Global profiling reveals common and distinct N6-methyladenosine (m6A) regulation of innate immune responses during bacterial and viral infections

N⁶-methyladenosine (m⁶A) is a dynamic post-transcriptional RNA modification influencing all aspects of mRNA biology. While m⁶A modifications during numerous viral infections have been described, the role of m⁶A in innate immune response remains unclear. Here, we examined cellular m⁶A epitranscriptomes during infections of Pseudomonas aeruginosa and herpes simplex virus type 1 (HSV-1), and lipopolysaccharide (LPS) stimulation to identify m⁶A-regulated innate immune response genes. We showed that a significant portion of cellular genes including many innate immune response genes underwent m⁶A modifications in 5'UTR and 3'UTR. We identified common and distinct m⁶A-modified genes under different stimulating conditions. Significantly, the expression of a subset of innate immune response genes was positively correlated with m⁶A level. Importantly, we identified genes that had significant enrichments of m⁶A peaks during P. aeruginosa infection following knockdown of m⁶A “eraser” ALKBH5, confirming the regulation of these genes by m⁶A and ALKBH5. Among them, we confirmed the association of m⁶A modification with gene expression in immune response genes TNFAIP3, IFIT1, IFIT2 and IFIH1. Taken together, our results revealed the vital role of m⁶A in regulating innate immunity against bacterial and viral infections. These works also provided rich resources for the scientific community.