EAGER:The Evolutionary Impact of Methylation on Grass Genomes and Gene Expression

EAGER：甲基化对草基因组和基因表达的进化影响

• 批准号: 1542703
• 负责人: Brandon Gaut
• 金额: $ 29.67万
• 依托单位: University of California-Irvine
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-07-01 至 2019-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1542703&HistoricalAwards=false
• 关键词: EAGER; Evolutionary; Impact; Methylation; Grass

To meet the food needs of future generations in a sustainable manner, an understanding of crop plant growth and development is essential. Information about growth and development is encoded in a plant's DNA, which has four fundamental chemical components, often referred to as A, C, G and T. However, the C can also be modified by a process called methylation, which allows it to function as a 5th information component in DNA. While it is apparent that methylated Cs play an important role in plant growth and development, their role has yet to be fully understood. In this proposal, the number and pattern of methylated Cs among different crop plants will be compared, including barley, einkorn wheat and sorghum. These comparisons will be used to investigate the influence of methylated Cs on the function of genes. The overall goal is to better understand the contribution of methylated Cs to plant growth and development, so that eventually this information can be used for crop improvement.DNA methylation is one of several epigenetic modifications that are crucial to plant genome function. Recent work has also shown that methylation has broad consequences for genome evolution, including the composition of intergenic DNA, as a fundamental evolutionary property of specific genes, and as a driver of compositional biases among genomic regions. Given the importance of epigenetic mechanisms, a thorough understanding of the evolution and function of plant genomes requires characterization of epigenetic variation among plant species. Yet, such a characterization is presently lacking. This project will generate and analyze whole genome bisulfite sequencing (BSseq) and transcript (RNAseq) data for an array of grass species. The data will be released to the Short Read Archive and Gene Expression Omnibus databases prior to publication. The goal is to use the data to better understand the relationship among DNA methylation, gene evolution and gene function, as measured by gene expression. To achieve this end, a series of unique evolutionary analyses will be developed that will address three specific hypotheses: 1) that gene-body methylation is a conserved feature of functionally important genes and maintained over evolutionary time by natural selection; 2) that evolutionary shifts in gene body methylation (and/or the methylation of flanking regions) drive shifts in gene expression between species; and 3) that DNA methylation variation among tissues - specifically in genes and flanking regions - contributes to tissue-specific gene expression.

为了以可持续的方式满足后代的粮食需求，了解作物的生长和发育至关重要。有关生长和发育的信息被编码在植物的DNA中，DNA有四种基本的化学成分，通常被称为A，C，G和T。然而，C也可以通过一种称为甲基化的过程进行修饰，这使得它可以作为DNA中的第五个信息成分。虽然甲基化Cs在植物生长和发育中起着重要作用，但其作用尚未完全了解。在本研究中，我们将比较不同作物（包括大麦、一粒小麦和高粱）中甲基化Cs的数量和模式。这些比较将用于研究甲基化Cs对基因功能的影响。总的目标是更好地了解甲基化Cs对植物生长和发育的贡献，以便最终这些信息可以用于作物改良。DNA甲基化是对植物基因组功能至关重要的几种表观遗传修饰之一。最近的研究还表明，甲基化对基因组进化具有广泛的影响，包括基因间DNA的组成，作为特定基因的基本进化特性，以及作为基因组区域之间组成偏差的驱动因素。鉴于表观遗传机制的重要性，深入了解植物基因组的进化和功能需要表征植物物种之间的表观遗传变异。然而，目前缺乏这样的特征。该项目将生成和分析一系列草物种的全基因组亚硫酸氢盐测序（BSseq）和转录（RNAseq）数据。数据将在出版前发布到Short Read Archive和Gene Expression Omnibus数据库。我们的目标是利用这些数据更好地了解DNA甲基化，基因进化和基因功能之间的关系，通过基因表达来衡量。为了实现这一目标，将开发一系列独特的进化分析，这些分析将解决三个特定的假设：1）基因体甲基化是功能重要基因的保守特征，并通过自然选择在进化过程中得以维持; 2）基因体甲基化的进化变化，（和/或侧翼区域的甲基化）驱动物种之间基因表达的转变;和3）组织间的DNA甲基化变异--特别是在基因和侧翼区域--有助于组织特异性基因表达。