Human brain microRNAs exhibit cell-type specificity and age dependence

Abstract MicroRNAs play key roles in regulating brain processes ranging from neurogenesis to neurological disease and contribute to many cell-type-specific pathways. However, technical limitations of single-cell small RNA sequencing have confined most studies to bulk analyses of whole-tissue specimens, limiting our capacity to resolve the cell-type specificity of brain microRNAs and to study their roles in depth. To generate a comprehensive, cell-type-resolved atlas of microRNAs in the human brain, we isolated neurons, astrocytes, microglia and oligodendrocytes from fresh neurosurgery-derived brain samples and profiled their small RNA repertoires by RNA sequencing. The results revealed pronounced cell-type-associated differences in microRNA profiles, identified novel cell-type-specific microRNA markers and shed new light on the contribution of their originating genomic loci to cell-type specificity. We further characterized the cell-type dependence of microRNA strand preference and isomiR processing, and identified cell-type-dependent microRNA programs associated with brain ageing. Combined with an accompanying statistical tool for cell-type signal enrichment, our atlas provides a publicly available resource for cell-type-resolved microRNA analysis in the human brain.