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

North Carolina State University, Raleigh NC

Investigators

Abstract

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.