Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease

• Published in: Human molecular genetics Vol. 15; no. 14; pp. 2250 - 2265
• Main Authors: LEE, Jennifer A, INOUE, Ken, CHEUNG, Sau W, SHAW, Chad A, STANKIEWICZ, Pawel, LUPSKI, James R
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.07.2006; Oxford Publishing Limited (England)
• Subjects: Base Sequence; Biological and medical sciences; Chromosome Breakage; Cohort Studies; Degenerative and inherited degenerative diseases of the nervous system. Leukodystrophies. Prion diseases; Female; Fundamental and applied biological sciences. Psychology; Gene Dosage; Gene Duplication; Gene Rearrangement; Genetics of eukaryotes. Biological and molecular evolution; Genome, Human; Humans; In Situ Hybridization, Fluorescence; Male; Medical sciences; Membrane Proteins - genetics; Models, Genetic; Molecular and cellular biology; Myelin Proteolipid Protein - genetics; Neurology; Pedigree; Pelizaeus-Merzbacher Disease - genetics; Recombination, Genetic; Terminal Repeat Sequences; Nervous system diseases; Pelizaeus-Merzbacher disease; Duplication; Genomics; Central nervous system disease; Genetics; Degenerative disease; Cerebral disorder; Genetic disease
• ISSN: 0964-6906; 1460-2083
• DOI: 10.1093/hmg/ddl150

Genomic architecture, higher order structural features of the human genome, can provide molecular substrates for recurrent sub-microscopic chromosomal rearrangements, or may result in genomic instability by forming structures susceptible to DNA double-strand breaks. Pelizaeus-Merzbacher disease (PMD) is a genomic disorder most commonly arising from genomic duplications of the dosage-sensitive proteolipid protein gene (PLP1). Unlike many other genomic disorders that result from non-allelic homologous recombination utilizing flanking low-copy repeats (LCRs) as substrates, generating a common and recurrent rearrangement, the breakpoints of PLP1 duplications have been reported not to cluster, yielding duplicated genomic segments of varying lengths. This suggests a distinct molecular mechanism underlying PLP1 duplication events. To determine whether structural features of the genome also facilitate PLP1 duplication events, we analyzed extensively the genomic architecture of the PLP1 region and defined several novel LCRs (LCR-PMDs). Array comparative genomic hybridization showed that PLP1 duplication sizes differed, but revealed a subgroup of patients with apparently similar PLP1 duplication breakpoints. Pulsed-field gel electrophoresis analysis using probes adjacent to the LCR-PMDs detected unique recombination-specific junction fragments in 12 patients, enabled us to associate the LCR-PMDs with breakpoint regions, and revealed rearrangements inconsistent with simple tandem duplications in four patients. Two-color fluorescence in situ hybridization was consistent with directly oriented duplications. Our study provides evidence that PLP1 duplication events may be stimulated by LCRs, possibly non-homologous pairs at both the proximal and distal breakpoints in some cases, and further supports an alternative role of genomic architecture in rearrangements responsible for genomic disorders.