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Abstract：
Ionotropic glutamate receptors (iGluRs) play key roles for signaling in the central nervous system. Alternative splicing and RNA editing are well-known mechanisms to increase iGluR diversity and to provide context-dependent regulation. Earlier work on isoform identification has focused on the analysis of cloned transcripts, mostly from rodents. We here set out to obtain a systematic overview of iGluR splicing and editing in human brain based on RNA-Seq data. Using data from two large-scale transcriptome studies, we established a workflow for the de novo identification and quantification of alternative splice and editing events. We detected all canonical iGluR splice junctions, assessed the abundance of alternative events described in the literature, and identified new splice events in AMPA, kainate, delta, and NMDA receptor subunits. Notable events include an abundant transcript encoding the GluA4 amino-terminal domain, GluA4-ATD, a novel C-terminal GluD1 (delta receptor 1) isoform, GluD1-b, and potentially new GluK4 and GluN2C isoforms. C-terminal GluN1 splicing may be controlled by inclusion of a cassette exon, which shows preference for one of the two acceptor sites in the last exon. Moreover, we identified alternative untranslated regions (UTRs) and species-specific differences in splicing. In contrast, editing in exonic iGluR regions appears to be mostly limited to ten previously described sites, two of which result in silent amino acid changes. Coupling of proximal editing/editing and editing/splice events occurs to variable degree. Overall, this analysis provides the first inventory of alternative splicing and editing in human brain iGluRs and provides the impetus for further transcriptome-based and functional investigations.
摘要：
离子型谷氨酸受体（iGluRs）在中枢神经系统中发挥关键作用。可变剪接和RNA编辑是增加iGluR多样性和提供环境依赖性调节的众所周知的机制。早期关于同工型鉴定的工作集中在克隆转录本的分析上，主要来自啮齿动物。我们在这里着手获得基于RNA-Seq数据的人脑中iGluR剪接和编辑的系统概述。利用两项大规模转录组研究的数据，我们建立了一个重新鉴定和量化选择性剪接和编辑事件的工作流程.我们检测到所有典型的iGluR拼接点，评估了文献中描述的替代事件的丰度，在AMPA中发现了新的剪接事件,Kainate,delta,和NMDA受体亚基。值得注意的事件包括编码GluA4氨基末端结构域的丰富转录物，GluA4-ATD,一种新的C端GluD1（δ受体1）亚型，GluD1-b,以及潜在的新GluK4和GluN2C亚型。C端GluN1剪接可以通过包含盒外显子来控制，这显示了对最后一个外显子中两个受体位点之一的偏好。此外，我们确定了可变非翻译区(UTR)和物种特异性剪接差异.相比之下,外显子iGluR区域的编辑似乎主要限于十个先前描述的位点，其中两个导致沉默的氨基酸变化。近端编辑/编辑和编辑/拼接事件的耦合以可变程度发生。总的来说,这项分析提供了人脑iGluRs中选择性剪接和编辑的第一个清单,并为进一步的基于转录组的功能研究提供了动力.
