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

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.