Transcriptome-Wide Identification and Analysis Reveals m6A Regulation of Porcine Intestinal Epithelial Cells Under TGEV Infection

Transmissible gastroenteritis virus (TGEV) represents a critical intestinal pathogen responsible for acute enteritis in pigs, posing significant challenges to global swine production biosecurity. N⁶-methyladenosine (m⁶A), the most abundant epitranscriptomic mark in eukaryotic messenger RNA, has emerged as a regulatory factor in host-virus interactions. Despite its recognized importance, the functional significance of m⁶A modifications during TGEV infection of porcine jejunal epithelial (IPEC-J2) cells remains unexplored. Here, we established a TGEV-infected IPEC-J2 cell model and we employed methylated RNA immunoprecipitation sequencing (MeRIP-seq) to comprehensively profile the m⁶A epitranscriptomic landscape and identify N⁶-methyladenosine-bearing transcripts in IPEC-J2 cells following TGEV challenge. A total of 14,813 m⁶A peaks were identified in the IPEC-J2, distributed in 7728 genes, mainly enriched in the CDS and 3'-UTRs. After TGEV infection, we identified 832 m⁶A peaks and 1660 genes with significant changes. Integrative analysis revealed a direct positive relationship between N⁶-methyladenosine modification abundance and transcript expression levels. Through integrated examination of MeRIP-Seq and RNA-Seq datasets, we identified 105 transcripts bearing m⁶A modifications, which were mainly enriched in the mTOR signaling pathway. Protein-protein interaction (PPI) network and RT-qPCR analysis demonstrated that <i>SOS2</i> probably acts an important moderator in TGEV infection. This work contributes to understanding the m⁶A modification landscape in the TGEV-swine model and suggests <i>SOS2</i> as potential target for future antiviral strategies.