Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians

• Published in: PloS one Vol. 11; no. 3; p. e0150840
• Main Authors: Marsh, Adam G, Hoadley, Kenneth D, Warner, Mark E
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 07-03-2016; Public Library of Science (PLoS)
• Subjects: Acclimation; Acclimatization; Acclimatization - genetics; Acidification; Acropora digitifera; Acropora millepora; Adaptation; Analysis; Animals; Annotations; Background levels; Baseline studies; Biology and life sciences; Climate change; Coral Reefs; Corals; CpG islands; CpG Islands - genetics; Crassostrea gigas; Cytosine; Deoxyribonucleic acid; DNA; DNA methylation; Earth Sciences; Environmental stress; Epigenesis, Genetic; Epigenetic inheritance; Epigenetics; Fitness; Functional groups; Gene expression; Genes; Genomes; Genomics; Global climate; Global temperature changes; Global warming; Guanosine; Heat resistance; Nematostella vectensis; Nucleotide Motifs - genetics; Ocean acidification; Ocean warming; Open access; Physical Sciences; Research and Analysis Methods; Sea Anemones - genetics; Sea Anemones - physiology; Temperature; Transcription; Urbanization; United States
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0150840

Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG) motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera) and an anemone (Nematostella vectensis). Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS) are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to environmental stress in reef corals and potential roles of epigenetics on survival and fitness in the face of global climate change.