Role of gene body methylation in coral acclimatization and adaptation

Abstract

Despite widespread taxonomic representation, the function of gene body methylation (GBM) remains uncertain. One hypothesis is that GBM mediates phenotypic plasticity. To investigate this hypothesis, we performed whole-genome methylation and transcriptome profiling on reciprocally transplanted colony fragments of the reef-building coral Acropora millepora. GBM was only slightly affected by transplantation but these small changes correlated with coral fitness in the new environment. Specifically, for transplanted corals, similarity in GBM patterns to native corals positively correlated with growth rate, as well as carbohydrate, protein, lipid and endosymbiont content. Between populations, elevated GBM positively correlated with transcription, supporting previous findings that GBM is associated with stable and active transcription. Contrary to expectations however, changes in transcription as a result of transplantation did not correlate with changes in GBM and did not predict fitness. This indicates that on physiological time scales GBM is not directly coupled to transcription, leaving open the question about the mechanism linking GBM to fitness during acclimatization.

Marine Environmental Epigenetics

“…The link between phenotypic plasticity and DNA methylation is supported by the exposure of an environmentally sensitive coral to ocean acidification conditions for six weeks, revealing a decline in growth, changes in metabolomic profiles, and an increase in the proportion of methylated DNA (Putnam et al 2016). Sequencing of methylation-enriched fractions and whole-genome bisulfite sequencing provides further mechanistic clarification regarding coral responses to transplantation between different thermal environments [Acropora millepora (Dixon et al 2017)] and exposure to low-pH environments [Stylophora pistillata (Liew et al 2018b)]. Additionally, several works have described a role for DNA methylation in Pacific oysters [Magallana (Crassostrea) gigas], including transcriptional control (Gavery & Roberts 2010, Olson & Roberts 2014, patterns of oyster DNA methylation through development (Riviere et al 2013(Riviere et al , 2017, a role for methylation in alternative splicing (Song et al 2017), and the potential for functionally important promoter methylation (Saint-Carlier & Riviere 2015).…”

“…Accordingly, an environmental parameter would induce an epigenetic effect that remains for some period of time and within that time incurs phenotypic consequences. While studies of methylation dynamics in marine systems are few and focus only on several time points (Dixon et al 2017, Liew et al 2018b, Putnam et al 2016, a role for epigenetics in reversible acclimatization is clear in other model systems (Feil & Fraga 2012). This flexibility in phenotype may provide a buffer against rapid environmental change, but the uncertainty of the role of epigenetics and acclimatization in climate change response comes from the wash-in and wash-out nature of these effects (Burggren 2015).…”