ArticleGigaScience2022
Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed, 3 citations in OpenAlex.
- Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia.bioRxiv : the preprint server for biology · 2026Article
- Cross-species single-cell transcriptomics reveals neuronal similarities and heterogeneity in amniote pallium.Zoological research · 2025Article
- Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells.GigaScience · 2022Article
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Authors and funding
17 authors at 2 institutions in 2 countries.
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Abstract
backgroundThe basal ganglia are a complex of interconnected subcortical structures located beneath the mammalian cerebral cortex. The degeneration of dopaminergic neurons in the basal ganglia is the primary pathological feature of Parkinson's disease. Due to a lack of integrated analysis of multiomics datasets across multiple basal ganglia brain regions, very little is known about the regulatory mechanisms of this area.
findingsWe utilized high-throughput transcriptomic and epigenomic analysis to profile over 270,000 single-nucleus cells to create a cellular atlas of the basal ganglia, characterizing the cellular composition of 4 regions of basal ganglia in adult macaque brain, including the striatum, substantia nigra (SN), globus pallidum, and amygdala. We found a distinct epigenetic regulation on gene expression of neuronal and nonneuronal cells across regions in basal ganglia. We identified a cluster of SN-specific astrocytes associated with neurodegenerative diseases and further explored the conserved and primate-specific transcriptomics in SN cell types across human, macaque, and mouse. Finally, we integrated our epigenetic landscape of basal ganglia cells with human disease heritability and identified a regulatory module consisting of candidate cis-regulatory elements that are specific to medium spiny neurons and associated with schizophrenia.
conclusionsIn general, our macaque basal ganglia atlas provides valuable insights into the comprehensive transcriptome and epigenome of the most important and populous cell populations in the macaque basal ganglia. We have identified 49 cell types based on transcriptomic profiles and 47 cell types based on epigenomic profiles, some of which exhibit region specificity, and characterized the molecular relationships underlying these brain regions.
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