National Center for Genome Resources 1800A Old Pecos Trail Santa Fe, NM 87505 USA
The structural organization of eukaryotic genomes plays an important role in the regulation of gene expression. Matrix attachment regions (MARs) are sequences at which euchromatin loops attach to the nuclear matrix, and have been shown to be: involved in maintaining higher chromatin structure, located near genes, and involved in the regulation of gene expression. Thus, these genomic structural elements are key to both genome organization and function. In humans, MARs have been shown to contain several classes of AT-rich sequence patterns, including topoisomerase II signals, regions associated with curved or kinked DNA, and origins of replication. MAR-Finder (www.ncgr.org/MarFinder) is a mathematical model developed by Dr. Singh to predict the location of matrix attachment regions (MARs) in human genomic sequences, based upon the occurrence of such sequence motifs. Our goal is to refine the MAR-Finder model to extend its utility to other eukaryotic genomes. We have analyzed the publicly available Arabidopsis thaliana genomic sequences with MAR-Finder. Arabidopsis thaliana was selected for this analysis because of its compact genome, and the availability of large amounts of genomic sequence. The MAR-Finder predictions are presented and discussed in relation to experimentally determined MARs.
Plant & Animal Genome VIII Conference Plant & Animal Genome VIII Conference