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

• Published in: Nature neuroscience 2024-09, Vol.27 (12), p.2512-2520
• Main Authors: Tegowski, Matthew, Prater, Anna K., Holley, Christopher L., Meyer, Kate D.
• Format: Article
• Language: English
• Subjects: 13/1; 13/51; 38/39; 38/90; 45; 45/77; 45/91; 631/337/1645/2570; 631/378; 64/60; 82/58; Age; Animal Genetics and Genomics; Behavioral Sciences; Biological Techniques; Biomedical and Life Sciences; Biomedicine; Brain; Brain mapping; Methylation; Microglia; N6-methyladenosine; Neurobiology; Neurosciences; Resource; RNA modification; Transcriptomes
• ISSN: 1097-6256; 1546-1726; 1546-1726
• DOI: 10.1038/s41593-024-01768-3

N 6 -methyladenosine (m 6 A) 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 m 6 A 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 m 6 A detection in any tissue of interest at single-cell resolution. We use these mice to map m 6 A 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 m 6 A than other cell types. Finally, we perform single-cell m 6 A mapping in aged mice and identify many transcripts with age-dependent changes in m 6 A. The authors perform the first single-cell profiling of m 6 A in the mouse brain. They uncover relative hypomethylation of microglial mRNA compared to other cell types, and they identify hundreds of RNAs that undergo differential methylation with age.