Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia.
Department of Medical Biology, University of Melbourne, Parkville 3052, Victoria, Australia.
RNA. 2021 Dec;27(12):1482-1496. doi: 10.1261/rna.078804.121. Epub 2021 Sep 17.
Conversion of adenosine to inosine in RNA by ADAR enzymes, termed "RNA editing," is essential for healthy brain development. Editing is dysregulated in neuropsychiatric diseases, but has not yet been investigated at scale at the level of individual neurons. We quantified RNA editing sites in nuclear transcriptomes of 3055 neurons from six cortical regions of a neurotypical female donor, and found 41,930 sites present in at least ten nuclei. Most sites were located within Alu repeats in introns or 3' UTRs, and approximately 80% were cataloged in public RNA editing databases. We identified 9285 putative novel editing sites, 29% of which were also detectable in unrelated donors. Intersection with results from bulk RNA-seq studies provided cell-type and spatial context for 1730 sites that are differentially edited in schizophrenic brain donors, and 910 such sites in autistic donors. Autism-related genes were also enriched with editing sites predicted to modify RNA structure. Inhibitory neurons showed higher overall transcriptome editing than excitatory neurons, and the highest editing rates were observed in the frontal cortex. We used generalized linear models to identify differentially edited sites and genes between cell types. Twenty nine genes were preferentially edited in excitatory neurons, and 43 genes were edited more heavily in inhibitory neurons, including , its target genes, and genes in the autism-associated Prader-Willi locus (15q11). The abundance of SNORD115/116 genes from locus 15q11 was positively associated with editing activity across the transcriptome. We contend that insufficient editing of autism-related genes in inhibitory neurons may contribute to the specific perturbation of those cells in autism.
ADAR 酶将 RNA 中的腺苷转换为肌苷，这种过程被称为“RNA 编辑”，对大脑的健康发育至关重要。编辑在神经精神疾病中失调，但尚未在单个神经元水平上进行大规模研究。我们对一名神经正常女性供体的六个皮质区域的 3055 个神经元的核转录组进行了 RNA 编辑位点的定量分析，发现至少有 10 个核中有 41930 个位点存在。大多数位点位于内含子或 3'UTR 中的 Alu 重复序列中，约 80%的位点被列入公共 RNA 编辑数据库。我们确定了 9285 个假定的新编辑位点，其中 29%在其他供体中也可检测到。与批量 RNA-seq 研究的结果交叉，为精神分裂症大脑供体中差异编辑的 1730 个位点和自闭症供体中 910 个这样的位点提供了细胞类型和空间背景。自闭症相关基因也富含预测可修饰 RNA 结构的编辑位点。抑制性神经元的总体转录组编辑水平高于兴奋性神经元，而在前额叶皮层观察到最高的编辑率。我们使用广义线性模型来识别细胞类型之间差异编辑的位点和基因。29 个基因在兴奋性神经元中优先编辑，43 个基因在抑制性神经元中编辑更为严重，包括其靶基因和自闭症相关 Prader-Willi 基因座（15q11）中的基因。来自 15q11 基因座的 SNORD115/116 基因的丰度与整个转录组的编辑活性呈正相关。我们认为，抑制性神经元中自闭症相关基因的编辑不足可能导致自闭症中这些细胞的特定扰动。
