Data from: Patterns of methylation and transcriptional plasticity during thermal acclimation in a reef-building coral

Phenotypic plasticity can buffer organisms against short-term
environmental fluctuations. For example, previous exposure to increased
temperatures can increase thermal tolerance in many species. Previous
studies have found that this acclimation response is associated with
changes in the magnitude of the gene expression response (hereafter,
“transcriptional response modulation”). However, mechanisms mediating this
gene expression response and, ultimately, phenotypic plasticity remain
largely unknown. Epigenetic modifications are good candidates for
modulating transcriptional response, as they broadly correlate with gene
expression. Here, we investigate changes in DNA methylation as a possible
mechanism controlling shifts in gene expression plasticity and thermal
acclimation in the reef-building coral Acropora nana. We find that gene
expression response to acute stress is altered in corals acclimated to
different temperatures, with many genes exhibiting a dampened response to
heat stress in corals pre-conditioned to higher temperatures. At the same
time, we observe shifts in methylation during both acclimation (11 days)
and acute heat stress (24 hours). We observed that the acute heat stress
results in shifts in gene-level methylation and elicits an acute
transcriptional response in distinct gene sets. Further,
acclimation-induced shifts in gene expression plasticity and differential
methylation largely occur in separate sets of genes. We found no overall
correlation between the magnitude of differential methylation and the
change in gene expression plasticity. We do find a small but statistically
significant number of genes exhibiting dampened expression response and
shifts in methylation (14 genes), which could be candidates for further
inquiry. Overall, our results suggest transcriptional response modulation
occurs independently of methylation changes induced by thermal
acclimation.