Transcriptome-wide dynamics of mA methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV.

Infectious spleen and kidney necrosis virus (ISKNV) is a highly virulent and rapidly transmissible fish virus that poses threats to the aquaculture of a wide variety of freshwater and marine fish. N6-methyladenosine (mA), recognized as a common epigenetic modification of RNA, plays an important regulatory role during viral infection. However, the impact of mA RNA methylation on the pathogenicity of ISKNV remains unexplored. Here, methylated RNA immunoprecipitation sequencing (MeRIP-seq) coupled with RNA sequencing (RNA-seq) was used to systematically detect variations in mA methylation and gene expression between ISKNV-infected and noninfected MFF-1 cells, followed by functional enrichment and co-expression joint analysis. The findings revealed that the mA methylation peaks were located mainly in coding sequences (CDSs), with more than 90% of the transcripts containing 1-5 mA peaks. Through MeRIP-seq, 4361 differentially mA-methylated mRNAs were identified. Gene enrichment analysis revealed that mA-related genes were enriched in biological processes and pathways such as gene expression, cellular structure, immune responses, and cell death. Co-expression analysis revealed that the genes differentially expressed at both the mRNA and mA modification levels were enriched in pathways such as the hippo, ErbB, and JAK-STAT pathways. The mA modification at the genome-wide transcription level of ISKNV was subsequently shown to be pronounced in several pivotal genes, such as putative vascular endothelial growth factor, ribonucleotide reductase small subunit, and E3 ubiquitin ligase. This study comprehensively describes the mA expression profile in ISKNV- and ISKNV-infected MFF-1 cells, providing a basis for investigating the role of mA modification during ISKNV infection.