Unbiased discovery of mechanisms regulating circRNA

circRNA调节机制的公正发现

• 批准号: 9332410
• 负责人: Julia Salzman
• 金额: $ 31.21万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-21 至 2020-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9332410
• 关键词: Address; Affect; Algorithms; Alternative Splicing; Attention; Biochemical; Biochemical Pathway; Biogenesis; Biological; Biology; Brain; CRISPR/Cas technology; Cardiomyopathies; Cells; Data; Data Set; Detection; Development; Disease; Engineering; Event; Evolution; Exons; Foundations; Gene Expression; Genes; Genetic Screening; Genetic Transcription; Genome; Genomics; Health; Heart; Human; Human Development; Introns; Kinetics; Length; Life; Malignant Neoplasms; Messenger RNA; Methods; Modeling; Molecular; Mutate; Nerve Degeneration; Nuclear Export; Organism; Play; Post-Transcriptional Regulation; Postdoctoral Fellow; Production; Protein Isoforms; Proteins; RNA; RNA Processing; RNA Splicing; Regulation; Reporter; Role; Screening Result; Signal Pathway; Signal Transduction; Site; Specificity; Statistical Algorithm; Statistical Data Interpretation; Statistical Methods; Statistical Models; Systems Analysis; Techniques; Testing; Time; Trans-Activators; Variant; Work; base; cell type; circular RNA; computer science; experimental study; genome editing; genome-wide; genome-wide analysis; human disease; improved; knock-down; novel; programs; public health relevance; tool; transcriptome sequencing

 DESCRIPTION (provided by applicant) RNA is an ancient carrier of biological information, whose many functions became necessary for the evolution of cellular life, and transcriptional and post-transcriptional regulation of RNA is central to health and the progression of human disease. Remarkably, we have discovered that thousands of human genes produce circular RNA (circRNA) isoforms and in hundreds of genes, the circRNA is more abundant than the linear isoform. Our recent work has shown that circRNA expression is particularly regulated during human development. We have also demonstrated that circular RNAs are produced in organisms separated by billions of years of evolution, which suggests that the machinery, and by implication, function, of circRNA is central to eukaryotic gene expression programs: either conserved over billions of years, or a feature that has re-evolved multiple times which implies a functional role for circRNAs in the cell. Together, our work suggests a fundamental hypothesis that alternative splicing has functional consequences apart from protein production, including the production of circRNA isoforms. Yet, the field lacks a predictive mechanistic model of the cis sequences and trans-acting factors that specifically regulate circRNA, meaning a) the biochemical signaling pathways used by the cell to produce circRNA are unknown; b) we lack molecular tools to specifically express circRNA without background transcription of off-target RNAs. Such tools are required for discovery and rigorous experimental tests of circRNA function. This proposal aims to discover the mechanisms controlling circRNA production and regulation and promises to reveal novel biology regarding how biochemical signals are transduced into alternatively spliced RNA molecules and provide crucial tools for discovering the function of circRNA. Specifically, we aim to 1) engineer statistical algorithms for detecting and quantifying circRNA variants, and statistical methods for integrating expression across datasets; 2) discover trans-acting factors regulating circRNA production, export and decay; 3) systematically discover cis sequence control of circRNA abundance. The work will build on our discoveries of regulated expression of circular in human development, to delineate their regulation under normal circumstances, and how dysregulation may contribute to diseases such as neurodegeneration and cardiomyopathy.

 描述（由申请人提供） RNA是一个古老的生物信息载体，其功能对于细胞寿命的演变而言是必要的，而RNA的转录和转录后调节对于健康和人类疾病的发展至关重要。值得注意的是，我们发现成千上万的人基因产生了圆形RNA（circRNA）同工型，在数百个基因中，circrna比线性同工型更丰富。我们最近的工作表明，在人类发展过程中特别调节circrna的表达。我们还证明，圆形RNA是在数十亿年进化的生物体中产生的，这表明机械以及circrnas的功能是真核基因表达程序的核心：要么保守数十亿年，要么是多次发展的功能，该功能已重复多次培养了CIRCRNAS的功能。总之，我们的工作表明了一个基本假设，即替代剪接除了蛋白质产生（包括生产circrna同工型）外，还具有功能后果。然而，该领域缺乏特异性调节ciRCRNA的顺式序列的预测机械模型和反式作用因子，这意味着a）细胞用于产生circrna的生化信号通路未知； b）我们缺乏分子工具来特异性表达circrna，而无需脱靶RNA的背景转录。此类工具是发现和严格的CIRCRNA功能实验测试所必需的。该建议旨在发现控制circrna生产和调节的机制，并有望揭示有关如何将生化信号转换为剪接的RNA分子的新生物学，并为发现CIRCRNA功能提供了重要的工具。具体而言，我们旨在1）工程师统计算法，用于检测和量化circrna变体，以及用于整合数据集表达式的统计方法； 2）发现控制circrna产生，出口和衰减的反式作用因子； 3）系统地发现CIRCRNA丰度的顺式序列控制。这项工作将建立在我们对人类发展中循环表达的发现，在正常情况下描述其调节，以及失调可能导致神经变性和心肌病等疾病。