Process-specific alternative splicing: a tool to monitor multiple alternative splicing events simultaneously in targeted plant genes

过程特异性选择性剪接：同时监测目标植物基因中多个选择性剪​​接事件的工具

• 批准号: BB/G000212/1
• 负责人: John Brown
• 金额: $ 12.71万
• 依托单位: University of Dundee
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG000212%2F1
• 关键词: Process; specific; alternative; splicing; tool

The majority of plant genes contain intervening sequences (introns). When a gene is turned on (transcribed), the DNA code is copied into a molecule of RNA called precursor messenger RNA (pre-mRNA). Intron sequences are removed from pre-mRNA by the process of splicing which joins the coding regions of genes (exons) together. The spliced mRNA is then translated into a protein. In many cases, in both plants and animals, pre-mRNAs can be spliced in different ways to generate different mRNAs / this is termed alternative splicing (AS). The alternative mRNAs produced can encode different proteins with different functions such that, for example, in humans, the 35,000 genes in the genome can give rise to more than 150,000 proteins. Thus, AS modulates gene function and expression and increases the number of proteins in higher eukaryotes. This flexibility allows the cells in an organism to fine-tune and subtly regulate cell activity. AS is not a random process but is highly regulated through the interaction of a large number of proteins called splicing factors with sequence signals in the pre-mRNA. Thus, in a particular cell type, the profile of splicing factors will determine the pattern of alternatively spliced transcripts of all of the genes being expressed. This will differ in different cell types, at different stages of development and in response to stimuli and, for example, stress conditions. To understand the regulation of gene expression at the level of alternative splicing, it is necessary to be able to measure changes in alternative splicing of multiple genes under different conditions. Over the last five years, estimates of the number of plant genes which undergo alternative splicing have risen from 7 to 35%. Despite at least a third of plant genes being alternatively spliced, little is known about how alternative splicing is regulated in plants. In particular, there is a need to better assess AS and its consequences, to address the co-ordinated regulation of AS in genes involved in the same biological process and to be able to examine cell- and tissue-specific alternative splicing. One of the major drawbacks currently is the lack of an accurate and reproducible system capable of monitoring multiple (10s to 100s) of AS events simultaneously. Research in animal systems has shown that alternative splicing is an essential aspect of gene expression with networks of alternative splicing regulation being superimposed on networks of transcriptional regulation. In plant systems, measuring global transcript levels is carried out routinely (transcriptomics) but alternative splicing and, in particular, the concept of co-ordinated and regulated alternative splicing has been largely ignored. We wish to establish a tool to monitor changes in alternative splicing of multiple plant genes in development and stress responses. The project will build collaborations between groups involved in aspects of developmental and stress biology of plants and the RNA biology/alternative splicing lab at the University of Dundee. The outcome of the project will be the demonstration that comprehensive process-specific AS RT-PCR panels can be used to accurately analyse changes in alternative splicing during development, under different conditions and in different mutant lines. By correlating patterns of changes in alternative splicing of specific genes or subsets of genes, information on the co-ordinated regulation of AS will be produced for the first time. Such information will be an integral part of systems approaches aimed at understanding interaction networks which regulate biological processes. The tool which we will develop will be of interest to plant scientists around the world. Although we will establish the tool by studying developmental processes and stress-induced genes in Arabidopsis, the system is very flexible and can be applied to examine any biological process in any plant species for which reasonable EST data exists.

大多数植物基因都含有中间序列（内含子）。当一个基因被打开（转录）时，DNA代码被复制到一个叫做前体信使RNA （pre-mRNA）的RNA分子中。内含子序列通过将基因编码区（外显子）连接在一起的剪接过程从mrna前体中移除。剪接的mRNA随后被翻译成蛋白质。在许多情况下，在植物和动物中，前mrna可以通过不同的方式剪接以产生不同的mrna /这被称为选择性剪接（AS）。产生的替代mrna可以编码具有不同功能的不同蛋白质，例如，在人类中，基因组中的35,000个基因可以产生超过150,000个蛋白质。因此，在高等真核生物中，AS调节基因功能和表达，并增加蛋白质的数量。这种灵活性使生物体中的细胞能够微调和微妙地调节细胞活动。AS不是一个随机过程，而是通过称为剪接因子的大量蛋白质与前mrna序列信号的相互作用而受到高度调节。因此，在特定的细胞类型中，剪接因子的特征将决定所有被表达基因的可选剪接转录本的模式。这在不同的细胞类型、不同的发育阶段和对刺激的反应，例如压力条件下，会有所不同。为了在选择性剪接水平上理解基因表达的调控，有必要能够测量不同条件下多个基因的选择性剪接的变化。在过去的五年中，对植物基因进行选择性剪接的数量的估计已经从7%上升到35%。尽管至少有三分之一的植物基因被选择性剪接，但人们对植物中如何调节选择性剪接知之甚少。特别是，有必要更好地评估AS及其后果，解决参与相同生物过程的基因中AS的协调调节，并能够检查细胞和组织特异性的选择性剪接。目前的主要缺点之一是缺乏能够同时监视多个（10到100个）AS事件的精确和可重复的系统。动物系统的研究表明，选择性剪接是基因表达的一个重要方面，选择性剪接调控网络叠加在转录调控网络上。在植物系统中，测量全球转录水平是常规的（转录组学），但选择性剪接，特别是协调和调节的选择性剪接的概念在很大程度上被忽视了。我们希望建立一种工具来监测多种植物基因在发育和胁迫反应中的选择性剪接变化。该项目将在涉及植物发育和胁迫生物学方面的小组与邓迪大学RNA生物学/选择性剪接实验室之间建立合作关系。该项目的结果将证明，综合过程特异性AS RT-PCR面板可用于准确分析发育过程中，不同条件下和不同突变系中选择性剪接的变化。通过将特定基因或基因亚群的选择性剪接的变化模式相关联，将首次产生关于AS协调调节的信息。这些信息将成为旨在理解调节生物过程的相互作用网络的系统方法的一个组成部分。我们将开发的工具将引起全世界植物科学家的兴趣。虽然我们将通过研究拟南芥的发育过程和胁迫诱导基因来建立工具，但该系统非常灵活，可以应用于检查任何植物物种的任何生物过程，只要存在合理的EST数据。

项目成果

Involvement of the plant nucleolus in virus and viroid infections: parallels with animal pathosystems.

• DOI: 10.1016/b978-0-12-385034-8.00005-3
• 发表时间: 2010
• 期刊: Advances in virus research
• 作者: Taliansky ME;Brown JW;Rajamäki ML;Valkonen JP;Kalinina NO
• 通讯作者: Kalinina NO

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis.

替代剪接和废话介导的衰减调节拟南芥中重要的调节基因的表达。

• DOI: 10.1093/nar/gkr932
• 发表时间: 2012-03
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kalyna M;Simpson CG;Syed NH;Lewandowska D;Marquez Y;Kusenda B;Marshall J;Fuller J;Cardle L;McNicol J;Dinh HQ;Barta A;Brown JW
• 通讯作者: Brown JW