome-wide Methylation Patterns Under Caloric Restriction in Daphnia magna.

Abstract

The degradation of epigenetic control with age is associated with progressive diseases of ageing, including cancers, immunodeficiency and diabetes. Reduced caloric intake slows the effects of aging and age-related diseases, a process likely to be mediated by the impact of caloric restriction on epigenetic factors such as DNA methylation. We used whole genome bisulphite sequencing to study how DNA methylation patterns change with diet in a small invertebrate, the crustacean Daphnia magna. Daphnia show the classic response of longer life under CR, and they reproduce clonally, which permits the study of epigenetic changes in the absence of genetic variation. Global CpG methylation was 0.7-0.9%, and there was no difference in overall methylation levels between normal and calorie restricted replicates. However, 453 regions were differentially methylated (DMRs) between the normally fed and calorie restricted (CR) replicates. Of these 61% were hypomethylated in the CR group, and 39% were hypermethylated in the CR group. Gene Ontogeny (GO) term enrichment of hyper and hypo-methylated genes showed significant over- and under-representation in three molecular function terms and four biological process GO terms. Notable among these were kinase and phosphorylation activity, which have a well-known functional link to cancers.