Integrative MeRIP-Seq and RNA-Seq Analyses Reveal Innate Immune and Infection-Related Transcriptomic Changes upon METTL3 Knockout.

Background: As a major regulator, methyltransferase-like 3 (METTL3) catalyzes N6-methyladenosine (m6A) modification in mRNA. The m6A modifications mediated by METTL3 influence RNA splicing, nucleocytoplasmic distribution, stability, and other functions, thereby playing a vital and indispensable role in genetic regulatory network. Although several studies have shown its critical role in mRNA fate, the global pattern of mRNA methylation alteration driven by METTL3 remain unclear. Methods: Here, a HEK293T cell line with METTL3 depletion was constructed, and RNA sequencing (RNA-seq) and methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) were implemented. Additionally, quantitative Reverse Transcription PCR (qRT-PCR) technology was used to confirm some of the differentially expressed genes. Result: The mRNA methylation alteration landscape was clarified and the regions altered by m6A modification due to METTL3 deletion that was annotated and characterized, with 5763 hypomethylated/269 hypermethylated genes after METTL3 silence. Several methylation-related innate anti-infection immune genes, including MYD88, RIG-1, CYLD and IRF9, were exposed through comprehensive analysis to MeRIP-seq and RNA-seq data, and these genes were principally enriched in pathogen infection and innate immune response pathways such as Shigellosis, Yersinia infection, and the HIV-1 viral life cycle. Conclusion: Our study discovered that the METTL3 association with differentially expressed genes, suggested that METTL3 and the genes it regulates might serve as targets for defense against infection.