A cell-type-resolved human brain atlas of microRNAs and tRNA fragments.
Small non-coding RNAs (sncRNAs), including microRNAs (miRs) and tRNA fragments (tRFs), regulate diverse brain molecular pathways involved in development, inflammation and neurodegeneration, and dynamically respond to stress insults in various neurological contexts. Nevertheless, the cell-type-specificity of brain miRs and tRFs remains poorly characterized, limiting the interpretation of their function. To address this issue, we generated a comprehensive, cell-type-resolved atlas of human brain small non-coding RNAs from live brain tissue. Specifically, we isolated neurons, astrocytes, microglia and oligodendrocytes from neurosurgery-obtained fresh human brain specimens and profiled their small RNA repertoires using small RNA-sequencing. Our atlas revealed multiple cell-type differences in miR and tRF expression and identified small RNA cell type biomarkers. Furthermore, we demonstrated that miR cell-type-specificity may be regulated by specific quantitative trait loci located in cell-type-associated enhancer regions. We identified higher levels of 5'-tRNA-halves in neurons, compared to glia, including a particular neuronal enrichment of 5'-tRNA-halves derived from Glycine, Leucine and Lysine-linked tRNAs. Intriguingly, these neuronal tRF families were significantly upregulated in Alzheimer's disease postmortem brain samples, compared to age-matched controls, possibly reflecting a neuronal response to disease. Our atlas and an accompanying statistical tool for miR cell-type-enrichment analysis together provide a novel publicly available resource for dissecting small RNA cell type origin and function in the fresh human brain. Overall design: Small RNA-seq profiling of lightly formalin fixed, neurosurgery-obtained fresh brain specimens, FACS-sorted to distinct cell-type-specific populations, representing neurons, astrocytes, microglia and oligodendrocytes.