Marsh Adam G, Hoadley Kenneth D, Warner Mark E
Marine Biosciences, School of Marine Science and Policy, University of Delaware, Lewes, DE, United States of America.
Center for Bioinformatics and Computational Biology/Delaware Biotechnology Institute/University of Delaware, Newark, DE, United States of America.
PLoS One. 2016 Mar 7;11(3):e0150840. doi: 10.1371/journal.pone.0150840. eCollection 2016.
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.
珊瑚礁正受到包括全球变暖、海洋酸化和城市化在内的多种压力因素的冲击。要了解这些因素如何影响珊瑚礁的未来命运，需要在生态、生物个体和细胞层面描绘压力反应。珊瑚礁生物学的最新进展将分子过程与生态适应性相结合，并在石珊瑚鹿角珊瑚中鉴定出了一套假定的温度适应基因。我们想知道这些基因的哪些独特特征决定了它们在温度适应过程中的协同表达，以及其他珊瑚和刺胞动物是否也具有这些特征。在这里，我们聚焦于胞嘧啶甲基化这种对环境压力有反应的表观遗传DNA修饰。我们在两种刺胞动物基因组中不同功能基因组的上游启动子区域，鉴定出了胞嘧啶 - 鸟嘌呤二核苷酸（CpG）基序频率的常见保守模式：一种珊瑚（多孔鹿角珊瑚）和一种海葵（星状海葵）。我们的分析表明，CpG基序频率在与环境适应相关的功能基因的启动子区域中很突出，特别是在鹿角珊瑚中鉴定出的那些基因。转录起始位点（TSS）附近上游启动子区域的CpG位点密度比TSS上游 -2000 bp处的基因组背景水平高1.38倍。CpG使用的增加表明存在选择作用，以使DNA甲基化事件在TSS的1 kb范围内更频繁地发生。此外，观察到的基因功能组之间CpG密度的变化表明，启动子区域内的表观遗传DNA甲基化可能在多孔鹿角珊瑚和星状海葵中影响功能基因的表达反应。在特定功能组的基因中识别启动子表观遗传序列基序，建立了一种描述珊瑚礁珊瑚对环境压力的综合细胞反应以及表观遗传学在面对全球气候变化时对生存和适应性的潜在作用的方法。
