Alternative Splicing and Long Non-coding RNAs in Polyploids

多倍体中的选择性剪接和长非编码 RNA

• 批准号: RGPIN-2014-04603
• 负责人: Adams, Keith
• 金额: $ 5.17万
• 依托单位: University of British Columbia
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2014
• 资助国家: 加拿大
• 起止时间: 2014-01-01 至 2015-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=566625
• 关键词: Alternative; Splicing; Long; Non; coding

Polyploids, organisms with an extra set of chromosomes, are common among plants and several crop plants are polyploid. Polyploidy can lead to novel morphological and developmental characteristics, larger cell sizes, and new gene functions and expression patterns. The formation of polyploids often involves hybridization (crossing) between two species followed by chromosome doubling. The goal of this research is to understand the consequences of polyploidy on gene expression with a focus on patterns of RNA splicing (alternative splicing) and long noncoding RNAs (genes whose products act as RNAs instead of as proteins). Expression and RNA splicing patterns of genes in Brassica napus (canola) polyploids will be compared with their diploid parents in response to stress conditions. Stress treatments will be done with heat, cold, and drought. RNA expression and splicing patterns will be examined on a genome-wide scale with high-throughput sequencing and computational analyses. Long noncoding RNA genes will be identified in Brassica species. Then their expression patterns will be assayed with high throughput sequencing in Brassica napus polyploids and their diploid parents to show how expression of this class of genes changes upon polyploidy. Duplicated long noncoding RNA genes, and their gene family histories, will be characterized in Arabidopsis thaliana and Brassica species, and the features will be compared with protein coding genes. The proposed research will provide the first insights into differences in RNA splicing patterns between duplicated genes in polyploid plants in response to stress conditions on a genome-wide scale. Also it will provide the first information about long noncoding RNA expression in polyploids. This research is likely to have a considerable impact on the fields of plant genomics, plant molecular biology, and molecular evolution. Some duplicate genes play a role in specifying traits of agronomic importance in plants. Some RNA splicing patterns in duplicated genes, as well as gene regulation by long noncoding RNAs, may be involved in conferring traits selected for during plant breeding. In particular, polyploid canola (Brassica napus) is important to Canada's economy and food supply and what is learned from studying RNA splicing and long noncoding RNAs in canola may lead to improvement of this crop plant. Understanding how RNA splicing patterns can change gene expression and function, as well as how long noncoding RNAs regulate gene expression, may lead to using RNA splicing and noncoding RNAs as tools for biotechnology applications to design crops with altered expression of genes of interest to create or improve desired characteristics.

多倍体是一种具有额外一组染色体的生物体，在植物中很常见，几种农作物都是多倍体。多倍体可以导致新的形态和发育特征，更大的细胞大小，和新的基因功能和表达模式。多倍体的形成通常涉及两个物种之间的杂交（杂交），然后是染色体加倍。本研究的目的是了解多倍体对基因表达的影响，重点关注RNA剪接（选择性剪接）和长链非编码RNA（其产物作为RNA而不是蛋白质的基因）的模式。将甘蓝型油菜多倍体的基因表达和RNA剪接模式与其二倍体亲本在胁迫条件下的差异进行比较。压力处理将在高温、低温和干旱条件下进行。RNA表达和剪接模式将在全基因组范围内通过高通量测序和计算分析进行检查。长链非编码RNA基因将在芸苔属植物中得到鉴定。然后利用高通量测序技术对其在甘蓝型油菜多倍体及其二倍体亲本中的表达模式进行分析，以揭示该类基因在多倍体发生时的表达变化。拟南芥和芸苔属植物中重复的长链非编码RNA基因及其基因家族史将被表征，并与蛋白质编码基因进行比较。该研究将首次在全基因组范围内深入了解多倍体植物在逆境条件下复制基因之间RNA剪接模式的差异。同时也为多倍体长链非编码RNA的表达提供了第一手信息。该研究将对植物基因组学、植物分子生物学、分子进化等领域产生重大影响。一些重复基因在植物中起着决定重要农艺性状的作用。一些复制基因的RNA剪接模式，以及长链非编码RNA的基因调控，可能与植物育种过程中所选择的性状的赋予有关。特别是，多倍体油菜（Brassica napus）对加拿大的经济和食物供应至关重要，研究油菜的RNA剪合和长链非编码RNA可能会导致这种作物的改良。了解RNA剪接模式如何改变基因表达和功能，以及非编码RNA调节基因表达的时间长短，可能会导致使用RNA剪接和非编码RNA作为生物技术应用的工具，设计具有改变感兴趣基因表达的作物，以创造或改善所需的特性。