RNA-based Mechanisms Specifying Heritable Epigenetic Change

现代遗传学和进化生物学是建立在孟德尔遗传原理之上的。这些原则将负责遗传性状的个体因素概念化为由DNA序列组成的静态实体，这些DNA序列由染色体携带并通过性传播给后代。这种关于遗传的观点与上个世纪的大多数实验研究完全一致。然而，某些特征因素在一代到下一代之间表现出动态的、可预测的变化的特殊行为长期以来表明，遗传的其他原则仍有待发现。本项目研究玉米植株中的一种非孟德尔表观遗传形式。表观遗传是指附属于DNA的可遗传信息，DNA是遗传的主要分子。最近的研究表明，小RNA分子和一些负责从DNA模板合成RNA的酶（RNA聚合酶）都是这种非孟德尔遗传的致病因子。在玉米中，RNA聚合酶的形式及其功能的多样性尤其广泛。最初的研究指出，不同RNA聚合酶共享的亚基蛋白之间的关系在很大程度上尚未被探索，这些亚基蛋白对基因组功能具有潜在的调节意义。该项目将描述玉米基因组中所有RNA聚合酶的多蛋白结构和机制功能，从而建立一个模型系统，以了解RNA聚合酶多样性在高度重复的真核生物基因组中的基本作用。所产生的工具和材料将用于表征农业上重要作物物种中RNA聚合酶的复杂性和功能，并测试有关这种负责指定可遗传表观遗传变化的基于RNA的机制的特定假设。更广泛的影响：该项目生产特定的植物种质材料、生物信息学资源和实验试剂，使社区能够长期努力了解DNA依赖的RNA聚合酶和小RNA分子在定义表观基因组中所起的作用——DNA或相关染色体结构的修饰，指定基因组编码信息的读出。这些研究活动为加州大学伯克利分校（UCB）的一名研究生、至少两名本科生和来自加州东湾地区的高中生提供生殖生物学、遗传、孟德尔遗传和遗传、遗传分析、染色体生物学和现代分子遗传学方面的教育和培训。传统上在科学领域代表性不足的少数民族通过现有的高中和本科研究项目的支持，参与了这些研究活动，促进了种族和社会经济多样性。本项目研究的非孟德尔遗传的具体例子影响了色素沉着基因，因此在概念上很容易传达给不同的受众，因为所涉及的特征是熟悉的和可见的。了解真核生物遗传学的这一特殊机制为rna遗传提供了一个新的视角，有望对未来从结构生物学到进化的广泛学科的生物学研究产生变革性影响。

Modern genetics and evolutionary biology are founded on the principles of Mendelian inheritance. These principles conceptualize the individual factors responsible for inherited traits as static entities comprised of DNA sequences that are borne on chromosomes and sexually transmitted to offspring. This view of inheritance conforms well to most experimental studies of the past century. However, exceptional behaviors in which certain trait factors display dynamic, yet predictable, changes from one generation to the next have long indicated that additional principles of inheritance remain to be discovered. This project investigates a form of non-Mendelian epigenetic inheritance occurring in the corn plant. Epigenetic refers to heritable information that is accessory to DNA, the primary molecule of inheritance. Recent studies indicate that both small RNA molecules and some of the enzymes responsible for synthesizing RNA from DNA templates (RNA polymerases) are causative agents in this type of non-Mendelian inheritance. The diversity of both RNA polymerase forms and their functions in corn is particularly extensive. Initial studies point to largely unexplored relationships of the subunit proteins shared by diverse RNA polymerases that have potential regulatory significance to genome function. This project will characterize both the multiprotein structures and mechanistic functions of all RNA polymerases of the corn genome and thereby develop a model system for understanding the fundamental roles of RNA polymerase diversity in a highly repetitive eukaryotic genome. The tools and materials generated will be used to characterize the complexity and function of RNA polymerases in an agriculturally important crop species and to test specific hypotheses regarding this RNA-based mechanism responsible for specifying heritable epigenetic changes.Broader Impacts: This project produces specific plant germplasm materials, bioinformatics resources, and experimental reagents that enable a long-term community effort to understand the roles that DNA-dependent RNA polymerases, and small RNA molecules, play in defining the epigenome -- modifications of the DNA or associated chromosome structure that specify readouts of genome-encoded information. The research activities provide education and training in reproductive biology, inheritance, Mendelian and transmission genetics, genetic analysis, chromosome biology, and modern molecular genetics for one University of California Berkeley (UCB) graduate student, at least two UCB undergraduates, and high school students from the California East Bay area. Minorities traditionally underrepresented in the sciences are engaged in these research activities through the support of existing high school and undergraduate research programs promoting ethnic and socioeconomic diversity. The specific example of non-Mendelian inheritance studied in this project affects a pigmentation gene and is therefore conceptually easy to convey to a diverse audience because the trait involved is familiar and visual. Understanding this particular mechanism of eukaryotic genetics provides a novel perspective of RNA-based inheritance promising transformative impacts to the future of biological research across broad disciplines from structural biology to evolution.