Plant Alternative Splicing and Abiotic Stress (PASAS)

植物选择性剪接和非生物胁迫 (PASAS)

• 批准号: BB/G024979/1
• 负责人: John Brown
• 金额: $ 50.41万
• 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: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG024979%2F1
• 关键词: Plant; Alternative; Splicing; Abiotic; Stress

Genetic variation is an important basis for biodiversity and phenotypic variation. How plants respond to external stimuli such as attack by pathogens/pests or stress conditions depends on the gene content of the plant species and the regulation of expression of the genes. Genes are regulated at many different levels. One important level is where genes are turned on or off or up or down - called transcriptional control. A second level occurs after the gene is transcribed or copied into RNA - called post-transcriptional control. There are many different mechanisms of post-transcriptional control and alternative splicing (AS) is one of the most important. Alternative splicing is where different portions of a gene transcript are joined in different combinations to generate more than one messenger RNA (mRNA) from a gene. The resultant mRNAs can be translated into proteins with different functions or can be targeted for degradation. Thus, AS increases the proteome complexity of an organism and can regulate mRNA levels. Alternative splicing affects all aspects of plant development, viability and adaptability to external conditions including abiotic stress. Nevertheless, AS in plants has been largely over-looked as a major contributor to global gene expression control despite its influence on transcript levels and on generation of differential protein functions. Current estimates suggest that a significant proportion of plant genes (35%) undergo alternative splicing. We have shown that this is clearly underestimated such that substantially more genes undergo AS and many genes have more AS events than have been described to date. In addition, alternative splicing patterns of many genes are regulated by different stress conditions and by altered levels of proteins which are involved in splicing. It is, therefore, essential to have a concerted effort to discover and identify AS events and to develop methods to accurately measure changes in AS at global and gene-specific levels. We will approach this by applying genomics and bioinformatics tools: 454 sequencing, whole genome tiling arrays, an RT-PCR system to quantify AS transcript levels and algorithms for comparing ESTs, to plants experiencing different abiotic stresses and with altered expression of splicing factors. We will identify new, un-annotated AS events, assess the technologies for their potential to provide quantitative analysis of AS and use these tools to study changes in AS under abiotic stress. We will also use these technologies to extend our examinations of the roles of specific trans-acting alternative splicing factors in regulating AS. The proposal is directly relevant to the themes of the ERA-PG call and brings together four research groups already involved in plant alternative splicing research and abiotic stress. The measurable outcomes will be novel, previously undescribed AS events deposited in appropriate databases; techniques for studying changes in AS; a database of AS events with their frequency and consequences; and information on the relationship between transcript levels and AS for many Arabidopsis genes. An overall outcome of this research will be a significantly increased awareness of the importance of AS and the need to consider AS and its consequences in post-transcriptional control of plant gene expression. Knowledge of the complexity and subtlety of all aspects of gene regulation is important in understanding how plants grow and survive and in the prediction of responses to changing environments and such awareness is the cornerstone of future plant breeding policies.

遗传变异是生物多样性和表型变异的重要基础。植物如何响应外部刺激，如病原体/害虫或胁迫条件的攻击，取决于植物物种的基因含量和基因表达的调控。基因在许多不同的水平上受到调控。一个重要的水平是基因的开启或关闭或向上或向下-称为转录控制。第二个层次发生在基因转录或复制成RNA后-称为转录后控制。转录后调控机制有很多种，选择性剪接（AS）是其中最重要的一种。选择性剪接是基因转录物的不同部分以不同的组合连接以从基因产生多于一个信使RNA（mRNA）的地方。所得到的mRNA可以被翻译成具有不同功能的蛋白质，或者可以被靶向降解。因此，AS增加了生物体的蛋白质组复杂性，并可以调节mRNA水平。选择性剪接影响植物发育、生存力和对包括非生物胁迫在内的外部条件的适应性的所有方面。然而，AS在植物中已在很大程度上被忽视的全球基因表达控制的主要贡献者，尽管它对转录水平和差异蛋白质功能的产生的影响。目前的估计表明，相当大比例的植物基因（35%）进行选择性剪接。我们已经表明，这显然是低估了，使更多的基因经历AS和许多基因有更多的AS事件比迄今为止已被描述。此外，许多基因的选择性剪接模式受不同胁迫条件和参与剪接的蛋白质水平改变的调节。因此，有必要共同努力，发现和识别AS事件，并开发方法，以准确地测量AS在全球和基因特异性水平上的变化。我们将通过应用基因组学和生物信息学工具：454测序，全基因组平铺阵列，RT-PCR系统来量化AS转录水平和算法比较EST，植物经历不同的非生物胁迫和剪接因子的表达改变。我们将确定新的，未注释的AS事件，评估其潜力的技术，提供定量分析的AS和使用这些工具来研究在非生物胁迫下AS的变化。我们还将利用这些技术来扩展我们的考试的作用，具体的反式作用的选择性剪接因子在调节AS。该提案与ERA-PG呼吁的主题直接相关，并汇集了已经参与植物选择性剪接研究和非生物胁迫的四个研究小组。可衡量的结果将是新的，以前未描述的AS事件存放在适当的数据库中;技术研究AS的变化; AS事件的数据库，其频率和后果;和信息之间的关系转录水平和AS的许多拟南芥基因。这项研究的总体成果将是一个显着提高认识的重要性，AS和需要考虑AS及其后果的转录后控制植物基因表达。了解基因调控各个方面的复杂性和微妙性对于理解植物如何生长和生存以及预测对变化环境的反应非常重要，这种认识是未来植物育种政策的基石。

项目成果

Plant SILAC: stable-isotope labelling with amino acids of arabidopsis seedlings for quantitative proteomics.

• DOI: 10.1371/journal.pone.0072207
• 发表时间: 2013
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Lewandowska D;ten Have S;Hodge K;Tillemans V;Lamond AI;Brown JW
• 通讯作者: Brown JW

Alternative Splicing of Barley Clock Genes in Response to Low Temperature.

大麦时钟基因响应低温的替代剪接。

• DOI: 10.1371/journal.pone.0168028
• 发表时间: 2016
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Calixto CP;Simpson CG;Waugh R;Brown JW
• 通讯作者: Brown JW

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

Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli.

• DOI: 10.1093/nar/gkp1241
• 发表时间: 2010-05
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kim SH;Spensley M;Choi SK;Calixto CP;Pendle AF;Koroleva O;Shaw PJ;Brown JW
• 通讯作者: Brown JW

A chloroplast retrograde signal regulates nuclear alternative splicing.

• DOI: 10.1126/science.1250322
• 发表时间: 2014-04-25
• 期刊: Science (New York, N.Y.)
• 作者: Petrillo E;Godoy Herz MA;Fuchs A;Reifer D;Fuller J;Yanovsky MJ;Simpson C;Brown JW;Barta A;Kalyna M;Kornblihtt AR
• 通讯作者: Kornblihtt AR