Novel Assay System and Analysis Algorithm in Detecting RNA Editing Events and Linked Splicing Isoforms

检测 RNA 编辑事件和连锁剪接亚型的新型检测系统和分析算法

• 批准号: 9184137
• 负责人: Ke Hao
• 金额: $ 17.4万
• 依托单位: CELETRIX, LLC
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2018-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9184137
• 关键词: 5' Untranslated Regions; Adenosine; Algorithms; Animals; Autopsy; Binding; Binding Sites; Biological Assay; Biological Sciences; Brain; Candidate Disease Gene; Code; Codon Nucleotides; Communities; Complementary DNA; Complex; Computational algorithm; DNA Methylation; Detection; Development; Disease; Event; Frequencies; Functional disorder; Gene Dosage; Gene Expression; Genes; Genome; Goals; Guanosine; Haplotypes; Heroin Abuse; Inosine; Introns; Length; Link; Mainstreaming; Major Depressive Disorder; Mediator of activation protein; Messenger RNA; Methods; MicroRNAs; Molecular; Molecular Biology; Neurologic; Nucleotides; Performance; Phase; Process; Protein Isoforms; Proteins; Protocols documentation; RNA; RNA Editing; RNA Splicing; Reading; Research; Research Personnel; Role; Sampling; Series; Serotonin Receptor 5-HT2C; Signal Transduction; Site; Specimen; Statistical Data Interpretation; Substance Use Disorder; System; Systems Analysis; Technology; Testing; Time; Untranslated RNA; Validation; Variant; abstracting; accomplished suicide; assay development; base; computerized tools; drug abuser; gene function; illicit drug use; nervous system disorder; novel; novel strategies; sequencing platform; serotonin receptor; single molecule; tool; transcriptome; vector

Abstract RNA editing is a process in which the genome-encoded information is altered in RNA. RNA editing is an efficient way to increase RNA complexity, thereby fine-tuning both gene function and dosage. Adenosine to Inosine (A-to-I) editing is the most common type of RNA editing known in animals. The cellular machinery recognizes inosine as guanosine, so A-to-I editing of codons and splicing signals directly modifies protein- coding gene function, whereas editing of microRNAs and their binding sites alter gene expression. The vast majority of A-to-I editing, however, is detected in non-coding regions (e.g. Alu-repeats within introns and 3' or 5' untranslated regions), strongly suggesting a still unknown regulatory role of this cellular mechanism. Dysregulation of mRNA editing was implicated in several neurological diseases. In addition, we and other groups showed that alterations in mRNA editing of one of the serotonin receptors (serotonin 2C receptor) is associated with completed suicide, major depression and possibly substance use disorder (SUD). Currently, short read Sanger or Illumina sequencing are the mainstream tools in RNA editing studies. However, these tools cannot detect the “phase” of editing events; i.e., they cannot detect simultaneous editing events at two or more sites which are situated further than 50-100bp from one another on the same mRNA molecule. In addition, the current tools, which focus on a small region in the vicinity of a given editing site, do not allow us to study RNA editing in the context of splicing. In the proposed project we aim to develop a state-of-the-art tool that can be used by the entire scientific community. If we are successful, this tool will enable a simultaneous detection and quantification of RNA editing and splicing isoforms in the brain hence allowing researchers to study RNA editing in the context of splicing. Moreover, this tool will enable determination of the haplotypes of mRNA molecules with multiple editing sites. We anticipate that this tool will have a great commercial potential and will facilitate research on RNA editing as one of the molecular mechanisms that is implicated in SUD.

抽象的 RNA编辑是改变RNA中基因组编码信息的过程。 RNA编辑是一种 增加RNA复杂性的有效方法，从而微调基因功能和剂量。腺苷 肌苷（A 到 I）编辑是动物中已知的最常见的 RNA 编辑类型。细胞机器 将肌苷识别为鸟苷，因此密码子和剪接信号的 A 到 I 编辑直接修饰蛋白质 编码基因功能，而编辑 microRNA 及其结合位点会改变基因表达。广阔的 然而，大多数 A 到 I 编辑是在非编码区域中检测到的（例如内含子和 3' 或 5' 内的 Alu 重复） 非翻译区），强烈表明这种细胞机制的调节作用仍然未知。 mRNA 编辑失调与多种神经系统疾病有关。此外，我们和其他 研究小组表明，其中一种血清素受体（血清素 2C 受体）的 mRNA 编辑的改变与 与完全自杀、重度抑郁症和可能的物质使用障碍（SUD）有关。现在， 短读长 Sanger 或 Illumina 测序是 RNA 编辑研究的主流工具。然而，这些 工具无法检测编辑事件的“阶段”；即，它们无法检测两个或多个同时编辑事件 同一 mRNA 分子上彼此相距超过 50-100bp 的更多位点。在 此外，当前的工具专注于给定编辑站点附近的小区域，不允许我们 研究剪接背景下的 RNA 编辑。在拟议的项目中，我们的目标是开发一种最先进的工具 整个科学界都可以使用。如果我们成功的话，这个工具将能够同时实现 大脑中 RNA 编辑和剪接异构体的检测和定量，从而使研究人员能够 研究剪接背景下的 RNA 编辑。此外，该工具将能够确定单倍型 具有多个编辑位点的 mRNA 分子。我们预计该工具将具有巨大的商业潜力 并将促进 RNA 编辑作为 SUD 涉及的分子机制之一的研究。