Computational tools and resources to study alternative splicing and mRNA isoform variation

项目总结 该项目的中心目标是开发广泛适用的计算工具和资源，用于 研究前信使核糖核酸选择性剪接(AS)和信使核糖核酸异构体的变化。AS是一种流行的机制， 产生监管和功能多样性。几乎所有哺乳动物基因组中的多外显子基因都经历AS， 导致外显子组成不同的mRNAs。AS在发育过程中发生广泛的变化，细胞 分化，和疾病。然而，许多问题仍然存在，关于模式、监管和功能 就像。公共资源库中大规模RNA-Seq数据的快速积累，出现了新的长期阅读 转录组分析的测序策略和深度学习技术的最新进展创造了 组学和大数据方法带来了令人兴奋的机会，以发现新的监管和功能特征 就像。为了充分利用这些强大的数据集和技术，迫切需要新的计算工具。 我们的实验室在开发和传播广泛采用的算法和 用于表征AS和信使核糖核酸异构体变异的计算工具。在这个R01项目中，在此基础上 专业知识，我们将开发新的计算工具和资源来研究内含子保留-仍然很差 了解人类细胞中基因调控的机制--并描述受基因调控的内含子 人群中的滞留事件(目标1)，并描述为模式和信使核糖核酸亚型变异 使用大量组织(目标2)和单个细胞(目标3)的长读RNA-SEQ数据。由此产生的用户友好型， 可扩展的工具以及相关的数据资源将大大增强生物医学的能力 研究人员使用内部和公共数据集研究AS和转录组的复杂性 病态的环境。在这个项目中开发的所有软件都将是开放源码的，并免费提供给 研究社区。我们将利用我们广泛的专家协作者网络和广泛的用户基础来 加强这些计算工具的开发、测试和传播。我们的努力将是整合的 由于我们对AS和mRNA异构体调控生物学的长期兴趣，确保我们的工作 解决重要的生物医学问题，并满足未得到满足的技术需求。重要的是，在每个目标中 计算工具和资源的开发将与它们对以下问题的应用相协同 AS的变异、调节和功能。总体而言，我们预计我们提议的R01项目将提供强大的 以及广泛用于研究的计算工具和资源，如在哺乳动物转录本中。

PROJECT SUMMARY The central objective of this project is to develop broadly applicable computational tools and resources for studying pre-mRNA alternative splicing (AS) and mRNA isoform variation. AS is a prevalent mechanism for generating regulatory and functional diversity. Almost all multi-exon genes in mammalian genomes undergo AS, resulting in mRNAs that vary in their exon composition. Widespread changes in AS occur in development, cell differentiation, and disease. However, many questions remain about the patterns, regulation, and functions of AS. Rapid accumulation of large-scale RNA-seq data in public repositories, emergence of new long-read sequencing strategies for transcriptome analysis, and recent advances in deep learning techniques create exciting opportunities for omics and big data approaches to uncover new regulatory and functional features of AS. To make full use of these powerful datasets and technologies, new computational tools are urgently needed. Our lab has an outstanding track record in developing and disseminating widely adopted algorithms and computational tools for characterizing AS and mRNA isoform variation. In this R01 project, building on that expertise, we will develop new computational tools and resources to study intron retention – a still poorly understood mechanism of gene regulation in human cells – and characterize genetically regulated intron retention events in the human population (Aim 1), and to delineate AS patterns and mRNA isoform variation using long-read RNA-seq data of bulk tissues (Aim 2) and single cells (Aim 3). The resulting user-friendly, scalable tools as well as associated data resources will substantially enhance the ability of biomedical researchers to study AS and transcriptome complexity using in-house and public datasets in diverse normal and diseased contexts. All software developed in this project will be made open source and freely available to the research community. We will leverage our extensive network of expert collaborators and broad user base to enhance the development, testing, and dissemination of these computational tools. Our efforts will be integrated with our long-standing interest in the biology of AS and mRNA isoform regulation, ensuring that our work addresses important biomedical questions and serves unmet technological needs. Importantly, in each aim the development of computational tools and resources will synergize with their applications to questions about the variation, regulation, and functions of AS. Overall, we expect that our proposed R01 project will provide powerful and widely used computational tools and resources for studying AS in mammalian transcriptomes.