Abstract: Coral reefs face significant challenges under rapid environmental change, driven by human activity throughout the last century. Steadily increasing sea surface temperatures, in conjunction with dramatic marine heat waves, induce an environmental stress response in corals that often leads to bleaching and death. During heat stress, corals must respond rapidly at the cellular level to regulate molecular processes and improve their chances of survival. Previous studies have characterized several transcriptomic shifts associated with the coral heat stress response. However, the upstream epigenetic mechanisms that regulate gene expression remain largely unknown in these organisms. To address this, we focused on chromatin packing, a process that controls the accessibility of genes to transcriptional machinery via chemical modifications of histone proteins. To study these mechanisms, we adapted a Chromatin Immunoprecipitation sequencing (ChIP-seq) protocol for reef-building corals. This technique uses immunoprecipitation to map enrichment of histone post-translational modifications across the genome through sequencing. After verifying the robustness of this protocol in coral tissues, we deployed ChIP-seq during an acute 24-hour heat stress assay to measure early epigenetic responses in the coral Pocillopora damicornis. To confirm whether specific histone modifications resulted in concomitant shifts in gene expression, we performed mRNA-sequencing at identical time points. We identified significant changes in the coral epigenome as early as ~3 hours after initiating heat stress, with differences increasing in magnitude under prolonged exposure. Notably, we observed significant increases in H3K27 acetylation—a marker associated with active transcription—on genes involved in protein misfolding, immune responses, cell signaling, and transcriptional regulation. In parallel, a loss of H3K27 acetylation was observed in genes related to transmembrane transport and metabolic processes. These findings are consistent with the cellular stress responses outlined in previous literature and provide novel mechanistic insight into how corals rapidly regulate their survival at the epigenetic level. To our knowledge, this study represents the first locus-specific epigenetic profiling of corals during heat stress.
Biosketch: George Warfel is a fourth-year undergraduate at Northwestern University studying Chemical Engineering and Biological Sciences. He works in the Marcelino lab within the Civil and Environmental Engineering department and Center for Physical Genomics and Engineering. His research focuses on probing the molecular mechanisms that drive environmental stress responses in reef-building corals using next-generation sequencing techniques. He was recently awarded the NSF Graduate Research Fellowship and plans to continue his studies at a PhD program in bioengineering or molecular sciences.
Andrew Liguori
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