Matrix attachment regions in the human dystrophin gene

Duchenne muscular dystrophy (DMD) is a lethal degenerative muscle disorder caused by mutations in the dystrophin gene. Dystrophin is a cytoskeletal protein associated with the plasma membrane. The dystrophin gene is exceptional with respect to its size and complexity. It is the largest gene identified to date, containing 79 exons across 2300 kb and at least seven distinct tissue-specific promoters. This X-linked gene is characterized by a high mutation rate, with most affected individuals having chromosomal rearrangements. Approximately 60% of males with the disease have deletions in the dystrophin gene and 6% have duplications.;In this study, the role of chromatin organization of the dystrophin gene in nuclear functions is investigated. The interactions of DNA with proteins of the nuclear matrix may be involved in such functions as defining chromatin loops or domains, DNA replication, transcriptional regulation and illegitimate recombination. The DNA regions involved in these interactions are specific DNA sequences called matrix attachment regions (MARs). This work examines the possible involvement of dystrophin gene MARs in both disease-causing chromosomal rearrangements and transcriptional regulation.;Specifically, points of attachment of the dystrophin gene to the nuclear matrix have been identified in this study at the breakpoints of a duplication from a DMD patient and in the muscle-specific promoter region. MARs have been identified at both the intron 7 and intron 9 breakpoints of a dystrophin gene duplication which resulted from a non-homologous recombination event. This finding indicates the possible positioning of these breakpoints in close proximity to one another on the nuclear matrix, providing the opportunity for recombination to occur. Both breakpoints contain topoisomerase I consensus cleavage sites, suggesting a molecular mechanism for DNA exchange in this recombination event. In addition, two MARs have been found to flank the internal muscle-specific promoter of the dystrophin gene. The proximity of these two MARs to this cis-acting regulatory element indicates a possible role for these MARs in transcriptional regulation from this promoter, perhaps through interactions with transcription factors on the nuclear matrix.;These results suggest important roles for dystrophin gene MARs in both illegitimate recombination and transcriptional regulation in this gene.