Global N-methyladenosine methylation analysis reveals the positive correlation between mA modification and mRNA abundance during Apostichopus japonicus disease development.

N-methyladenosine (mA), the most abundant epitranscriptomic modification in eukaryotic messenger RNA (mRNA), plays important roles in regulation of gene expression for fundamental biological processes and diverse physiological functions, including combating with pathogen infection. Here, we were first profile transcriptome-wide mA sequencing in four stages of skin ulceration syndrome-diseased Apostichopus japonicus following Vibrio splendidus infection, including Control (healthy), Early (small ulcer), Later (extensive ulcer), and Resistant (no ulcer) groups. Our results revealed that three experimental groups were all extensively methylated by mA and the proportion of the mA modified genes were also significantly increased to 28.90% (Early), 27.97% (Later), and 29.98% (Resistant) when compared with Control group (15.15%), indicating mA modification could be induced by V. splendidus infection. Intriguingly, we discovered a positive correlation between the mA methylation level and mRNA abundance, indicating a positive regulatory role of mA in sea cucumber gene expression during V. splendidus infection. Moreover, genes with specific and differentially expressed mA methylation in Later group were both enriched in cell adhesion, while Early and Resistant groups were both mainly involved in DNA conformation change and chromosome organization when compared with Control, suggesting the higher-methylated mA might serve as "conformational marker" and associated to the initiation of related anti-disease genes transcription in order to improve disease resistance of sea cucumber. Subsequently, we selected the pivotal genes enriched in cell adhesion pathway and found that the IggFc-binding protein (FcGBP) and Fibrocystin-L both had higher levels of mA methylation and higher level of mRNA expressions in Later group. Conversely, Fibrinogen C domain-containing protein 1 (F1BCD1) gene presented as an antibacterial role in sea cucumber and showed higher mRNA expression and higher mA methylation in Resistant group and lower mRNA level in Later group. The levels of mA methylation and mRNA abundance of FcGBP and F1BCD1 genes indicates disease occurrence or disease resistant were also verified by MeRIP-qPCR. Overall, our study presents the first comprehensive characterize of dynamic mA methylation modification in the different stages of disease in sea cucumber. These data provide an invaluable resource for future studies of function and biological significance of mA in mRNA in marine invertebrates.