M6A modifications regulate intestinal immunity and rotavirus infection.

Anmin Wang,Gaopeng Hou,Decai Wang,Wanyiin Tao,Runzhi Li,Kaiguang Zhang,Huabing Li,Jinghao Wang,Jiyu Tong,Shu Zhu,Wen Pan,Richard A Flavell,Siyuan Ding,Guorong Zhang,Juanzi Gao,Chen Qian,Xingxing Ren

doi:10.7554/elife.73628

Abstract

N6-methyladenosine (m6A) is an abundant mRNA modification and affects many biological processes. However, how m6A levels are regulated during physiological or pathological processes such as virus infections, and the in vivo function of m6A in the intestinal immune defense against virus infections are largely unknown. Here, we uncover a novel antiviral function of m6A modification during rotavirus (RV) infection in small bowel intestinal epithelial cells (IECs). We found that rotavirus infection induced global m6A modifications on mRNA transcripts by down-regulating the m6a eraser ALKBH5. Mice lacking the m6A writer enzymes METTL3 in IECs (Mettl3ΔIEC) were resistant to RV infection and showed increased expression of interferons (IFNs) and IFN-stimulated genes (ISGs). Using RNA-sequencing and m6A RNA immuno-precipitation (RIP)-sequencing, we identified IRF7, a master regulator of IFN responses, as one of the primary m6A targets during virus infection. In the absence of METTL3, IECs showed increased Irf7 mRNA stability and enhanced type I and III IFN expression. Deficiency in IRF7 attenuated the elevated expression of IFNs and ISGs and restored susceptibility to RV infection in Mettl3ΔIEC mice. Moreover, the global m6A modification on mRNA transcripts declined with age in mice, with a significant drop from 2 weeks to 3 weeks post birth, which likely has broad implications for the development of intestinal immune system against enteric viruses early in life. Collectively, we demonstrated a novel host m6A-IRF7-IFN antiviral signaling cascade that restricts rotavirus infection in vivo.

Highlights

N6-methyladenosine (m6A) is the most abundant internal mRNA modification and modulates diverse cellular functions through m6A-related writers, erasers, and readers[1,2,3]
Total RNA m6A modifications in the mouse ileal tissues, revealed by a m6A dot blot and mass spectrum (MS) analysis, significantly declined from 2 weeks to 3 weeks post birth (Figure 1a, 1b and 1c), which caused by increased Alkbh5 expression (Figure 1d, Figure 1-figure supplement 1a and Figure 1-figure supplement 1b) and development of microbiota might be involved (Figure 1-figure supplement 2). overexpression of Alkbh5 in mouse intestinal epithelial cells (IECs) cell line caused decreased m6A level (Figure 1-figure supplement 1c), supporting the role of Alkbh5 in regulating global m6A levels in intestine
We hypothesize that RV may induce an enriched cellular m6A modification environment and a weakened innate immune response to facilitate virus replication

Summary

Introduction

N6-methyladenosine (m6A) is the most abundant internal mRNA modification and modulates diverse cellular functions through m6A-related writers, erasers, and readers[1,2,3]. M6A RNA modification-mediated down-regulation of the α-ketoglutarate dehydrogenase (KGDH)-itaconate pathway inhibits viral replication independent of the innate immune response[9]. 77 The m6A modification of the enterovirus 71 (EV71) RNA genome is important for viral propagation, and EV71 infection increases the expression of m6A writers in vitro[11]. Rotaviruses encode multiple viral proteins to inhibit innate immune responses by degrading interferon regulatory factors (IRFs) and mitochondrial antiviral-signaling protein (MAVS), facilitating efficient virus infection and replication[15, 16]. We identified IRF7, a master regulator of IFN responses[17], as one of the primary m6A targets during virus infection. In the absence of METTL3, IECs showed increased Irf mRNA stability and enhanced type I and III IFN expression. We identified a novel regulation and function of m6A modifications in an enteric viral infection model in vivo

Methods

Results

Conclusion