Structural, Functional, and Evolutionary Analysis of Long Non-coding RNAs in Control of Stress Response and the Epigenome in Diverse Plant Species

PI：Brian D.Gregory(宾夕法尼亚大学)共同PI：Eric Lyons和Mark Beilstein(亚利桑那大学)Long-Non-Coding RNAs(LncRNAs)是一类新兴的分子，因其在各种生物过程中的作用而受到关注。LncRNAs的定义是，它们不编码蛋白质，因此不是mRNAs。此外，它们不适合于其他定义明确的小干扰RNA产生类别，如小干扰RNA(SiRNA)和微小RNA(MiRNAs)。尽管lncRNAs在发育、表观遗传修饰和逆境反应中具有重要作用，但关于其结构、蛋白质相互作用和功能仍有许多需要了解，特别是在模式植物和作物物种中。该项目将结合基因组学、进化学和生物信息学的方法解决这一重大差距。预计该项目开发的数据、网络可访问的基因组分析工具和数据管理系统将为通过LncRNAs调控植物基因表达提供新的见解，并为专注于改良大量作物和遗传模式植物的研究提供重要的新发现和资源。关于推广和培训，该项目将为学生和博士后提供核糖核酸生物学、计算科学和进化生物学方面的跨学科研究培训。此外，该项目将开发一门名为“RNA生物学中的应用概念”的跨学科课程，该课程将利用大规模计算和数据集来了解RNA在生物系统中作用的各个方面。这门基于项目的课程将教授RNA生物学的基础知识、下一代测序技术、分布式和高性能计算、数据密集型科学以及将用于学生主导的研究项目的协作研究技术。这门课程将在宾夕法尼亚大学和亚利桑那大学同时教授，双向音频/视频会议和讲座主题将在每个地点轮流教授。所有项目成果将通过项目网站(https://genomevolution.org/wiki/index.php/EPIC-CoGe_Tutorial)，、iPLANT协作库和长期储存库，如基因库和短期阅读档案，随时提供给更广泛的研究界。这个项目的独特之处在于提供对lncRNAs的结构和功能的见解，以及它们与基因组中特定的表观基因组调节修饰的相互作用。该项目的具体目标是定义在正常发育和应激反应中对适当的基因调控至关重要的lncRNAs的子集。具体地说，该项目将集中于识别和功能描述那些(1)核，(2)高度结构，(3)胁迫响应，(4)蛋白质结合，和(5)进化保守的在遗传模型(Eutrema salsugineum和Arabiopsis thaliana)和作物物种(Camelina sativa，Brassica Rapa，Zea Mays，and Sorghum biolor)中保守的lncRNAs，重点关注它们在胁迫适应中的作用。最后，该项目将扩展EPIC-COGE，这是一个跨所有物种的植物表观基因组数据的中央存储库，具有先进的数据集成、可视化和分析工具，以允许集成功能基因组数据，以提供对全基因组表观基因组相互作用的新见解。

PI: Brian D. Gregory (University of Pennsylvania)Co-PIs: Eric Lyons and Mark Beilstein (University of Arizona) Long non-coding RNAs (lncRNAs) are an emerging class of molecules gaining attention for their roles in various biological processes. lncRNAs are defined by the fact that they do not code for proteins and are therefore not mRNAs. In addition, they do not fit into other well-defined small silencing RNA-producing categories such as small interfering RNAs (siRNA) and microRNAs (miRNAs). Despite the importance of lncRNAs in development, epigenetic modification, and stress responses, there is still much to be learned about their structure, protein interactions, and functions, especially in model and crop plant species. This project will address this significant gap using a combination of genomic, evolutionary, and bioinformatics approaches. It is anticipated that the data, web-accessible genome analytical tools, and data management systems developed by the project will provide novel insights into plant gene expression regulation by lncRNAs, and provide important new findings and resources for studies focused on the improvement of numerous crop and genetic model plants. With regard to outreach and training, this project will provide interdisciplinary research training in RNA biology, computational science and evolutionary biology for students and postdoctoral associates. In addition, the project will develop an interdisciplinary course entitled "Applied Concepts in RNA Biology" that will leverage large-scale computing and datasets to understand various aspects of the role of RNA in biological systems. This project-based course will teach the fundamentals of RNA biology, next-generation sequencing techniques, distributed and high performance computing, data-intensive science, and collaborative research techniques that will be used in student-driven research projects. The course will be taught simultaneously at the University of Pennsylvania and the University of Arizona, with two-way audio/video conferencing and lecture topics alternatively taught at each site. All project outcomes will be made readily accessible to the broader research community through a project website (https://genomevolution.org/wiki/index.php/EPIC-CoGe_Tutorial), the iPlant Collaborative and long-term repositories such as GenBank and the Short Read Archive (SRA). This project is uniquely positioned to provide insights into the structure and function of lncRNAs, and their interaction with specific epigenomic regulatory modifications in the genome. The specific goals of the project are to define a subset of lncRNAs that are important for proper gene regulation in both normal development and stress response. Specifically, the project will focus on identifying and functionally characterizing those lncRNAs that are (1) nuclear, (2) highly structured, (3) stress responsive, (4) protein bound, and (5) evolutionary conserved in genetic models (Eutrema salsugineum and Arabidopsis thaliana) and in crop species (Camelina sativa, Brassica rapa, Zea mays, and Sorghum bicolor), focusing on their roles in stress adaptation. Finally, the project will expand EPIC-CoGe, a central repository for plant epigenomics data across all species, with advanced data integration, visualization, and analysis tools to allow for the integration of functional genomics data to provide new insight into genome-wide epigenomic interactions.