Comparative genomic and spatial analysis of DNA replication in maize and sorghum

所有生物在生长发育过程中都必须准确、完整地复制其DNA基因组。在真核生物中，DNA复制发生在细胞核内，并且在空间和时间上都是紧密编排的。本项目将比较玉米和高粱两种重要品种的DNA复制定时程序及其与染色体组织和功能的相互作用。这些植物品系的高水平遗传多样性将被用来进一步了解它们的复制定时程序是如何被调控的。了解这一过程很重要，因为染色体事件发生在发育早期，并与DNA复制相结合，可能影响基因表达程序和整个植物生命周期的可观察性状。该项目将培训下一代科学家进行跨学科研究，并帮助他们发展合作技能和专业网络，以应对生物学和农业领域的重大挑战。该项目还将通过夏季研究经验，向代表性不足群体的本科生和高中生介绍玉米遗传学和现代植物研究。它还将为公众提供一个机会，通过实地演示和制作一本说明玉米突变体的艺术性和科学性的书，了解玉米等重要作物的遗传学和育种。DNA复制是一个高度调控的过程，整合了基因组结构和功能的许多方面，包括转录活性、染色质结构、表观遗传状态和三维结构。该项目将通过利用玉米和高粱优良的遗传、基因组和细胞学资源来探索植物中的这些联系。该项目建立在早期研究的基础上，该研究使用体内标记新复制的DNA，结合细胞核的流动分选来表征B73玉米根尖分生组织的复制时间（RT）程序。第一个目标将使用B73根分生组织来定义和可视化复制起始区（IRs），定义全基因组转录率，并在间期和复制核的细胞学和分子相互作用的背景下检查复制。将这些数据与现有的RT和染色质可及性数据相结合进行分析，将为B73根分生组织的复制定时程序提供强有力的机制视图。第二个目的是将玉米B73基因谱与高粱（S. bicolor）和玉米Mo17自交系的RT程序、IR分布、转录活性、基因组特征和染色质接近性进行比较。这些实验将定义在不同基因型中复制被改变的区域，并开始理解复制程序是如何被遗传决定的过程。该项目将进一步确立复制时间作为重要的整合基因组注释，并阐明植物基因组的功能分区。该奖项是由植物基因组研究计划在综合有机体系统部门和遗传机制计划在分子和细胞生物学部门共同资助。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

All living organisms must accurately and completely duplicate their DNA genomes during growth and development. In eukaryotes, DNA replication occurs within cell nuclei, and is tightly choreographed in both space and time. This project will compare the DNA replication timing programs and their interplay with chromosome organization and function in two important cultivars of maize and their close relative, sorghum. The high level of genetic diversity in these plant lines will be exploited to learn more about how their replication timing programs are regulated. Understanding this process is important because chromosomal events that occur early in development, and are coupled to DNA replication, may impact gene expression programs and observable traits throughout the plant life cycle. The project will train the next generation of scientists to conduct interdisciplinary research, and help them develop collaborative skills and professional networks needed to address major challenges in biology and agriculture. The project will also introduce undergraduates and high school students from underrepresented groups to maize genetics and modern plant research through summer research experiences. It will also provide an opportunity for the general public to learn about genetics and breeding of important crops like maize through field demonstrations and the production of a book illustrating the artistry and science of maize mutants.DNA replication is a highly regulated process that integrates many aspects of genome structure and function, including transcriptional activity, chromatin structure, epigenetic state, and 3-D structure. This project will explore these linkages in plants by exploiting the excellent genetic, genomic, and cytological resources for maize and sorghum. The project builds upon earlier studies that used in vivo labeling of newly replicated DNA in combination with flow sorting of nuclei to characterize replication timing (RT) programs in the root tip meristem of B73 maize. The first aim will use B73 root meristems to define and visualize replication initiation regions (IRs), to define genome-wide transcription rates, and to examine replication in the context of cytological and molecular interactions in both interphase and replicating nuclei. Analysis of these data in combination with existing data on RT and chromatin accessibility will provide a strong mechanistic view of the replication timing program in B73 root meristems. In the second aim, the maize B73 profiles will be compared to RT programs, IR distributions, transcriptional activity, genomic features and chromatin accessibility in sorghum (S. bicolor) and the maize Mo17 inbred line. These experiments will define regions in which replication is altered in different genotypes and begin the process of understanding how replication programs are genetically determined. The project will further establish replication time as an important integrative genomic annotation and shed light on the functional compartmentation of plant genomes.This Award was co-funded by the Plant Genome Research Program in the Division of Integrative Organismal Systems and the Genetic Mechanisms Program in the Division of Molecular and Cellular Biology.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.