Integrative Analysis to Identify Regulation Targets of RNA-Binding Proteins

 描述(由申请人提供)：在过去的几十年里，大量的发现揭示了RNA调控在细胞过程中的核心作用。环状RNA(CircRNAs)是由线性转录体的两端连接而成的一大类转录后调控因子，在生物系统中发挥着广泛的功能。RNA在转录后的所有阶段都受到RNA结合蛋白的调控，包括剪接、运输、稳定和翻译。识别这些限制性商业惯例的功能靶点(包括线状和环状RNA)是生物医学研究的关键问题之一，并为药物发现开辟了新的方向。此外，由于一种将交联性免疫沉淀与高通量测序(CLIP-SEQ)相结合的技术的出现，现在可以在全基因组范围内研究RBP-RNA结合。这项研究的总体目标是开发新的分析模型和一个全面的研究平台来研究限制性商业惯例，以及更广泛的RNA调控。随着快速增长的CLIP-SEQ数据以及衡量特定RBP结合引起的全基因组功能变化的功能数据，引发了对系统分析限制性商业惯例功能靶标的计算方法的迫切需求。为此，我们已经收集了大量的CLIP-SEQ数据以及RNA-SEQ数据，它们代表了RBP结合引起的功能变化。整合来自不同来源的这些大规模和互补的数据集将为确定限制性商业惯例的功能目标和审查限制性商业惯例与CircRNA之间的直接相互作用提供一个很好的机会。更重要的是，我们的计算分析结果将得到我们的合作者的实验验证。在这项研究的目标1.1中，我们将提出一种新的统计方法来改进对CLIP-SEQ数据的分析和RBP结合位点的识别。我们将使用公共领域的基准数据集，以及通过生成我们自己的实验数据和实验验证，来比较和评估这些新的计算方法。在本研究的目标1.2中，我们将开发一个强大的计算模型，通过整合RNA序列、二级结构、RBP结合和功能数据集来识别限制性商业惯例的功能靶点。我们的合作者将对前景看好的功能目标进行实验验证。环状RNA(CircRNA)可以结合和隔离限制性商业惯例发挥调节作用，研究RBP-CircRNA的相互作用可能有助于深入了解CircRNA在疾病发病机制中的作用及其作为治疗靶点的潜力。然而，到目前为止，还没有开发出研究RBP-CircRNA相互作用的计算方法。在目标2中，我们将提出一种新的计算方法，利用CLIP-SEQ数据和RNA-SEQ数据系统地研究RBP-CircRNA相互作用及其功能。在本研究的目标3中，我们将开发一个公开可用的、全面的RBP-RNA相互作用门户网站，具有用户友好的界面和强大的分析引擎。这个门户网站将包括这项研究中使用的所有结果、计算算法和数据集。我们将在门户网站中将这些数据集与根据这项研究开发的分析算法整合在一起，以便世界各地的研究人员可以利用我们生成的数据和计算工具。我们计划与银河团队合作，为RNA调控开发一个用户友好和可重复使用的研究环境。

 DESCRIPTION (provided by applicant): Over the past couple of decades, a surge of discoveries have revealed RNA regulation as a central player in cellular processes. Circular RNAs (circRNAs), formed when the two ends of linear transcripts are joined together, were recently identified as a large class of post-transcriptional regulators that perform a range of functions in biological systems. RNAs are regulated by RNA-binding proteins (RBPs) at all post- transcriptional stages, including splicing, transportation, stabilization and translation. Identifyng the functional targets (including both linear and circular RNAs) of these RBPs ranks among the key biomedical research questions and opens a new direction for drug discoveries. Moreover, investigating RBP-RNA binding is now possible on a genome-wide scale, due to the advent of a technique that couples cross-linking immunoprecipitation with high-throughput sequencing (CLIP-seq). The overall goal of this study is to develop novel analytical models and a comprehensive research platform to study RBPs and, more broadly, RNA regulation. A rapidly-expanding amount of CLIP-seq data together with function data, which measure the genome-wide functional changes caused by the binding of a specific RBP, has triggered a critical need for computational methods to systematically analyze the functional targets of RBPs. For this purpose we have already collected extensive CLIP-seq data as well as RNA-seq data, which represent the functional changes caused by RBP-binding. Integrating these large-scale and complementary data sets from different sources will unlock a great opportunity to identify the functional targets of RBPs and to examine the direct interactions between RBPs and circRNAs. More importantly, the findings from our computational analysis will be experimentally validated by our collaborators. In Aim 1.1 of this study, we will propose a novel statistical approach to improve the analysis of CLIP- seq data and the identification of RBP-binding sites. We will compare and evaluate these new computational approaches by using benchmark datasets from the public domain, as well as by generating our own experimental data with experimental validations. In Aim 1.2 of this study, we will develop a powerful computational model to identify the functional targets of RBPs by integrating RNA sequence, secondary structure, RBP-binding and functional data sets. Promising functional targets will be experimentally validated by our collaborators. Circular RNA (circRNA) may bind and sequester RBPs into regulatory roles, and studying RBP- circRNA interactions may provide insights into the role of circRNAs in disease pathogenesis and their potential as therapeutic targets. However, as of yet no computational method has been developed to study RBP- circRNA interactions. In Aim 2, we will propose a novel computational method to systematically study RBP- circRNA interactions and their functions using CLIP-Seq data and RNA-seq data. In Aim 3 of this study, we will develop a publicly-available, comprehensive RBP-RNA interaction web portal with a user-friendly interface and a powerful analysis engine. This web-portal will include all the results, computational algorithms and datasets used in this study. We will integrate these datasets in the web portal together with analytic algorithms developed from this study, so that researchers worldwide can utilize the data and computational tools we have generated. In partnership with the Galaxy team, we plan to develop a user- friendly and reproducible research environment for RNA regulation.