Remodeling of the Epigenetic Landscape in Rainbow Trout, Oncorhynchus mykiss, Offspring in Response to Maternal Choline Intake

The objective of this paper was to determine whether shifts in the methylome in rainbow trout (Oncorhynchus mykiss) are correlated with transcriptomic changes during early development in response to maternal dietary choline intake. Three experimental diets were formulated to have different levels of choline: (a) 2065 ppm choline (Low Choline, 0% supplementation), (b) 5657 ppm choline (Medium Choline, 0.6% supplementation), and (c) 9248 ppm choline (High Choline, 1.2% choline supplementation). Six rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Reduced representational bisulfite sequencing (RRBS) was utilized to measure genome-wide methylation differences in offspring immediately after hatching. When comparing to the Medium Choline offspring, differential DNA methylation occurred more in the Low Choline offspring than High Choline, especially in genic features like promoters. The differentially methylated CpGs (q ≤ 0.01) were identified evenly between CpG islands and shores in the genome, mostly found in the introns of genes. Genes such as fabp2 and leap2B associated with protein binding, fatty acid binding, DNA binding, and response to bacteria were differentially methylated and detected as differentially regulated genes by previous RNA-seq analysis. Although these findings indicate that levels of dietary choline available in broodstock diets alters offspring DNA methylation; most differentially expressed genes were not associated with differential DNA methylation, suggesting additional mechanisms playing a role in regulating gene expression in response to maternal choline intake. To identify metabolic regulatory mechanisms affected by choline availability in rainbow trout broodstock diets associated with improved offspring growth performance, we fed one of three commercial diets formulated with different levels of choline: Low (2065 ppm choline), Medium (5657 ppm choline), and High (9248 ppm choline). We then performed gene expression profiling analysis using data obtained from RNA-seq of 18 rainbow trout sac-fry at 0-days post-hatch (dph) and 14-dph through a main effect of diet and diet-by-broodstock family interaction. Differential methylation analysis from reduced representational bisulfite sequencing (RRBS) was performed to investigate methylation levels concurrently with gene expression levels at 0-dph.