Environmental Change-Dependent Inherited Epigenetic Response

Abstract

Epigenetic modifications are a mechanism conveying environmental information to subsequent generations via parental germ lines. Research on epigenetic responses to environmental changes in wild mammals has been widely neglected, as well as studies that compare responses to changes in different environmental factors. Here, we focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to either diet (~40% less protein) or temperature increase (10 °C increased temperature). Because both experiments focused on the liver as the main metabolic and thermoregulation organ, we were able to decipher if epigenetic changes differed in response to different environmental changes. Reduced representation bisulfite sequencing (RRBS) revealed differentially methylated regions (DMRs) in annotated genomic regions in sons sired before (control) and after the fathers' treatments. We detected both a highly specific epigenetic response dependent on the environmental factor that had changed that was reflected in genes involved in specific metabolic pathways, and a more general response to changes in outer stimuli reflected by epigenetic modifications in a small subset of genes shared between both responses. Our results indicated that fathers prepared their offspring for specific environmental changes by paternally inherited epigenetic modifications, suggesting a strong paternal contribution to adaptive processes.

Keywords: DNA methylation; RRBS; adaptation; exposure; inheritance; plasticity; wild mammal species.

Figure 1

Experimental setup and study aim. Male wild guinea pigs (n = 5) were exposed for two months either to an altered diet (“experiment D”, left side, green) or to an increase in temperature (“experiment H”, right side, red). Each male mated with the same two females before (first mating, T_C) and after the period of exposure (second mating, T_D and T_H). Sons sired before the father’s environmental change represented the control groups (F1_CD = control diet and F1_CH = control heat), and sons sired afterwards represented the diet (F1_D) or heat (F1_H) group. We then analyzed DNA methylation patterns before and after the treatment to identify epigenetic inheritance. In the current study, we aimed to compare genes and gene pathways of the two environmental factors by comparing epigenetic diet effects versus heat effects.

Figure 2

Total number and number of annotated differentially methylated regions (DMRs) after “experiment D” and after “experiment H”; total number of DMRs (dark-colored bars) and the number of annotated DMRs (light-colored bars) between control sons (F1L_C) and sons sired by fathers either fed a low-protein diet (F1L_D, left two bars in green) or exposed to a prolonged temperature increase (F1L_H, right two bars in red). We considered DMRs to be “annotated” when they overlapped with gene coding sequences (CDS), promoters, or CpG islands (CGIs).

Figure 3

STRING gene network of genes from annotated DMRs in livers of F1 sons after paternal exposure to a low-protein diet; STRING gene network of genes from annotated DMRs detected in the livers of all five father-sorted son groups after paternal diet change (“experiment D”). The main metabolic pathways identified are labeled by colored circles (colors of dots were chosen by the STRING database and do not account for a certain gene function), and connections between dots indicate the interaction of gene products.

Figure 4

STRING gene network of genes from annotated DMRs in livers of F1 sons after paternal exposure to temperature increase; STRING gene network of genes from DMRs detected in the livers of at least four of the five father-sorted son groups after paternal exposure to increased temperature (“experiment H”). Gene network analysis identified genes encoding for proteins (dots) with a function in the immune system, cell structure, and RNA splicing (colors of dots were chosen by the STRING database and do not account for a certain gene function).

Figure 5

Venn diagram of genes with DMRs after both environmental factors. Of the 155 genes with DMRs identified in the livers of sons sired after a paternal protein diet and the 98 genes with DMRs identified after paternal heat exposure, 21 DMRs were shared between both experiments (diet and heat). Of those, three DMRs were overlapping promoter regions, and 18 DMRs were overlapping CDSes (listed in Table 1).