Global Analysis of Functional Units in Plant Chromosomes: DNA Replication, Domain Structure, and Transcription

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It is well known that higher organisms, including plants, begin the process of replicating their DNA at many different places in their genomes. However, as yet we know very little about how these starting points ("replication origins") are defined, or how they relate to other chromosomal features. An interdisciplinary team from three leading research institutions will pool their efforts and expertise to investigate this question and attain a deeper understanding of spatial and biochemical parameters affecting genome function. Specific objectives:(1) A primary goal of their research project is to construct maps of replication origins in large regions of representative plant chromosomes, as well as to construct and overlay maps of key chromosomal features such as matrix attachment regions, regions enriched in modified histones or methylated DNA. (2) A parallel effort will map DNA replication activity and gene activity (transcription) in the same chromosomal regions under several different developmental conditions, which will lead to a better understanding of the interrelationship of chromosome structure and function. Outcomes:When completed, the project will help scientists understand how chromosome functions are spatially organized and coordinated in structural and functional domains, and help define chromosomal features that play key roles in these functions. The proposed experiments will combine powerful genomic technologies with molecular, cellular and biochemical tools. The team will focus on the short arm of rice chromosome 1 and the full length of Arabidopsis chromosome 4, thus providing extensive data for model organisms representing each of the two major groups of crop plants. Comparing chromosomal features for these plant species with data for animals and other organisms will help identify chromosomal features important enough to be broadly conserved in evolution, as well as highlight features that may be unique to the plant kingdom. New genomic information and tools that are generated (including the carefully designed set of sequences to be used as mapping landmarks on genomic microarrays) will be made available to other members of the scientific community via the web as well as through conventional publications. Data will be submitted to the Gene Expression Omnibus homepage (http://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress, a public repository (http://www.ebi.ac.uk/arrayexpress/) . All sequence annotation for the chromosomal elements will be submitted to GenBank.The basic information on chromosome structure generated by this project will help support a new generation of genetic engineering technologies, which may include new methods for directing gene expression, targeted gene insertion, and construction of artificial chromosomes. In addition, the project will provide training in state-of-the-art functional genomic and bioinformatics techniques. Trainees at the undergraduate, graduate and postdoctoral levels will participate in the research, and workshops will be organized for scientists in the southeastern US, including faculty and students at historically black and minority institutions. The team will also work with local educators to develop teaching tools useful for presenting genomics concepts to high school students.