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

Jian Feng,Zhao Lai,Weiming Yuan,Shou-Jiang Gao,Yidong Chen,Xinquan Zhang,Yufei Huang,Océane Sorel,Wen Meng,Teng Zhang

doi:10.1038/s41419-022-04681-4

Abstract

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.

Highlights

Innate immunity, the first line of defense against infection, relies on pattern recognition receptors (PRRs) to sense pathogens by recognizing pathogen-associated molecular patterns (PAMPs) [1, 2]
Regulation by m6A is dynamic and reversible, which is executed by methyltransferases (“writers”) [7, 8], demethylases (“erasers”) including alkB homolog 5 (ALKBH5) and fat mass and obesity associated (FTO) [9, 10], m6A-binding proteins (“readers”) [11–13], and proteins that preferentially bind to mRNAs in the absence of m6A (“antireaders”) [14, 15]. m6A modification on RNA participates in RNA metabolism but is involved in diverse biological functions [9, 10]
Since the TLR4 pathway is primarily activated by LPS in Gramnegative bacteria [29], we examined m6A epitranscriptome following treatment of RAW264.7 cells with LPS for 6 h, which innate immune response genes, providing further insights into the biological roles of m6A modifications

Summary

INTRODUCTION

The first line of defense against infection, relies on pattern recognition receptors (PRRs) to sense pathogens by recognizing pathogen-associated molecular patterns (PAMPs) [1, 2]. (10.50%) and 228 (9.78%) genes were consistently hypermethylated and hypomethylated, respectively, at all the time points, indicating more dynamic m6A alterations during bacterial infection (Fig. 1B). Gene Set Enrichment Analysis revealed that among DEs, numerous immune response pathways including Immune system and Cytokine signaling in the immune system were highly enriched, and that these pathways were upregulated following bacterial infection (Supplementary Fig. 3A and Supplementary Table 1). We did not observe enrichment of any immune response pathways among DEs (Supplementary Fig. 7A and Supplementary Table 7), DMs

Feng et al 3

DISCUSSION

Findings

MATERIALS AND METHODS