Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians
Date
2016-03-07
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Publisher
Public Library of Science (PLOS)
Abstract
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.
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Citation
Marsh AG, Hoadley KD, Warner ME (2016) Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians. PLoS ONE 11(3): e0150840. doi:10.1371/journal.pone.0150840