The UEA Small RNA Workbench: New and improved tools for high throughput small RNA analysis

RNA沉默是一种复杂的高度保守的调控机制，参与了多种过程，如发育，病原体控制，基因组维持和对环境变化的反应。RNA沉默自最近被发现以来，已成为植物和动物分子生物学中非常重要的快速发展的研究领域。它的发现不仅是我们对活细胞中复杂调控过程的理解的重大突破，而且也为人类疾病的新疗法的开发打开了大门。2006年诺贝尔医学奖的颁发强调了这些发现对于发现RNA干扰的重要性。小RNA分子（sRNA）在RNA沉默机制中起着至关重要的作用，因为它们可以以序列特异性的方式与其他核酸相互作用，将它们标记为失活靶点。研究人员利用尖端测序技术获得大量sRNA序列数据集，（多达2亿个序列，长度约20-30个核苷酸）。随着这些技术变得越来越容易获得和负担得起，现在可以获得多个大规模数据集，从而可以分析完整sRNA群体的变化。这些变化可以表明RNA沉默途径参与感兴趣的生物过程，例如调节生物体的关键发育阶段。在以前的BBSRC资助的工作中，我们通过开发UEA sRNA工作台解决了分析大量sRNA数据集所面临的一些挑战。这是一个可下载的程序，吸引了学术和商业用户，并且允许生物学家在没有生物信息学支持的情况下识别数据集中的关键sRNA。自2012年推出以来，工作台已被下载4 000多次，随着用户群迅速扩大，网站每天收到约50个RSS提要请求。然而，工作台需要一些新的功能和改进，这些功能和改进的需求是由sRNA的新研究、用户反馈以及更深入、更便宜的测序技术的快速发展驱动的。在这个项目中，我们将建立在我们公开的sRNA分析软件工具的基础上，旨在提供新的尖端工具，包括本地和通过云计算，以便继续为植物和动物sRNA数据集的分析提供世界领先的解决方案。这将包括增加新的工具，用于准备和访问sRNA序列数据的质量，预测新的sRNA类别，以及分析sRNA数据与RNA-seq数据。这将为生物学家提供急需的资源，以帮助识别新的sRNA及其功能，从而指导进一步的湿实验室研究。

RNA silencing is a complex and highly conserved regulatory mechanism that is involved in diverse processes such as development, pathogen control, genome maintenance and response to environmental change. Since its recent discovery, RNA silencing has become a fast moving area of research of great importance in both plant and animal molecular biology. Its discovery has not only been a major breakthrough for our understanding of complex regulatory processes in living cells, but has also opened the door to the development of novel therapeutics for human diseases. The award of the Nobel Prize for medicine highlighted the importance of these findings in 2006 for the discovery of RNA interference. Small RNA molecules (sRNAs) play a crucial role in the RNA silencing machinery in that they can interact with other nucleic acids in a sequence specific manner to mark them as targets for inactivation.To learn more about this mechanism and its implications, researchers employ cutting-edge sequencing technologies to obtain huge datasets of sRNA sequences (up to 200 million sequences about 20-30 nucleotides in length) from a number of organisms. With these technologies becoming more accessible and affordable, it is now possible to obtain multiple large-scale data sets, which allow the analysis of changes in complete sRNA populations. These changes can indicate the involvement of RNA silencing pathways in biological process of interest, such as regulation of key developmental stages in an organism.In previous BBSRC-funded work, we have addressed some of the challenges involved in analysing massive sRNA data sets through the development of the UEA sRNA workbench. This is a downloadable program that has attracted both academic and commercial users, and that allows biologists to identify key sRNAs in their data sets without bioinformatics support. Since its introduction in 2012, the workbench has been downloaded over 4,000 times and the website receives around 50 requests for the RSS feed per day as its user base rapidly expands. However, there are several new features and improvements that the workbench requires whose need are being driven by new research in sRNAs, user feed-back, and the rapid development of ever deeper and cheaper sequencing technologies. In this project, we will build on our publicly available software tools for sRNA analysis, with the aim of providing new cutting edge tools, both locally and through the cloud-computing, so as to continue to provide a world-leading solution for the analysis of plant and animal sRNA datasets. This will include the addition of new tools for preparing and accessing the quality of sRNA sequence data, predicting new classes of sRNAs, and for analysing sRNA data in tandem with RNA-seq data. This will provide biologists with much needed resources to help identify novel sRNAs and their function in order to direct further wet-lab studies.