State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China.
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, PR China.
Fish Shellfish Immunol. 2022 Aug;127:748-757. doi: 10.1016/j.fsi.2022.07.008. Epub 2022 Jul 11.
Circular RNAs (circRNAs) are novel endogenous non-coding RNAs (ncRNAs) and can be acted as competing endogenous RNAs (ceRNAs) to regulate microRNA (miRNA) and downstream gene expression. Recently, mA modification has been found in circRNA, and mA circRNAs also play important roles in various biological processes and a variety of diseases. Our previous study had been demonstrated that circRNAs were differentially expressed in skin ulceration syndrome (SUS) diseased sea cucumber Apostichopus japonicus. However, whether the function of circRNAs are dependent on mA levels are largely unknown. Here, we firstly investigated the genome-wide map of mA circRNAs in sea cucumbers with different stages of Vibrio splendidus challenge, that's Control group, SUS-diseased group, and SUS-resistant group. MeRIP-seq revealed that mA abundances were enriched in circRNAs in all three groups, especially for SUS-resistant group. Among them, more than 62% of modified circRNAs harbor only a single mA peak and about 55% of mA sites in circRNAs were derived from sense overlapping in each group. After V. splendidus infection, we found that most of mA peaks in circRNAs were upregulated and less were downregulated in both SUS-diseased and SUS-resistant groups when compared with Control. Furthermore, GO analysis indicated that the host genes of circRNAs with dysregulated mA peaks in SUS-diseased and SUS-resistant groups were both mainly enriched in the adhesion pathway. More importantly, we discovered that more than 50% mA circRNAs showed a positive correlation between the circRNAs expression and mA methylation levels both in SUS-diseased and SUS-resistant groups. Therefore, a core circRNA-miRNA-mRNA (ceRNA) network whether influenced by mA modification was constructed based on conjoint analysis. Our results indicated that several selected mA circRNAs bind with miRNAs were mainly targeting to ubiquitylation system and adhesion pathway. What's more, three candidate mA circRNAs and three target genes were validated by MeRIP-qPCR and qPCR, whose mA levels in circRNA and mRNA expressions were consistent with disease occurrence or disease resistance. All of our current findings suggested that mA circRNAs could play important roles during pathogen infection and might be served as a new molecular biomarker in SUS disease diagnose of A. japonicus.
环状 RNA（circRNA）是一种新型的内源性非编码 RNA（ncRNA），可以作为竞争性内源性 RNA（ceRNA）来调节 microRNA（miRNA）和下游基因表达。最近，circRNA 中的 mA 修饰已被发现，mA circRNA 也在各种生物过程和多种疾病中发挥重要作用。我们之前的研究表明，在患有皮肤溃疡综合征（SUS）的海参中，circRNA 存在差异表达。然而，circRNA 的功能是否依赖于 mA 水平还知之甚少。在这里，我们首次研究了不同阶段的灿烂弧菌（Vibrio splendidus）攻毒下海参的全基因组 mA circRNA 图谱，即对照组、SUS 患病组和 SUS 抗性组。MeRIP-seq 显示，mA 丰度在所有三组的 circRNA 中都富集，尤其是 SUS 抗性组。其中，超过 62%的修饰 circRNA 只含有一个 mA 峰，并且在每组中，约 55%的 mA 位点来源于 sense 重叠。在 V. splendidus 感染后，我们发现与对照组相比，SUS 患病组和 SUS 抗性组中大多数 circRNA 的 mA 峰都上调，下调的较少。此外，GO 分析表明，SUS 患病和 SUS 抗性组中差异表达的 mA 峰的 circRNA 的宿主基因主要富集在黏附途径中。更重要的是，我们发现，超过 50%的 mA circRNA 在 SUS 患病和 SUS 抗性组中表现出 circRNA 表达和 mA 甲基化水平之间的正相关。因此，基于联合分析构建了一个核心 circRNA-miRNA-mRNA（ceRNA）网络，该网络是否受 mA 修饰的影响。我们的结果表明，几个选定的与 mA 结合的 circRNA 主要靶向泛素化系统和黏附途径。更重要的是，通过 MeRIP-qPCR 和 qPCR 验证了三个候选 mA circRNA 和三个靶基因，circRNA 和 mRNA 的 mA 水平与疾病发生或疾病抗性一致。我们目前的所有发现都表明，mA circRNA 在病原体感染过程中可能发挥重要作用，并可能成为 A. japonicus SUS 疾病诊断的新分子生物标志物。
