Nuclease Profiling as an Integrative Resource for Maize Epigenomics

Florida State University, Tallahassee FL

Investigators

Abstract

PI: Henry W. Bass (Florida State University-Tallahassee) CoPIs: Jonathan H. Dennis, Jinfeng Zhang, and Daniel L. Vera (Florida State University-Tallahassee), Oghenekome U. Onokpise and Violeta Tsolova (Florida A & M University) Eukaryotic chromosomes consist of DNA-protein complexes referred to as chromatin. The current understanding of the relationship between chromatin structure and genome behavior is still relatively underdeveloped. The goal of this project is to identify and map genome-wide changes in chromatin structure in five diverse tissues of maize using a novel method developed with previous NSF funding. It is expected that chromatin mapping will reveal previously undetected and biochemically functional regions of the maize genome, while integrating genetic information from maize and other plant genome research projects. Together these efforts will provide basic information about chromatin structure that could accelerate crop improvement strategies to address current and future challenges in food and biofuel production. With regard to outreach and training, the project will provide research training for postdoctoral associates, graduate and undergraduate students, particularly from underrepresented groups. The project will organize public field displays and hold summer science camps for high school students to engage a diverse group of people in several Science, Technology, Engineering, and Mathematics (STEM) disciplines related to agriculture, genomics, and bioinformatics. A novel assay for genome-wide nuclease profiling using micrococcal nuclease (MNase) will be used to develop reference nuclease profiles for chromatin from five core tissues of maize: stem cells from root and shoot tips, the immature ear, developing nutritive seed tissue (endosperm), and pollen sperm nuclei. Measuring the differential nuclease sensitivity (DNS-seq) across the entire maize genome will uncover localized sites coupled to evolutionarily conserved sequences, transcription factor binding sites, and gene expression levels. This method uniquely maps specialized and functionally important regions of the genome while greatly enhancing the information content of nucleosome position data, providing new opportunities to connect epigenomic data across disparate projects. All data will be made accessible to the public through various long-term repositories and portals. These include the NCBI's GEO and SRA as well as the UCSC Genomaize (http://genomaize.org/), EPIC-CoGe (https://www.plant-epigenome.org/), and the iPlant Collaborative (Data Store, Discovery Environment, Powered-by-iPlant genome browsers).