Discovering mechanisms of gene regulation in plant cell specific transcriptomes using bioinformatics and microgenomics

利用生物信息学和微观基因组学发现植物细胞特异性转录组中的基因调控机制

• 批准号: RGPIN-2015-04571
• 负责人: Stromvik, Martina
• 金额: $ 2.04万
• 依托单位: McGill University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2018
• 资助国家: 加拿大
• 起止时间: 2018-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=666102
• 关键词: Discovering; mechanisms; gene; regulation; plant

Functional cells and organs are the products of an amazing collection of tens of thousands of genes, orchestrated by different levels of regulation. At the most basic level, each gene's possibility of expression is controlled by gene switches, regulatory sequence motifs, to which proteins called transcription factors bind. These regulatory motifs and combinations of them probably exists in the thousands, however, the exact number is unknown. Few of them are well-known or well-studied, yet they are crucial for development of functional cells, organs and organisms.*** My NSERC Discovery funded research program focuses on regulatory motifs and plant transcriptional gene regulation using an approach that integrates bioinformatics (computational methods) with genomics (molecular methods). The long-term objective is to understand different gene regulating layers and mechanisms of gene expression and how they contribute to plant functional anatomy. My approach is to 1) measure the transcriptome in cells of interest (using laser capture microdissection and RNA-Sequencing) to identify co-regulated genes, 2) discover regulatory motifs using de novo motif discovery algorithms (e.g. Seeder, developed in my lab) in the gene flanking regions, and 3) validate the function of the motifs in planta through transient and stable genetic transformation and targeted genome editing (CRISPR/Cas9). Our model system is soybean, an increasingly popular crop plant in Canada that has long been at the forefront of functional genomics research, with a sequenced genome and a multitude of other genetic and genomic resources available. We are in an excellent position to embark on truly cell specific gene expression studies, where we will explore promoters and other regulatory motifs in groups of co-regulated genes. The proposed research pursues exciting findings on master regulators (transcription factors) and linked motifs in soybean meristems, as well as cells at the interface of soybean host and soybean associated bacteria (pathogens and symbionts) and soybean cyst nematode (the cause of the most economical losses to soybean crops). This research has invaluable impact by increasing our basic knowledge of plant development and function, by making progress for biotechnology and crop improvement strategies, by continuing to develop bioinformatics tools for better sequence analysis and by crucial training of highly qualified graduate students in this exciting and rapidly expanding field. The training of HQP to take place during the proposed research will continue with the same high standards to provide opportunities for undergraduate and graduate students and postdocs to learn modern molecular, genomics and bioinformatics techniques and scientific thinking, allowing them to publish in high impact journals and to be competitive with skills and knowledge that are in great demand in academia as well as in industry. **

功能细胞和器官是成千上万个基因的惊人集合的产物，由不同水平的调控精心编排。在最基本的层面上，每个基因表达的可能性是由基因开关、调控序列基序控制的，而转录因子则与之结合。这些调控基序和它们的组合可能有数千个，然而，确切的数量是未知的。它们很少为人所知或被充分研究，但它们对功能性细胞、器官和生物体的发育至关重要。***我的研究项目由NSERC Discovery资助，主要研究调控基序和植物转录基因调控，使用生物信息学（计算方法）和基因组学（分子方法）相结合的方法。长期目标是了解不同的基因调控层和基因表达机制，以及它们如何对植物功能解剖学做出贡献。我的方法是1)测量感兴趣细胞中的转录组（使用激光捕获显微解剖和rna测序）以识别共调控基因，2)在基因侧翼区域使用de - novo motif发现算法（例如Seeder，在我的实验室开发）发现调控基序，以及3)通过短暂和稳定的遗传转化和靶向基因组编辑（CRISPR/Cas9）验证基序在植物中的功能。我们的模型系统是大豆，这是一种在加拿大日益流行的作物植物，长期以来一直处于功能基因组学研究的前沿，具有测序基因组和大量其他遗传和基因组资源。我们处于一个非常有利的位置，可以开始真正的细胞特异性基因表达研究，在那里我们将探索共同调节基因组中的启动子和其他调控基序。该研究计划在大豆分生组织中的主要调控因子（转录因子）和相关基序，以及大豆寄主和大豆相关细菌（病原体和共生体）和大豆囊线虫（造成大豆作物最经济损失的原因）的界面细胞方面取得令人兴奋的发现。这项研究通过增加我们对植物发育和功能的基本知识，通过在生物技术和作物改良策略方面取得进展，通过继续开发生物信息学工具以更好地进行序列分析，以及通过在这个令人兴奋和迅速发展的领域培养高素质的研究生，具有无价的影响。在拟议的研究期间，HQP的培训将继续保持同样的高标准，为本科生、研究生和博士后提供学习现代分子、基因组学和生物信息学技术和科学思维的机会，使他们能够在高影响力的期刊上发表文章，并在学术界和工业界都有很大需求的技能和知识方面具有竞争力。**