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

MicroRNA 是短 RNA 分子（约 20 至 24 个核苷酸），其功能是调节动物和植物中的基因表达水平。 microRNA 的靶标在许多关键细胞过程中发挥作用，包括发育、生物和非生物应激反应。在农作物中，microRNA 已表现出支持对生育力和产量至关重要的表型的作用，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跨基因组一致地编目和跟踪 microRNA 基因至关重要。这需要统一和严格的标识符分配、使用最新标准定期重新评估和筛选以及社区的意见。至关重要的是，不同的出版物和数据库对特定的 microRNA 使用相同的名称，并且不同物种的同源物最好应该获得一致的名称。自 2004 年起，就有了一个用于 microRNA 命名和质量控制的单一中央注册中心，用于命名和编目 microRNA：miRBase。 miRBase 在当前“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管理。基因组和小 RNA 的廉价测序极大地提高了 microRNA 的发现率，超出了 miRBase 手动管理新条目的能力。然而，为了快速注册新的 microRNA 以及评估现有注释和新注释，对单一可信资源的需求比以往任何时候都更加迫切。唐纳德·丹福斯植物科学中心、美国宾夕法尼亚州立大学和英国曼彻斯特大学之间的这一合作项目将为 miRbase 开发自主且自动化的 microRNA 注册系统。这将与 miRBase 命名协议集成并添加额外的质量控制。该项目将解决小RNA领域持续发展的一个关键问题，特别是在植物中。通过自动提交、管理和发布新注释，该项目将消除当前对耗时的手动注释来维护 miRBase 的依赖。这将使 miRBase 能够继续促进生物学所有领域的基础发现。因此，该项目将建立在现有工具的基础上，对植物小 RNA 深度测序数据集中的高置信度 microRNA 进行注释。该项目将开发一个管道，自动为用户从这些深度数据集中生成的新型植物 microRNA 注释分配一致的基因名称。该项目将把新的界面纳入 miRBase 基础设施中，以接受和显示用户提交的新型 microRNA 数据，并扩展用户可视化数据的选项。该项目的一项成果是对研究人员进行生物大数据分析和全栈网络开发方面的培训，这是科学界及其他领域急需的技能。该项目还将研究与本科教育相结合，并将以扩大代表性不足群体的参与为基础。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.