Figure 2.

Methylated (m⁶A) RNA immunoprecipitation (meRIP) coupled with sequencing analysis identifies polyadenylated RNAs with reduced m⁶A methylation at their 3′-UTRs and exons in liver-specific METTL3 knockout (M3LKO) livers compared with WT livers. A: Normalized distribution of high-confidence m⁶A sites on mRNAs and long noncoding RNAs (lncRNAs) in 5-week–old wild-type (WT) and M3LKO mice. Black lines indicate distribution of all m⁶A sites identified. Red lines denote distribution of all m⁶A sites found to have significantly altered enrichment in M3LKO livers (fold change in m⁶A enrichment (WT/M3LKO ≠ 0). Significant enrichment was calculated using ExomePeak finder with a rescaled hypergeometric test false discovery rate cut-off of P < 0.05 and absolute fold change enrichment >1. B: Motif enrichment for each peak type (all sites or altered sites) was identified by running Homer Motif Analysis. Only the most significant and prevalent motifs are shown. C: Peak distribution normalized to input in the genomic regions of 3 critical transcripts (Agpat2, Ctnnb1, and Elovl1) in the WT and M3LKO mice are shown. Sequencing tracks of these genes and enrichment in the m⁶A immunoprecipitation and input in the WT and M3LKO livers were visualized using Integrated Genome Viewer (IGV) software version 2.4.16 (Broad Institute, Cambridge, MA). Arrowheads indicate m⁶A peaks. n = 4 per genotype (A). TSS, transcription start site; TTS, transcription termination site.