Using Natural Variation to Probe the Evolution, Mechanisms and Function of Imprinting in Plants

智力优势：生物体从母亲和父亲那里继承的基因通常表达水平相似。然而，一些基因表现出印记表达现象，即母系和父系遗传的基因拷贝或等位基因不能同等表达。印记被认为是表观遗传，因为母系和父系遗传等位基因的表达水平不是由DNA序列决定的。印记对于开花植物和哺乳动物的正常发育至关重要。在植物中，印记主要发生在胚乳中，胚乳是种子中发现的胚胎营养组织。胚乳中母系和父系遗传等位基因的差异表达通常与差异胞嘧啶DNA甲基化有关，胞嘧啶DNA甲基化是对作为关键表观遗传标记的DNA的化学修饰。甲基化差异经常出现在类似转座元件的序列上，转座元件是一种侵入性DNA片段，可以在基因组中移动，通常是甲基化的。这些结果导致了一种假设，即印记基因的表达是转座元件表观遗传控制的副产品。由于转座元件的存在、基因组位置和表观遗传修饰在密切相关的物种内和物种之间是不同的，因此本研究将检验这一假设，即许多印记实例可能是特定遗传背景的等位基因所特有的。利用高通量全基因组方法，利用自然遗传和表观遗传变异，将评估三个具有不同繁殖模式和基因组结构的植物物种的印记表达和DNA甲基化，以检验关于植物印记的机制、进化和功能的特定假说。在了解物种内部和物种之间印记的保存程度或可变性方面，几乎没有什么努力。远缘植物如拟南芥和玉米之间的保守印记的例子可能反映了在特定基因上重复采用印记过程来调节胚乳发育的例子。这项研究可能会在进一步确定印记的功能后果以及理解转座元件的控制如何导致重要的发育调控过程方面取得实质性成果。此外，该项目还将更好地了解植物物种母本和父本对后代的贡献差异。更广泛的影响：该项目为高中生、本科生、研究生和博士后提供跨学科的教育和培训机会。这项研究将需要整合经典遗传学、分子生物学、基因组学和生物信息学。这为生物学家提供了一个宝贵的机会来熟练地进行生物信息学分析，为计算机科学家提供了一个熟悉生物学的机会。随着新技术推动生物学变得更加量化，这些技能变得越来越必要。来自以本科为主的少数民族服务机构的本科生如果无法获得一流的研究设施，将在博士后研究员的指导下为该项目工作三个夏天。这一经验将为本科生提供重要的研究经验，并为博士后研究员提供重要的指导培训。此外，高中生将利用作为这项研究的一部分创建的工具来了解植物的生命周期和遗传机制。

Intellectual merit: The genes that an organism inherits from its mother and father are usually expressed at similar levels. However, some genes exhibit the phenomenon of imprinted expression, in which the maternally and paternally inherited gene copies, or alleles, are not expressed equally. Imprinting is considered epigenetic because the expression level of maternally and paternally inherited alleles is not determined by the DNA sequence. Imprinting is critical for normal development in flowering plants and mammals. In plants, imprinting primarily occurs in endosperm, the embryo-nourishing tissue found within seeds. Differential expression of maternally and paternally inherited alleles of a gene in the endosperm is often correlated with differential cytosine DNA methylation, a chemical modification to the DNA that serves as a key epigenetic mark. The methylation differences frequently occur at sequences that resemble transposable elements, invasive pieces of DNA that can move throughout the genome and are usually methylated. These results have led to the hypothesis that imprinted gene expression arises as a byproduct of epigenetic control of transposable elements. Because the presence, genomic location, and epigenetic modification of transposable elements are variable within and between closely related species, this research will test the hypothesis that many instances of imprinting could be specific to alleles from certain genetic backgrounds. Using high-throughput genome-wide approaches to take advantage of natural genetic and epigenetic variation, imprinted expression and DNA methylation will be assessed in three plant species with distinct modes of reproduction and genome structure, Arabidopsis thaliana, Arabidopsis lyrata, and Zea mays, to test specific hypothesis about the mechanism, evolution, and function of imprinting in plants. There has been relatively little effort directed at understanding the degree of conservation or variability of imprinting within and between species. Examples of conserved imprinting between distantly related plant species like Arabidopsis and maize might reflect instances in which the process of imprinting has been repeatedly adopted at a particular gene to regulate endosperm development. This research is likely to have substantial outcomes in further determining the functional consequences of imprinting and in understanding how the control of transposable elements can lead to important developmental regulatory processes. In addition, the project will provide a better understanding of the differences in maternal and paternal contributions to offspring in plant species. Broader Impacts: This project provides interdisciplinary education and training opportunities for high school students, undergraduates, a graduate student and a postdoctoral fellow. The research will require the integration of classical genetics, molecular biology, genomics, and bioinformatics. This provides a valuable opportunity for biologists to become skilled in bioinformatics analysis and computer scientists to become conversant in biology. These skills are increasingly necessary as new technologies drive biology to become more quantitative. Undergraduate students from primarily undergraduate minority-serving institutions who do not have access to top-notch research facilities will work on the project for three summers under the guidance of the postdoctoral fellow. This experience will provide critical research experience for the undergraduates and important training in mentoring for the postdoctoral fellow. Additionally, high school students will take advantage of tools created as part of this research to learn about the plant life cycle and mechanisms of inheritance.