METTL3 regulates microglial inflammation through the m6A modification

Microglia, the most abundant type of brain-resident immune cells, continuously surveil the environment and play a central role in shaping the inflammatory state of the central nerve system (CNS). We discovered that the protein expression of METTL3 (a m6A methyltransferase) were up-regulated in inflammatory microglia. We conducted MeRIP-seq analyses in LPS-stimulated microglial cells with or without METTL3 knockout. In the MeRIP-seq analysis, the m6A modifications are primarily located in a consensus “RRACH” motif, and m6A peaks mainly occur in coding sequences (CDSs), 3′ untranslated regions (3′ UTRs), and near stop codons.Further study identified that METTL3 promoted the expression of Basic Leucine Zipper Transcriptional Factor ATF-Like (BATF), which in turn directly bound to a cohort of characteristic inflammatory cytokines and chemokine genes. Collectively, our findings identified METTL3-m6A-BATF axis as a potential therapeutic target for terminating detrimental microglial inflammation In order to identify the key regulators involved in mediating METTL3-m6A-associated effects on microglial response, we conducted MeRIP-seq and RNA-seq analyses in LPS-stimulated microglial cells with or without METTL3 knockout. In the MeRIP-seq analysis, the m6A modifications are primarily located in a consensus “RRACH” motif (Figure 4A), and m6A peaks mainly occur in coding sequences (CDSs), 3′ untranslated regions (3′ UTRs), and near stop codons, which were consistent with previous reports. To determine the correlation between m6A modification and gene expression, we plotted the m6A peak data against the RNA-seq data. Given that the knockout of METTL3 leads to the blocking of its methyltransferase activity and the downregulation of global m6A levels, we speculated that mRNA transcripts that carry hypomethylated m6A peaks, including the hypo-up and hypo-down genes, might be the potential targets of METTL3. Setting diffPeak.log2fc to 2 and diffExp.gene.log2fc to 2 resulted in the identification of 15 highly reliable genes with diminished m6A peaks while expression was down- or up-regulated. BATF, the only transcription factor among these genes, was reported to have binding sites in the regulatory regions of numerous inflammatory cytokines and pro-inflammatory genes. Collectively, these results suggest BATF as a vital target of METTL3 in microglia.