A genomic study of the nuclear matrix attachment region recognition signature

Abstract

Matrix attachment regions (MAR) are the sites on genomic DNA that interact with the nuclear matrix. A complex bipartite motif, the MAR recognition signature (MRS), has been proposed as a DNA sequence marker for MAR but its specificity and sensitivity remain unresolved. I describe here the distribution of the MRS in the genomes of a number of species from across animals and plants. The MRS is shown to have a distinctive, nonrandom distribution, with a particular relationship to genes. This relationship was studied in detail in the genome of Caenorhabditis elegans, revealing striking peaks of average MRS frequency in the regions flanking C. elegans genes. The occurrence of similar peaks in C. briggsae, Danio rerio, Arabidopsis thaliana, Drosophila melanogaster and Homo sapiens was also investigated. The nucleotide content in the vicinity of genes is examined and it too is shown to have striking peaks in regions surrounding genes. C. elegans genes associated with MRS were found to be significantly enriched for receptor activity annotations but not for some other features. Using this analysis of the genomic distribution of the MRS, the relevance of the MRS as a marker for MAR is discussed. The potential for MRS to play a functional role, as indicated by their peculiar frequency in the vicinity of genes, is also explored.