DNA methylation dynamics in Atlantic salmon (Salmo salar) challenged with high temperature and moderate hypoxia
In this study, we employed Multiplex Bisulfite Sequencing (MBS) to measure CpG methylation within a ~500 bp region around the transcription start of six thermal/hypoxia biomarker genes (cirbp, jund, pdk3, prdx6, serpinh, ucp2) in the liver of post-smolt Atlantic salmon following short-term (3 days) and prolonged (4 weeks) exposure to i) high temperature (20°C) and normoxia (~100% air saturation) (Warm & Normoxic - WN); or ii) high temperature (20°C) and moderate hypoxia (~70% air saturation) (Warm & Hypoxic - WH) as compared to iii) control conditions (12°C, ~100% air saturation) (Control - CT).We found distinct CpG methylation profiles for each treatment group based on responsive CpG sites that were strongly dependent on the duration of the exposure (i.e., 3 days vs. 4 weeks at 20°C) and also differed between regulatory genomic regions (i.e., 5'upstream region, 5'UTR, first exon, and first intron). Several of these changes in CpG methylation were highly correlated with changes in gene expression, and can be considered as potential epigenetic marks (epimarkers). Overall design: Atlantic salmon were exposed to following treatments: (1) Control (CT) constant temperature of 12°C and 100 % air saturation; (2) Warm&Normoxic (WN) incremental temperature increase (1°C per week from 12 - 20°C)  at 100% air saturation; and (3) Warm&Hypoxic (WH) decrease in oxygen content of 70% air saturation over one week, followed by two weeks of acclimation to this oxygen level, and then incremental temperature increase (1°C per week from 12 - 20°C) at 70% air saturation.