Genome-wide Methylation Patterns Under Caloric Restriction inDaphnia magna

Abstract

28The degradation of epigenetic control with age is associated with progressive diseases of 30 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 32 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 34 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 36 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. 38However, 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 40 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 42 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 44 cancers. 46 48 piRNAs in transposon silencing. Science

Daphnia magna modifies its gene expression extensively in response to caloric restriction revealing a novel effect on haemoglobin isoform preference

“…To contrast gene expression between food levels, we selected one genotype that demonstrated increased longevity here. We have previously established that life history traits (Garbutt & Little, 2014, DNA methylation (Hearn, Pearson, Blaxter, Wilson, & Little, 2019) and miRNA expression in the selected strain (Hearn et al, 2018) respond to CR; indeed, the miRNA was sequenced from the same set of RNA extractions. Using geneand transcript-level expression change of this CR-responsive genotype of D. magna, we now identify known and novel gene families and metabolic pathways implicated in CR.…”

“…Gene ontology term enrichment was tested in topGO (Alexa & Rahnenfuhrer, 2016) for each category of significant gene from geneand transcript-level analyses using D. magna GO term annotations following Hearn et al (2018) and Hearn, Pearson, et al (2019). A conservative p-value threshold of 0.01 was applied with no multiple testing correction in line with topGO author recommendation (Section 6.2.…”

“…Average TPM gene expressions calculated in tximport and normalized in DESeq2 for CR and NF were correlated with the proportion of methylation within genes for the corresponding treatment using data taken from Hearn, Pearson, et al (2019). A schematic of the relationships between data sets in this work is given in File S1.…”

“…A schematic of the relationships between data sets in this work is given in File S1. Proportion methylated was defined as the count of methylated reads over the total reads at CpG sites within a genic region (exons + introns) aligned against the D. magna genome assembly (version 2.4) using Bismark (Krueger & Andrews, 2011), see Hearn, Pearson, et al (2019) for further detail. Genic regions were defined from the D. magna reference annotation (downloaded from http:// arthr opods.eugen es.org/Evide ntial Gene/daphn ia/daphn ia_magna/ Genes/ early acces s/dmags et7fi nloc9c.puban.gff.gz).…”

“…Genic regions were defined from the D. magna reference annotation (downloaded from http:// arthr opods.eugen es.org/Evide ntial Gene/daphn ia/daphn ia_magna/ Genes/ early acces s/dmags et7fi nloc9c.puban.gff.gz). CpG counts for CR or NF were extracted by combining CpG counts of the six replicates per treatment from Hearn, Pearson, et al (2019) from Bismark bam files.…”