Quantifying genome-wide cytosine methylation in response to hypoxia in the gills, muscle, and brain of an African cichlid fish

Phenotypic responses to the environment may be controlled via cytosine methylation (5mC) and its effects on gene expression. We test whether hypoxia influences plastic or heritable changes in the quantity of 5mC in the genomes of a widespread African cichlid, the Egyptian mouth-brooder, Pseudocrenilabrus multicolor (Scholler, 1903). Fish were collected from three sites in southwestern Uganda: one hypoxic swamp, one swamp-river ecotonal area, and one well-oxygenated river site. F1 offspring were raised in a split-brood experiment under both high- (normoxic) and low-oxygen (hypoxic) conditions. Previous work on morphological and physiological variation that stemmed from this experiment showed that the majority of responses to hypoxia were plastic, with some genetic variation in plasticity observed among populations. To partition evolutionary and plastic effects on 5mC, we estimated the percentage of methylated cytosines in the genomes of the muscle, gills, and brain. Our results showed that the quantity of 5mC varied among tissues, and there were significant differences between rearing treatments for the gills in families from the swamp site, with higher cytosine methylation levels under hypoxic laboratory conditions. No other significant differences were observed, but more extensive sampling schemes, as well as contrasting genomic 5mC patterns to transcriptional variation, could shed additional light on the molecular basis of plasticity in response to hypoxia.