Epigenetic plasticity is a driver of heritable pollution tolerance in Atlantic killifish [RNA-seq]

Heritable epigenetic adaptation to environmental stressors is a compelling but highly contested possibility. Previously, we showed evidence of a generationally heritable epigenetic memory at the cytochrome P450 1A (CYP1A) gene in wild Atlantic killifish (Fundulus heteroclitus) with evolved tolerance to PAH. This memory leads to blunted induction of CYP1A by PAH; this blunting that protects against polycyclic aromatic hydrocarbon (PAH)-induced cancer. Here, using Oxford Nanopore long-read sequencing in PAH-tolerant and sensitive wild-type embryos, we show that genome-wide, PAH-tolerant embryos showed reduced plasticity in DNA methylation response to PAH vs. PAH sensitive embryos that was not due to mutational loss of CpG sites. Notably, we observed population differences in gene methylation in pathways linked to the PAH tolerance phenotype, including AHR and voltage-gated potassium channel signaling, as well as developmental processes and energy metabolism. Specifically, we observed PAH-induced loss of CYP1A gene body methylation in PAH-sensitive (86% CpG methylation in control, decreased to 63% in exposed), but not -tolerant (84% control, 86% exposed), embryos. We observed similar patterns at CYP1B, CYP1C, and the aryl hydrocarbon receptor repressor, AHRR, which show similarly blunted expression. This genic methylation loss was correlated with decreased levels of natural anti-sense RNA transcripts in cis (cis-NATs), which may regulate transcription of these genes. Our data support the existence of stable epigenetic responses to chronic environmental stressors in a natural experimental setting, with broad implications for natural or directed adaptation strategies for other populations. Overall design: Stranded, paired-end RNA sequencing in four pools of embryos (N=10 embryos/pool): two pools each from PAH-sensitive and PAH-tolerant populations, one control and one challenged with PAH (Elizabeth River sediment extract, ERSE).