Affiliations: 1) Princeton University, Princeton, NJ; 2) University of Montana, Missoula, MT
Keywords: Molecular Evolution
Epigenetic modifications such as DNA methylation act as means for phenotypic plasticity, as these changes drive quick and reversible phenotypic responses in comparison to sequence-level genetic changes. Peromyscus maniculatus populations can span altitudinal gradients, and consequently harbor plastic physiological mechanisms to adapt to low oxygen conditions typically found in high altitudes. However, studying DNA methylation changes specific to oxygen metabolism can be challenging, as wild mice can harbor non-specific methylation differences due to a large number of environmental variables and lab mice can accumulate epigenetic changes that could make results less representative of mechanisms driven by natural environmental variation. We used reduced representation bi-sulfite sequencing of left ventricle tissue to identify sites that are differentially methylated in response to hypobaric hypoxia. We conducted two statistically controlled analyses of these data. In the first, we compared lab-reared mice exposed experimental hypoxia to those housed under normoxia, and in the second, we compared wild mice sampled in lowland (450 m a.s.l.) and highland conditions (4350 m a.s.l). We identified common differentially methylated sites across the two analyses, with methylation differences in the same direction for both low-oxygen conditions. Some of these sites were present within genes Zfp142, Egln3, Ppt2 and Stard13, and have at least 25% methylation difference between the low and high oxygen conditions in both analyses. Strikingly, Egln3 encodes the Egl-9 Family Hypoxia Inducible Factor 3. Egln3 is involved in the regulation of hypoxia inducible factor, a transcription factor that mediates physiological responses to hypoxic conditions and plays is a critical role in maintaining oxygen homeostasis. We also found Egln3, Ppt2 and Stard13 are connected through a common gene network, which is significantly enriched for gene ontology terms such as “protein hydroxylation”, “response to decreased oxygen levels” and “L-ascorbic acid binding”. These results underscore the prevalence of environmentally induced epigenetic modifications, possibly causing intra-specific physiological differences in deer mice populations spanning an altitudinal gradient.