Project description: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.
Project description:Here, we generated multiome (coupled scRNA-seq and scATAC-seq) data over a time course of mid- and hindbrain organoid development to map cell composition and explore the regulatory mechanisms underlying cell type maturation. The dataset incorporates 5 time points from day 7 to day 120 from 3 human induced pluripotent stem cell (iPSC) lines using 2 previously established protocols. The protocols differentially generate ventral and dorsal cell types, and together cover regions such as floor-plate, dorsal and ventral midbrain, cerebellum, and additional parts of hindbrain. Comparing the data to a reference atlas of the developing human brain and to an integrated neural organoid cell atlas, we find that the gene regulatory architecture in organoid cells is predictive of primary counterparts and also that multiple regions are under-represented in existing organoid models.
Project description:The majority of common genetic risk variants associated with neuropsychiatric disease are non-coding and are thought to exert their effects by disrupting the function of cis regulatory elements (CREs), including promoters and enhancers. Within each cell, chromatin is arranged in specific patterns to expose the repertoire of CREs required for optimal spatiotemporal regulation of gene expression. To further our understanding of the complex mechanisms that modulate transcription in the brain, we utilized frozen postmortem samples to generate the largest human brain and cell type-specific open chromatin dataset to date. Using the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq), we created maps of chromatin accessibility in 2 cell types (neurons and non-neurons) across 14 distinct brain regions of 5 individuals. Chromatin structure varies markedly by cell type, with neuronal chromatin displaying higher regional variability than that of non-neurons. Among our findings is an open chromatin region (OCR) specific to neurons of the striatum. When placed in the mouse, a human sequence derived from this OCR recapitulates the cell-type and regional expression pattern predicted by our ATAC-seq experiments. Furthermore, differentially accessible chromatin overlaps with the genetic architecture of neuropsychiatric traits and identifies differences in molecular pathways and biological functions. By leveraging transcription factor binding analysis, we identify protein coding and long noncoding RNAs (lncRNAs) with cell-type and brain region specificity. Our data provides a valuable resource to the research community and we provide this human brain chromatin accessibility atlas as an online database “Brain Open Chromatin Atlas (BOCA)” to facilitate interpretation.