Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation

N⁶-methyladenosine (m⁶A) is an abundant mRNA modification in the brain that has important roles in neurodevelopment and brain function. However, because of technical limitations, global profiling of m⁶A sites within the individual cell types that make up the brain has not been possible. Here, we develop a mouse model that enables transcriptome-wide m⁶A detection in any tissue of interest at single-cell resolution. We use these mice to map m⁶A across different brain regions and within single cells of the mouse cortex and discover a high degree of shared methylation across brain regions and cell types. However, we also identify a small number of differentially methylated mRNAs in neurons that encode important regulators of neuronal signaling, and we discover that microglia have lower levels of m⁶A than other cell types. Finally, we perform single-cell m⁶A mapping in aged mice and identify many transcripts with age-dependent changes in m⁶A.