Yang Y et al. (2020), Genome-Wide DNA Methylation Signatures of Sea C...

ECB-ART-49641

Genes (Basel) 2020 Aug 31;119:. doi: 10.3390/genes11091020.

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Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation.

Yang Y , Zheng Y , Sun L , Chen M .

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Organisms respond to severe environmental changes by entering into hypometabolic states, minimizing their metabolic rates, suspending development and reproduction, and surviving critical ecological changes. They come back to an active lifestyle once the environmental conditions are conducive. Marine invertebrates live in the aquatic environment and adapt to environmental changes in their whole life. Sea cucumbers and sponges are only two recently known types of marine organisms that aestivate in response to temperature change. Sea cucumber has become an excellent model organism for studies of environmentally-induced aestivation by marine invertebrates. DNA methylation, the most widely considered epigenetic marks, has been reported to contribute to phenotypic plasticity in response to environmental stress in aquatic organisms. Most of methylation-related enzymes, including DNA methyltransferases, Methyl-CpG binding domain proteins, and DNA demethylases, were up-regulated during aestivation. We conducted high-resolution whole-genome bisulfite sequencing of the intestine from sea cucumber at non-aestivation and deep-aestivation stages. Further DNA methylation profile analysis was also conducted across the distinct genomic features and entire transcriptional units. A different elevation in methylation level at internal exons was observed with clear demarcation of intron/exon boundaries during transcriptional unit scanning. The lowest methylation level occurs in the first exons, followed by the last exons and the internal exons. A significant increase in non-CpG methylation (CHG and CHH) was observed within the intron and mRNA regions in aestivation groups. A total of 1393 genes were annotated within hypermethylated DMRs (differentially methylated regions), and 749 genes were annotated within hypomethylated DMRs. Differentially methylated genes were enriched in the mRNA surveillance pathway, metabolic pathway, and RNA transport. Then, 24 hypermethylated genes and 15 hypomethylated genes were Retrovirus-related Pol polyprotein from transposon (RPPT) genes. This study provides further understanding of epigenetic control on environmental induced hypometabolism in aquatic organisms.

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References [+] :

Akalin, methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. 2012, Pubmed

	Figure 1. Gene expression levels of DNA methyltransferases, Methyl-CpG binding domain proteins, and DNA demethylase in sea cucumber intestine during aestivation. Significant levels are indicated by * (p < 0.05).
	Figure 2. Heat maps of CpG density patterns (Sample A1 and Sample C1 as representative samples for aestivation and control groups). CpG density (x-axis) is defined as the number of CpG dinucleotides in 200 bp windows. The methylation level (y-axis) is defined as the average methylation level of cytosines in CpGs. The thin black lines denote the median methylation level of CpGs at the given local density. The red color gradient indicates an abundance of CpGs that fall into bins of given methylation levels and CpG densities. The blue bar charts show the distribution of CpG densities. The green bar charts show the distribution of methylation levels.
	Figure 3. Canonical DNA methylation profiles of the entire transcriptional units (Sample A1 and Sample C1 as representative samples for aestivation and control groups). The canonical gene structure is defined by seven different features. The length of each feature was normalized and divided into equal numbers of bins. Each dot denotes the mean methylation level per bin, and the respective lines denote the 5-bin moving average. The green vertical line indicates the mean location of the transcription start sites.
	Figure 4. GO analysis of differentially methylated regions (DMRs)-related genes. The x-axis represents three domains of GO while the y-axis represents the gene number in every pathway and processes.
	Figure 5. Pathway analysis of DMRs-related genes.