非蛋白编码反义 RNA 在与自闭症谱系障碍相关的基因组区域中的表达。
Expression of non-protein-coding antisense RNAs in genomic regions related to autism spectrum disorders.
机构信息
Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave,, BRB-407, Miami, FL 33136, USA.
出版信息
Mol Autism. 2013 Sep 4;4(1):32. doi: 10.1186/2040-2392-4-32.
BACKGROUND
Autism spectrum disorders (ASD) manifest with neurodevelopmental phenotypes including communicative, social and behavioral impairments that affect as many as 1 in 88 children. The majority of autism cases have no known genetic cause, suggesting complex genetics of the disorder, but a few genes of large effect have been identified.
METHODS
In order to identify novel ASD genetic correlates, we investigated non-protein coding RNAs (ncRNAs) which are abundantly transcribed from the human genome, enriched in the brain, and have been implicated in neurodevelopmental disorders. Using an algorithm that we developed, we examined a publicly available transcriptomics database, AceView, to identify the natural antisense transcripts (NATs) that overlap with known autism-related genes. We validated the presence and differential expression of NATs in different brain regions of ASD and control brains using qRT-PCR. Additionally, we investigated the subcellular localization of these transcripts in a neuronal cell line using RNA-sequencing (RNA-seq).
RESULTS
We found noncoding antisense RNA transcripts at approximately 40% of loci previously implicated in ASD. We confirmed the expression of 10 antisense RNAs in different postmortem human brain tissues. The expression of five antisense transcripts was found to be region-specific, suggesting a role for these ncRNAs in the development and function of specific brain regions. Some antisense RNAs overlapping suspected ASD genes exhibited concordant expression relative to their sense protein-coding genes, while other sense-antisense pairs demonstrate a discordant relationship. Interestingly, the antisense RNA corresponding to the SYNGAP1 locus (SYNGAP1-AS) was found to be differentially expressed in brain regions of patients with ASD compared to control individuals. RNA-seq analysis of subcellular compartments from SH-SY5Y human neuroblastoma cells demonstrated that antisense RNAs to ASD candidate genes are predominantly expressed in the nucleoplasmic or chromatin compartments, implying their involvement in nuclear-associated processes.
CONCLUSIONS
Our data suggests that NATs are abundantly expressed from ASD-related loci and provide evidence for their roles in target gene regulation, neurodevelopment and autism pathogenesis. This class of RNA should therefore be considered in functional studies aimed at understanding genetic risk factors for ASD.
背景
自闭症谱系障碍（ASD）表现为神经发育表型，包括交流、社交和行为障碍，影响多达 1/88 的儿童。大多数自闭症病例没有已知的遗传原因，这表明该疾病的遗传具有复杂性，但已经确定了一些具有较大影响的基因。
方法
为了确定新的 ASD 遗传相关性，我们研究了丰富转录自人类基因组的非蛋白编码 RNA（ncRNA），它们在大脑中富集，并与神经发育障碍有关。我们使用我们开发的一种算法，检查了一个公开的转录组学数据库 AceView，以鉴定与已知自闭症相关基因重叠的自然反义转录本（NAT）。我们使用 qRT-PCR 验证了 ASD 和对照大脑不同脑区中 NAT 的存在和差异表达。此外，我们使用 RNA 测序（RNA-seq）研究了这些转录本在神经元细胞系中的亚细胞定位。
结果
我们在大约 40%以前被认为与 ASD 相关的基因座上发现了非编码反义 RNA 转录本。我们在不同的死后人类脑组织中证实了 10 种反义 RNA 的表达。发现 5 种反义转录本的表达具有区域特异性，表明这些 ncRNA 在特定脑区的发育和功能中起作用。一些与疑似 ASD 基因重叠的反义 RNA 的表达与其有意义的蛋白质编码基因一致，而其他 sense-antisense 对则表现出不一致的关系。有趣的是，与 SYNGAP1 基因座（SYNGAP1-AS）相对应的反义 RNA 在 ASD 患者的大脑区域中与对照个体相比表现出差异表达。对 SH-SY5Y 人神经母细胞瘤细胞的亚细胞区室进行 RNA-seq 分析表明，ASD 候选基因的反义 RNA 主要在核质或染色质区室中表达，暗示它们参与了与核相关的过程。
结论
我们的数据表明，NAT 从 ASD 相关基因座大量表达，并为它们在靶基因调控、神经发育和自闭症发病机制中的作用提供了证据。因此，在旨在了解 ASD 遗传风险因素的功能研究中，应考虑这一类 RNA。
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