Distribution of CpG motifs in upstream gene domains in a reef coral and sea anemone: Implications for epigenetics in cnidarians

Abstract

Coral reefs are under aault from streors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stre responses acro ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular procees with ecological fitne 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 expreion in response to temperature acclimation, and whether or not other corals and cnidarians would likewise poe these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental streors. 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 aociated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (T) are 1.38x higher than genomic background levels upstream of -2000 bp from the T. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the T. 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 expreion 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 stre in reef corals and potential roles of epigenetics on survival and fitne in the face of global climate change.