Chromatin Structure and Genome Response in Maize

Florida State University, Tallahassee FL

Investigators

Abstract

Chromatin Structure and Genome Response in Maize. PI: Henry W. Bass (Florida State University) Co-PI(s): Jonathan H. Dennis (Florida State University), Karen M. McGinnis (Florida State University) and Oghenekome U. Onokpise (Florida Agricultural and Mechanical University) Understanding how genomes are organized functionally is a major challenge in biology. Structurally, the genomes of eukaryotes, such as plants, animals or fungi, are organized into chromatin, which is a complex of DNA and associated proteins. The basic subunit of chromatin is the nucleosome, comprising ~150 base pairs of DNA wrapped around eight histone proteins. It is known that nucleosome positions in the genome vary with changes in gene expression levels. However, the specific relationship between genome structure and gene expression has not been clearly defined. The overall goal of this project is to characterize the chromatin structure of the maize genome in relation to function, specifically with respect to nucleosome occupancy and gene expression. The research uses computational, biochemical, genetic, and microscopic methods to accomplish three specific objectives: (1)DNA microarrays will be developed for genome-wide studies of chromatin structure. In the process new predictive tools will be adapted to the maize genome from technology developed for study of the human genome, (2) genome changes will be investigated in a mutant called mop1, which is thought to regulate chromatin structure through small RNAs and by silencing potentially deleterious genome changes; and (3) chromatin structure of normal plants and mop1 mutants will be visualized using 3D molecular cytology. The project will deliver plots that map sites of nucleosome occupancy in the maize genome and new tools for investigation of chromatin structure. In addition, custom microarrays will be available for use by the broader plant genomics community. All data will be released to GenBank and will be available on the project website (www.maizenucleosome.org) and on public databases including www.maizegdb.org, www.gramene.org, and www.maizesequence.org. Direct involvement of diverse students in field and laboratory activities will provide training opportunities and exposure to plant genetics and genomic research. The project will continue a unique outreach activity for the public through a Maize-10-Maze chromosome-map field: each of the ten maize chromosomes is displayed as a single row to scale and with mutants in appropriate map positions. This life-size view of the maize chromosomes provides a tangible understanding of genome organization and engages participants in discussion about the importance of genomics research to meet societal challenges.