Unbiased discovery of mechanisms regulating circRNA

 描述（由申请人提供） RNA是一种古老的生物信息载体，其许多功能对于细胞生命的进化是必需的，并且RNA的转录和转录后调节对于健康和人类疾病的进展至关重要。值得注意的是，我们已经发现数千个人类基因产生环状RNA（circRNA）同种型，并且在数百个基因中，circRNA比线性同种型更丰富。我们最近的研究表明，circRNA的表达在人类发育过程中受到特别的调节。我们还证明了环状RNA是在经过数十亿年进化分离的生物体中产生的，这表明circRNA的机制和功能对真核基因表达程序至关重要：要么是数十亿年来保守的，要么是一种经过多次重新进化的特征，这意味着circRNA在细胞中的功能作用。总之，我们的工作提出了一个基本假设，即选择性剪接除了产生蛋白质外，还具有功能性后果，包括产生circRNA亚型。然而，该领域缺乏特异性调节circRNA的顺式序列和反式作用因子的预测机制模型，这意味着a）细胞用于产生circRNA的生物化学信号传导途径是未知的; B）我们缺乏在没有脱靶RNA的背景转录的情况下特异性表达circRNA的分子工具。这些工具是发现和严格实验测试circRNA功能所必需的。该提案旨在发现控制circRNA产生和调节的机制，并有望揭示关于生化信号如何被转导到选择性剪接的RNA分子的新生物学，并为发现circRNA的功能提供关键工具。具体来说，我们的目标是：1）设计用于检测和定量circRNA变体的统计算法，以及用于整合数据集表达的统计方法; 2）发现调节circRNA产生，输出和衰变的反式作用因子; 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育中循环表达调控的发现的基础上，以描述它们在正常情况下的调节，以及调节异常如何导致神经退行性疾病和心肌病等疾病。

 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.