Single-cell discovery of m⁶A RNA modifications in the hippocampus

Heterogeneous and homogeneous m⁶A sites in single cells. (A) m⁶A site counts over mutation per read (m/k) ratio (left) and C-to-U edit E-YTH^mut background over mutation per read (m/k) ratio (middle) for WT mice. m⁶A site counts over m/k ratio for Mettl3 knockout (KO) mice (Mettl3^−/−:Emx1-Cre; right). Minimum threshold: 5%. (B) Normalized m⁶A scaled density 500 nt 5′ and 500 nt 3′ from stop codon (0 nt) for ASC, EC, IMC, NEUR, and OLG. (Left) m⁶A sites with m/k = 1 (homogenous m⁶A). (Right) m⁶A sites with m/k < 1 (heterogenous m⁶A). (ASC) astrocyte cell lineage, (EC) endothelial cell lineage, (IMC) immune cell lineage, (NEUR) neuronal cell lineage, (OLG) oligodendrocyte cell lineage. (C) Disease gene enrichment analyses (GO). GO terms with an adjusted Q-value < 0.05 and P-value < 0.05 are shown for NEUR and ASC. (D) Localization of m⁶A for gene. (Left) UMAP plot of single-cell expression for one gene. Legend color represents transcript density. (Middle) UMAP density plot of m⁶A on RNA transcribed from one gene, per cell. Legend color represents m⁶A density on RNA transcribed from one gene. (Right) IGV RefSeq gene annotation with editing sites representing adjacent m⁶A sites is shown. Last exon with 3′ UTR region is illustrated with higher magnitude.