Landscape of N6-methyladenosine (m6A) methylation in porcine cells identifies candidate genes associated with porcine epidemic diarrhea virus infection.

Porcine epidemic diarrhea virus (PEDV) infection leads to serious intestinal disease in piglets, often leading to high mortality rates and substantial economic losses. Understanding host-PEDV interactions is crucial for PEDV therapeutic strategies. N6-methyladenosine (m6A) methylation has been proven to play an important role in host antiviral immunity. However, transcriptome-wide profiling patterns and the biological functions of host m6A methylation in response to PEDV infection remain incompletely understood. This study first observed significant upregulation of m6A regulators (METTL3, FTO, WTAP, YTHDC1, and YTHDF2) in PEDV infection. Following transcriptome-wide m6A methylation and gene expression profiling, this study identified 803 differentially methylated peaks with 674 differentially expressed m6A-methylated genes and 345 differentially expressed genes (DEGs) after PEDV infection. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these differentially methylated genes were enriched mainly in lysine degradation, histidine metabolism, and the ubiquitin-mediated proteolysis pathway, whereas these DEGs were enriched in negative regulation of viral genome replication, viral protein interaction with cytokines and cytokine receptors, nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling, and immune response-related signaling pathways. Furthermore, the joint analysis of RNA sequencing (RNA-seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) identified 16 differentially expressed genes with m6A methylation (AMDHD1, CPM, DCTPP1, GIMAP1, GVIN1, HERC6, LOC100522040, LOC106510546, NFAT5, PIM3, PPARGC1B, RASSF2, SAPCD2, URB2, XRRA1, and ZC3HAV1L), which were associated with immune response and metabolism. Taken together, the study results map the dynamic landscape of host m6A methylation and demonstrate the functional enrichment of m6A methylated genes during PEDV infection, thereby providing a theoretical framework for future research on the role of m6A methylation in resistance to PEDV infection.