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Deciphering the RNA degradome: A new tool for small RNA target discovery

破译 RNA 降解组：发现小 RNA 靶标的新工具

基本信息

批准号：
BB/H023895/1
负责人：
Vincent Moulton
金额：
$ 12.68万
依托单位：
University of East Anglia
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2010
资助国家：
英国
起止时间：
2010 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FH023895%2F1
关键词：
Deciphering RNA degradome new tool

项目摘要

RNA silencing is a complex and highly conserved regulatory mechanism that is now known to be involved in diverse processes such as development, pathogen control, genome maintenance and response to environmental changes. Since its recent discovery, RNA silencing has become a fast moving area of research of great importance in both plant and animal molecular biology. Research in this field has greatly profited from new developments in novel high-throughput sequencing technologies (such as 454 and Solexa/Illumina) which, in a single run, can generate several datasets each containing millions of small RNA (sRNA) molecules, the key players in all RNA silencing phenomena. A key challenge in sRNA research at present is to understand the function of the millions of sRNAs that have been recently sequenced and deposited in public databases. A first step in meeting this challenge is to find which (if any) genes are being regulated by each sRNA. Several computational approaches have been devised for sRNA target prediction in plants and animals but these are only predictions and cannot be relied upon without experimental validation. However, in the last year or so a new high-throughput experimental technique has been described for sequencing of the 5'-ends of uncapped mRNAs including those transcripts that are targeted by sRNAs and subjected to endonucleolytic cleavage. In plants, degraded mRNA fragments provide evidence of the interaction between sRNAs and their complimentary mRNA targets that lead to cleavage and degradation of the mRNA. Thus the possibility of sequencing the ''RNA degradome' of an organism in this manner is set to revolutionise target validation in plants since it permits the genomic scale sequencing of cleaved mRNAs for the first time. Currently there is only one tool available for degradome analysis and it has several limitations which make it unsuitable for large-scale analysis of such data. In this proposal we will develop and implement a novel approach to high-throughput analysis of degradome data which will allow users to validate targets across the entire sRNAome and produce a network of sRNA/mRNA interactions based on degradome evidence. The tool will be made available online and for download through the UEA Plant sRNA Toolkit, a collection of user-friendly tools allowing the analysis of high-throughput plant sRNA datasets with high-performance computing without the need for expert knowledge or dedicated bioinformatics support.

RNA沉默是一种复杂且高度保守的调控机制，目前已知它涉及多种过程，如发育、病原体控制、基因组维持和对环境变化的反应。自RNA沉默被发现以来，它已成为植物和动物分子生物学中一个快速发展的重要研究领域。该领域的研究得益于新型高通量测序技术（如454和Solexa/Illumina）的新发展，这些技术在一次运行中可以生成多个包含数百万小RNA （sRNA）分子的数据集，这些小RNA （sRNA）分子是所有RNA沉默现象的关键参与者。目前sRNA研究的一个关键挑战是了解最近测序并存储在公共数据库中的数百万sRNA的功能。应对这一挑战的第一步是找出哪些（如果有的话）基因受到每个sRNA的调节。已经设计了几种计算方法来预测植物和动物的sRNA靶标，但这些只是预测，没有实验验证不能依赖。然而，在过去一年左右的时间里，一种新的高通量实验技术被描述为对无帽mrna的5'端进行测序，包括那些被sRNAs靶向并受到核内溶解切割的转录本。在植物中，降解的mRNA片段提供了sRNAs与其互补的mRNA靶标之间相互作用导致mRNA切割和降解的证据。因此，以这种方式对生物体的“RNA降解”进行测序的可能性将彻底改变植物中的靶标验证，因为它首次允许对裂解mrna进行基因组规模的测序。目前只有一种工具可用于降解分析，它有几个限制，使其不适合大规模分析这类数据。在本提案中，我们将开发和实施一种高通量降解数据分析的新方法，该方法将允许用户验证整个sRNAome的靶标，并基于降解证据产生sRNA/mRNA相互作用的网络。该工具将在线提供，并可通过东英吉利大学植物sRNA工具包下载，该工具包是一个用户友好的工具集合，允许使用高性能计算分析高通量植物sRNA数据集，而无需专家知识或专门的生物信息学支持。