Genome-wide analysis of short RNAs as modulators in dehydration stress tolerance using tolerant and genetic model systems

使用耐受和遗传模型系统对短 RNA 作为脱水应激耐受调节剂进行全基因组分析

• 批准号: BB/E024866/1
• 负责人: Tamas Dalmay
• 金额: $ 39.94万
• 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: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FE024866%2F1
• 关键词: Genome; wide; analysis; short; RNAs

Drought stress is a common adverse environmental condition that seriously affects crop productivity worldwide. The prediction is that the drought stress, in the form of unpredictable changes in rainfall or competition for fresh water with growing urban populations, will continue to be the major single abiotic factor likely to affect crop yields globally. Drought stress affects practically every aspect of plant growth and metabolism. Plant responses to water deficit depend upon factors such as duration and degree of stress, growth stage and time of stress exposure. Most environmental stresses result in water-deficit stress. Frozen soil can reduce water uptake and thus produce water stress; in the same way, salt accumulation in the soil decreases the water potential that makes soil water less available. In order to survive under water deficit conditions, plants have to maintain their water status to maintain ion homeostasis. The common responses to different stresses indicate similar functions of the gene products for plants under stress conditions involving water deficit. The existence of interacting signal perception and transduction pathways, which promote the plant stress response, is suggested by studies on gene expression during dehydration. Endogenous abscisic acid (ABA) levels increase as result of water deficit and it is thought to be involved in signal transduction. Up to now the protein coding regions have been analysed with respect to transgenic approaches to improve drought tolerance, but it has become clear that important regulatory determinants are missing. sRNAs have been recently recognised as important regulatory components of gene expression. There are two classes of sRNAs: microRNAs (miRNAs) and short interfering RNAs (siRNAs). miRNAs are endogenous regulatory sRNAs that derive from stem-loop regions of endogenous precursor transcripts. miRNAs anneal to the messages of protein-coding genes which result in the cleavage of the mRNAs. The genome wide analysis of sRNAs will allow us to identify novel sRNAs that are differentially accumulated in well watered and dried tissues. Therefore, sRNAs will be cloned and sequenced from well watered and dehydrated tissues of two different dehydration tolerant model species (C. plantagineum and M. truncatula) using high-throughput sequencing technology. The genome wide analysis of sRNAs will allow us to identify novel sRNAs that are differentially accumulated in well watered and dried tissues. The expression profile of known and novel sRNAs will be determined by microarray hybridisation and validated by Northern blots. Target genes will be predicted or experimentally determined for sRNAs that are differentially accumulated in well watered and dehydrated tissues. The biological relevance of the sRNA regulation of validated target genes will be analysed by over-expressing sRNAs or sRNA insensitive target genes. Several genomics tools are integrated in this approach, such as high-throughput sequencing and microarray hybridisation. This project is not feasible without these tools because the scale of sRNA regulation requires genome wide analysis. The advantage of the chosen methodology is that it will reveal novel sRNAs and the function of known and novel sRNAs in drought tolerance. Although it is more difficult to carry out this project using plant species without complete genome sequences, the advantages are that it allows (i) the identification of novel sRNAs that do not exist in Arabidopsis and rice and (ii) the analysis of sRNAs in two drought tolerant model species will reveal different networks regulating dehydration tolerance.

干旱胁迫是一种常见的不利环境条件，严重影响全球作物生产力。据预测，干旱胁迫（表现为降雨量不可预测的变化或城市人口不断增长对淡水的竞争）将继续成为可能影响全球作物产量的主要单一非生物因素。干旱胁迫几乎影响植物生长和新陈代谢的各个方面。植物对缺水的反应取决于胁迫持续时间和程度、生长阶段和胁迫暴露时间等因素。大多数环境压力都会导致缺水压力。冻土会减少吸水量，从而产生水分胁迫；同样，土壤中的盐分积累会降低水势，从而使土壤水的利用率降低。为了在缺水条件下生存，植物必须保持水分状态以维持离子稳态。对不同胁迫的共同反应表明，在缺水胁迫条件下植物的基因产物具有相似的功能。对脱水过程中基因表达的研究表明，存在促进植物应激反应的相互作用的信号感知和转导途径。缺水会导致内源性脱落酸 (ABA) 水平升高，人们认为它与信号转导有关。到目前为止，已经针对提高耐旱性的转基因方法对蛋白质编码区进行了分析，但很明显，重要的调控决定因素仍然缺失。 sRNA 最近被认为是基因表达的重要调控成分。 sRNA 有两类：微小 RNA (miRNA) 和短干扰 RNA (siRNA)。 miRNA 是内源性调节 sRNA，源自内源性前体转录本的茎环区域。 miRNA 与蛋白质编码基因的信息退火，从而导致 mRNA 的裂解。 sRNA 的全基因组分析将使我们能够识别在水分充足和干燥的组织中差异积累的新型 sRNA。因此，将使用高通量测序技术从两个不同耐脱水模式物种（C. plantagineum 和 M. truncatula）的充足水分和脱水组织中克隆 sRNA 并进行测序。 sRNA 的全基因组分析将使我们能够识别在水分充足和干燥的组织中差异积累的新型 sRNA。已知和新型 sRNA 的表达谱将通过微阵列杂交确定，并通过 Northern 印迹进行验证。将预测或通过实验确定在水分充足和脱水组织中差异积累的 sRNA 的靶基因。将通过过表达 sRNA 或 sRNA 不敏感靶基因来分析已验证靶基因的 sRNA 调节的生物学相关性。该方法集成了多种基因组学工具，例如高通量测序和微阵列杂交。如果没有这些工具，这个项目就不可行，因为 sRNA 调控的规模需要全基因组分析。所选方法的优点是它将揭示新型 sRNA 以及已知和新型 sRNA 在耐旱性中的功能。尽管使用没有完整基因组序列的植物物种来开展该项目比较困难，但其优点是它可以（i）鉴定拟南芥和水稻中不存在的新型sRNA，以及（ii）对两个耐旱模型物种中的sRNA进行分析将揭示调节脱水耐受性的不同网络。

项目成果

High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families.

• DOI: 10.1186/1471-2164-9-593
• 发表时间: 2008-12-09
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Szittya G;Moxon S;Santos DM;Jing R;Fevereiro MP;Moulton V;Dalmay T
• 通讯作者: Dalmay T