Whole-transcriptome RNA editing analysis in single cortical neurons links locus 15q11 with psychiatric illness

Abstract

11Conversion of adenosine to inosine in RNA by ADAR enzymes occurs at thousands of sites in the human transcriptome, and is 12 essential for healthy brain development. This process, known as 'RNA editing', is dysregulated in many neuropsychiatric 13 diseases, but is little understood at the level of individual neurons. We examined full-length nuclear transcriptomes of 3,055 14 neurons from six cortical regions of a neurotypical post-mortem female donor and identified 40,861 high-confidence edited 15 sites. The majority of sites were located within Alu repeats in introns or 3' UTRs, and were present in previously published RNA 16 editing databases. We identified 15,784 putative novel RNA editing sites, 30% of which were also detectable in independently 17 generated neuronal transcriptomes from unrelated donors. The strongest correlates of global editing rates were expression 18 levels of small nucleolar RNAs from the SNORD115 and SNORD116 cluster (15q11), known to modulate serotonin receptor 19 processing and to colocalize with ADAR2, one of three known RNA editing enzymes in humans. As expected, expression of 20 DNA and RNA binding proteins were negatively associated with editing. We present evidence for dysregulated RNA editing in 21 six rare genetic conditions; and report 117 differentially edited sites between cortical regions and neuronal subtypes. These 22 results provide spatial and neurophenotypic context for 1,871 and 998 sites that are differentially edited in the brains of 23 schizophrenic and autistic patients respectively, and a reference for future studies of RNA editing in single brain cells from 24 these cohorts. 2526 29 conversion of adenosine to inosine (A>I) in nascent RNA transcripts by ADAR1 and ADAR2 enzymes, known as 'RNA editing', is 30 the most abundant RNA modification in the primate central nervous system, and confers transcriptomic diversity beyond that 31 encoded in the genome [1]. RNA editing is essential for healthy brain development and increases with age [2]. 32 33 Dysregulated editing is implicated in epilepsy [3], glioblastoma [4], major depression [5], autism spectrum disorder [6] and 34 schizophrenia [7]. ADAR1 primarily edits adenosine within repetitive regions; ADAR2 primarily edits non-repetitive regions, and 35ADAR3 is a catalytically inactive inhibitor of editing [8]. ADAR2-null mice die in utero and partial knock-out neonatal animals 36 succumb to severe seizures [9]. In humans, mutations in ADAR1 cause skin dyschromatosis (MIM 127400) and Aicardi-Goutieres 37 encephalopathy (MIM 615010) with sub-types including striatal and motor neurodegeneration [10,11]. Mislocalization of ADAR 38 was recently discovered in human and mouse models of C9orf72-mediated amyotrophic lateral sclerosis (ALS) [12]. Common 39SNPs in this gene family are also implicated in 18 complex human traits including hippocampal volume, type II diabetes, and 40 aspects of Alzheimer's disease and lung cancer [13]. 42Recently thousands of edited sites were identified in bulk RNA sequencing of human tissues [...