MBD4 from the pearl oyster Pinctada fucata martensii involved in immune response by binding to methylated DNA sequences

DNA methylation is a conserved epigenetic modification with a critical role in regulating gene expression and maintaining genomic stability. Methyl-CpG-binding protein 4 (MBD4) binds to the methylated sequences and regulates gene expression. The Pearl oyster Pinctada fucata martensii is a commercial oyster species used for cultivating seawater pearls in China. To clarify the function of MBD4 from P. f. martensii (PmMBD4), we obtained the regulatory genes of PmMBD4 by DNA affinity purification sequencing (DAP-seq) and RNA interference (RNAi) techniques and analyzed the binding ability of PmMBD4 to methylated DNA sequences. The results of subcellular localization analysis showed that PmMBD4 was present in both nucleus and cytoplasm. The combined analysis of DAP-seq and whole genome bisulfite sequencing revealed that all the binding fragments of PmMBD4 were methylated. The downregulated expression of PmMBD4 by RNAi decreased the enzyme activities of superoxide dismutase, catalase, and inducible nitric oxide synthase. The combined analysis of DAP-seq and transcriptome showed that PmMBD4 inhibited the immune response through the Lysosome and other signaling pathways. These results indicate that PmMBD4 is involved in regulating the immune response in pearl oysters by binding to methylated DNA sequences. • PmMBD4 was mainly localized in the nucleus. • All of the binding fragments of PmMBD4 contained methylation modification. • Down-regulation of PmMBD4 decreased the activities of SOD, CAT and iNOS. • PmMBD4 inhibited the immune response of Pearl oyster.