Integrative MeRIP-seq and RNA-seq analysis reveals m⁶A-mediated epigenetic regulation of host-virus interactions during HSV-2 infection.

Herpes simplex virus type 2 (HSV-2), a highly prevalent pathogen responsible for genital herpes, is characterized by neurotropism and the ability to establish lifelong latent infection. N6-methyladenosine (m6A) is a widespread epitranscriptomic modification that plays a critical role in regulating RNA metabolism and gene expression. In this study, we used methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to profile m6A modifications and transcriptomic changes in human foreskin fibroblasts (HFF-1) infected with HSV-2. We identified 9477 common m6A peaks and 15,842 differentially methylated peaks, with a predominant localization within coding sequences. Analysis of m6A modification sites on HSV-2 gene transcripts from MeRIP-seq data identified a total of 145 m6A sites across 63 viral genes. Functional enrichment analysis revealed that differentially m6A-modified genes are involved in key biological processes, including gene expression, neural signaling, and immune responses. Pathway analysis highlighted significant enrichment in the NOD-like receptor signaling pathway, Rap1 signaling, endocytosis, and adherens junction pathways. RNA-seq analysis identified 6172 differentially expressed genes, of which 3181 were upregulated and 2991 were downregulated. Integrative analysis of the two datasets revealed that genes exhibiting both altered m6A methylation and differential expression were significantly enriched in pathways including TNF signaling and the NOD-like receptor pathway. This study provides the first comprehensive landscape of m6A epitranscriptomic modifications and their association with transcriptomic reprogramming during HSV-2 infection, offering new insights into the epigenetic mechanisms of virus-host interactions.