Collaborative Research: The Epigenetic Regulatory Role of the Maize Ufo1 Gene

合作研究：玉米 Ufo1 基因的表观遗传调控作用

• 批准号: 1051576
• 负责人: Blake Meyers
• 金额: $ 53.57万
• 依托单位: University of Delaware
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2015-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1051576&HistoricalAwards=false
• 关键词: Collaborative; Research; Epigenetic; Regulatory; Role

Intellectual Merit: One of the mechanisms that allow diversification of form and function is epigenetic regulation. Epigenetic changes are alterations in the DNA or protein components of chromatin that affect gene expression. Epigenetic modifications that are of transient nature are widespread in the plant kingdom, but are rarely isolated or identified because the associated phenotypes are not easy to see and the modifications are not stable from generation to generation. Using the pericarp color1 (p1) gene and its red pigmentation as a marker in maize, allelic variation at the p1 locus has been shown to be a function of gene structure and organization, which is further regulated by epigenetic mechanisms. To understand the basis of allelic diversity modulated through epigenetic regulation of gene expression, molecular and genetic characterization of a dominant mutation called Ufo1 (Unstable factor for orange1) has been performed. Plants with a particular p1 allele, called P1-wr, produce ears with colorless kernel pericarps and red cob glumes, and this silent pericarp phenotype is stable; however, in the presence of Ufo1 the P1-wr allele confers variably enhanced pigmentation phenotypes in several tissues. Expression studies demonstrated that the gain of pigmentation is associated with increased steady state levels of P1 transcript. Enhanced P1 expression in P1-wr; Ufo1 plants was shown to correlate with a decrease in DNA methylation at the promoter and coding sequence of the P1-wr allele. In the current project, map based cloning of ufo1 gene will be carried out. New alleles of ufo1 will be generated using transposon mutagenesis. Evidence for Ufo1-mediated effects on epigenetic regulation will be analyzed using high throughput sequencing methods for global profiling of chromatin, transcript (mRNA and small RNA), and DNA methylation of Ufo1 mutant and wild type plants. A database will be developed to visualize and analyze data generated from ChIP-seq, RNA-seq and bisulfite sequencing. The results will establish the role of the Ufo1 mutation (and wild type ufo1 gene) in effecting global changes in transposons, DNA methylation, histone modifications and RNA profiles. Because Ufo1 does not appear to act in the same way as other known epigenetic regulators in maize, this project will expand understanding of how overlapping epigenetic pathways regulate gene expression in this important crop plant.Broader Impacts: This project will provide training opportunities in plant epigenetics and study of allelic variation of plant genes. The collaboration between Pennsylvania State University and the University Delaware will enhance professional interactions in the area of plant biology and bioinformatics. Specifically, two postdoctoral fellows and two graduate students will be cross-trained in computational biological aspects and epigenetic gene regulation. Undergraduate students, including women and minority students, will learn classical and cutting-edge plant biology techniques that are used understand and dissect the molecular basis of regulation of tissue-specific gene expression. In addition, high school students and teachers will participate in a summer biotechnology workshop to learn gene expression techniques in maize.This project is co-funded by the Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences and by the Plant Genome Research Program in the Division of Integrative Organismal Systems.

智力优势：允许形式和功能多样化的机制之一是表观遗传调控。表观遗传变化是影响基因表达的DNA或染色质蛋白质成分的改变。短暂的表观遗传修饰在植物界广泛存在，但很少被分离或鉴定出来，因为相关的表型不容易看到，而且这种修饰在一代一代之间不稳定。以玉米果皮色素1 （p1）基因及其红色色素沉着为标记，p1位点的等位基因变异已被证明是基因结构和组织的功能，并进一步受到表观遗传机制的调控。为了了解通过基因表达的表观遗传调控调控等位基因多样性的基础，研究人员对显性突变Ufo1（不稳定因子）进行了分子和遗传表征。具有特定p1等位基因的植物，称为p1 -wr，产生的穗子果皮无色，穗轴颖片红色，这种沉默的果皮表型是稳定的；然而，在Ufo1存在的情况下，P1-wr等位基因会在几种组织中不同程度地增强色素沉着表型。表达研究表明，色素沉着的增加与P1转录物稳态水平的增加有关。P1-wr中P1表达增强；研究表明，Ufo1植物与启动子和P1-wr等位基因编码序列的DNA甲基化降低有关。在目前的项目中，将进行基于图谱的ufo1基因克隆。利用转座子诱变产生新的ufo1等位基因。研究人员将利用高通量测序方法对Ufo1突变体和野生型植物的染色质、转录物（mRNA和小RNA）和DNA甲基化进行全局分析，分析Ufo1介导的表观遗传调控效应的证据。将开发一个数据库，以可视化和分析从ChIP-seq， RNA-seq和亚硫酸盐测序产生的数据。这些结果将确定Ufo1突变（和野生型Ufo1基因）在影响转座子、DNA甲基化、组蛋白修饰和RNA谱的全局变化中的作用。由于Ufo1似乎与玉米中其他已知的表观遗传调控因子的作用方式不同，因此该项目将扩大对这种重要作物中重叠表观遗传通路如何调节基因表达的理解。广泛影响：本项目将提供植物表观遗传学和植物基因等位基因变异研究方面的培训机会。宾夕法尼亚州立大学和特拉华大学之间的合作将加强植物生物学和生物信息学领域的专业互动。具体来说，两名博士后和两名研究生将在计算生物学和表观遗传基因调控方面进行交叉训练。本科学生，包括女性和少数民族学生，将学习经典和尖端的植物生物学技术，用于理解和剖析组织特异性基因表达调控的分子基础。此外，高中生和教师将参加夏季生物技术研讨会，学习玉米基因表达技术。本项目由分子和细胞生物科学部的遗传机制项目和综合生物系统部的植物基因组研究项目共同资助。