Abstract
The rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brains. We identify gene modules associated with specific brain regions like the cerebral cortex, pituitary, and thalamus. In addition, we discover 9703 novel intergenic transcripts, including 1701 coding transcripts and 2845 lncRNAs. Most of the novel transcripts are only expressed in specific brain regions or cortical regions of specific individuals. We further survey the open chromatin regions in the hippocampal CA1 and several cerebral cortical regions of the rhesus macaque brain using ATAC-seq, revealing CA1- and cortex-specific open chromatin regions. Our results add to the growing body of knowledge regarding the baseline transcriptomic and open chromatin profiles in the brain of the rhesus macaque.
Highlights
The rhesus macaque is a prime model animal in neuroscience
Samples from the midbrain were excluded from downstream analysis except for de novo transcriptome assembly, due to possible mixture of residual tissue from the ventral tegmental area (VTA) and substantia nigra (SN)
To gain a high-level understanding of the rhesus brain transcriptome, we visualized the samples in two dimensions using t-distributed stochastic neighbor embedding (t-SNE)
Summary
The rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. We further survey the open chromatin regions in the hippocampal CA1 and several cerebral cortical regions of the rhesus macaque brain using ATAC-seq, revealing CA1- and cortex-specific open chromatin regions. Region- and cell-specific patterns of open chromatin have been reported in human and mouse brain using ATAC-seq[12,13] (Assay for Transposase-Accessible Chromatin using sequencing) It remains unknown whether region- or individualassociated open chromatin pattern exists in the rhesus macaque brain. We perform RNA-sequencing (RNA-seq) on 416 samples from 52 regions (anatomically and functionally related to human counterparts) of the rhesus macaque brain, revealing transcriptomic differences among different brain areas. We survey the open chromatin regions in several cerebral cortical regions and hippocampal CA1 (cornu Ammonis 1) of the rhesus macaque brain using ATAC-seq, revealing region-specific patterns of chromatin accessibility
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