Gene body methylation (GBM) has been hypothesized to modulate responses to environmental change, including transgenerational plasticity, but the evidence thus far has been lacking. Here we show that coral fragments reciprocally transplanted between two distant reefs respond predominantly by increase or decrease in genome-wide GBM disparity: The range of methylation levels between lowly and highly methylated genes becomes either wider or narrower. Remarkably, at a broad functional level this simple adjustment correlated very well with gene expression change, reflecting a shifting balance between expressions of environmentally responsive and housekeeping genes. In our experiment, corals in a lower-quality habitat up-regulated genes involved in environmental responses, while corals in a higher-quality habitat invested more in housekeeping genes. Transplanted fragments showing closer GBM match to local corals attained higher fitness characteristics, which supports GBM’s role in acclimatization. Fixed differences in GBM between populations did not align with plastic GBM changes and were mostly observed in genes with elevated F_ST, which suggests that they arose predominantly through genetic divergence. However, we cannot completely rule out transgenerational inheritance of acquired GBM states.

据推测，基因体甲基化（GBM）可以调节对环境变化的响应，包括跨代可塑性，但迄今为止尚缺乏证据。在这里，我们显示了相互移植在两个遥远珊瑚礁之间的珊瑚片段主要通过增加或减少全基因组GBM差异来响应：低甲基化和高度甲基化基因之间的甲基化水平范围变宽或变窄。值得注意的是，在广泛的功能水平上，这种简单的调节与基因表达的变化非常相关，反映了环境响应基因和管家基因的表达之间的平衡转移。在我们的实验中，低质量栖息地的珊瑚上调基因参与环境响应，而高质量栖息地的珊瑚在管家基因上投入更多。移植后的碎片显示出与当地珊瑚更接近的GBM匹配度，获得了更高的适应性，这支持了GBM在适应环境中的作用。人群之间GBM的固定差异与GBM的塑性变化并不吻合，并且大多数在具有高表达的基因中观察到F _ST，表明它们主要是通过遗传差异产生的。但是，我们不能完全排除获得性GBM状态的跨代继承。