Chrysemys picta bellii Raw sequence reads

DNA methylation alters gene expression but not DNA sequence, and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylationin TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear. Here we test for broad differences in genome-wide DNA methylation between male and female hatchling gonads of the TSD painted turtle Chrysemys picta using Methyl DNA Immunoprecipitation sequencing (MeDIP-seq), to identify differentially methylated candidates for future study. We also examine the genome-wide nCpG distribution (which affects DNA methylation) in painted turtlesand test for historic methylation in genes regulating vertebrate gonadogenesis.Turtle global methylation was consistent with other vertebrates (57% of the genome, 78% of all CpG dinucleotides). Numerous genes regulating turtle gonadogenesis exhibited sex-specific methylation and were proximal to methylated repeats. nCpG distribution predicted actual turtle DNA methylation, and was bimodal in gene promoters (as other vertebrates) and introns (unlike other vertebrates). Differentially-methylated genes, including regulators of sexual development, had lower nCpG content indicative of higher historic methylation. Ours is the first demonstration that sexually dimorphic DNA methylation is pervasive in turtle gonads (perhaps mediated by repeat methylation) and targets numerous regulators of gonadal development, consistent with the hypothesis that it may regulate thermosensitive transcription in TSD vertebrates. However, further research during embryogenesis will help test this hypothesis and the alternative that instead, most differential methylation observed in hatchlings is the byproduct of sexual differentiation and not its cause..