Collaborative Research: BBSRC-NSF/BIO: An autonomous registry system for plant microRNAs

合作研究：BBSRC-NSF/BIO：植物 microRNA 自主注册系统

• 批准号: 2130884
• 负责人: Michael Axtell
• 金额: $ 19.43万
• 依托单位: Pennsylvania State Univ University Park
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-12-01 至 2024-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2130884&HistoricalAwards=false
• 关键词: Collaborative; Research; BBSRC; NSF; BIO

MicroRNAs are short RNA molecules (~20 to 24 nucleotides) that function to regulate levels of gene expression in animals and plants. The targets of microRNAs function in many key cellular processes, including development, biotic and abiotic stress responses. In crop plants, microRNAs have demonstrated roles supporting phenotypes important for fertility and yield, and thus contribute to food security and the agricultural economy. As with all features of genomes, cataloging and tracking microRNA genes consistently and across genomes using appropriate gene names is crucial. This requires uniform and rigorous assignment of identifiers, periodic reassessment and screening using the latest criteria, and community input. It is crucial that different publications and databases use the same name for a particular microRNA, and homologs in different species should ideally receive consistent names. A single, central registry for microRNA nomenclature and quality control has existed since 2004 to name and catalogue microRNAs: miRBase. miRBase faces challenges in the current era of 'big data'. In particular, registration of new microRNAs currently relies on time-consuming, manual curation. Inexpensive sequencing of genomes and small RNAs has massively increased the discovery rate of microRNAs, exceeding the capacity of miRBase for manual curation of new entries. Yet the need for a single trusted resource is more acute than ever, for rapid registration of new microRNAs, and to assess both existing annotations and new. This collaborative project between the Donald Danforth Plant Science Center and Pennsylvania State University in the US and the University of Manchester in the UK will develop an autonomous and automated microRNA registry system for miRbase. This will be integrated with miRBase naming protocols and adding additional quality controls. The project will resolve a critical problem for the continued growth of the small RNA field, particularly in plants. By automating submission, curation, and release of new annotations, this project will eliminate the current reliance on time-consuming manual annotations to maintain miRBase. This will allow miRBase to continue to catalyze fundamental discoveries in all areas of biology. The project will thus build on existing tools to annotate high-confidence microRNAs from plant small RNA deep sequencing datasets. The project will develop a pipeline to automatically assign consistent gene names to novel plant microRNA annotations generated by users from these deep datasets. And the project will incorporate new interfaces into the miRBase infrastructure to accept and display user submissions of novel microRNA data, and to expand options for users to visualize data. An output of the project is training researchers in the analysis of biological big data and full stack web development -- skill sets in high demand across the sciences and beyond. The project will also integrate research with undergraduate education, and it will build on programs to broaden participation by under-represented groups.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

microRNA是短的RNA分子（约20至24个核苷酸），可调节动物和植物中基因表达水平。 microRNA的靶标在许多关键的细胞过程中起作用，包括发育，生物和非生物应力反应。在作物工厂中，microRNA表现出了支持对生育和产量重要的表型的作用，从而有助于粮食安全和农业经济。与基因组的所有特征一样，使用适当的基因名称始终如一地编目和跟踪microRNA基因至关重要。这需要使用最新标准以及社区意见的定期重新评估和筛选的统一和严格分配。至关重要的是，不同的出版物和数据库为特定microRNA使用相同的名称，并且不同物种中的同源物理想地应获得一致的名称。自2004年以来，已经存在一个单一的MicroRNA命名和质量控制的中央注册表来命名和编目MicroRNA：Mirbase。 Mirbase在当前的“大数据”时代面临挑战。特别是，新microRNA的注册目前依赖于耗时的手动策展。基因组和小RNA的廉价测序大大提高了microRNA的发现率，超过了Mirbase在新条目的手动策划中的能力。然而，对单一可信赖的资源的需求比以往任何时候都更加敏锐，对新microRNA的快速注册，并评估现有注释和新的注释。唐纳德·丹佛斯植物科学中心和美国宾夕法尼亚州立大学和英国曼彻斯特大学之间的合作项目将开发出Mirbase的自动和自动化的MicroRNA注册系统。这将与mirbase命名协议集成并添加其他质量控制。该项目将解决小小的RNA场的持续生长，特别是在植物中的持续增长。通过自动提交，策展和发布新注释，该项目将消除当前对耗时的手动注释的依赖，以维护Mirbase。这将使Mirbase能够继续催化生物学所有领域的基本发现。因此，该项目将建立在现有工具的基础上，以注释植物小RNA深度测序数据集的高信心microRNA。该项目将开发一条管道，以自动为这些深数据集用户生成的新型植物microRNA注释分配一致的基因名称。该项目将将新的接口纳入MIRBASE基础架构，以接受和显示新型MicroRNA数据的用户提交，并扩展以用户可视化数据的选项。该项目的一个输出是培训研究人员在分析生物大数据和完整的堆栈网络开发的分析中 - 在整个科学及其他方面的需求较高的技能。该项目还将将研究与本科教育相结合，并将基于扩大代表性不足的小组参与的计划。该奖项反映了NSF的法定任务，并认为使用该基金会的知识分子优点和更广泛的影响审查标准，认为值得通过评估来获得支持。