title: Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination.
abstract: We describe genomic structures of 59 X-chromosome segmental duplications that include the proteolipid protein 1 gene (PLP1) in patients with Pelizaeus-Merzbacher disease. We provide the first report of 13 junction sequences, which gives insight into underlying mechanisms. Although proximal breakpoints were highly variable, distal breakpoints tended to cluster around low-copy repeats (LCRs) (50% of distal breakpoints), and each duplication event appeared to be unique (100 kb to 4.6 Mb in size). Sequence analysis of the junctions revealed no large homologous regions between proximal and distal breakpoints. Most junctions had microhomology of 1-6 bases, and one had a 2-base insertion. Boundaries between single-copy and duplicated DNA were identical to the reference genomic sequence in all patients investigated. Taken together, these data suggest that the tandem duplications are formed by a coupled homologous and nonhomologous recombination mechanism. We suggest repair of a double-stranded break (DSB) by one-sided homologous strand invasion of a sister chromatid, followed by DNA synthesis and nonhomologous end joining with the other end of the break. This is in contrast to other genomic disorders that have recurrent rearrangements formed by nonallelic homologous recombination between LCRs. Interspersed repetitive elements (Alu elements, long interspersed nuclear elements, and long terminal repeats) were found at 18 of the 26 breakpoint sequences studied. No specific motif that may predispose to DSBs was revealed, but single or alternating tracts of purines and pyrimidines that may cause secondary structures were common. Analysis of the 2-Mb region susceptible to duplications identified proximal-specific repeats and distal LCRs in addition to the previously reported ones, suggesting that the unique genomic architecture may have a role in nonrecurrent rearrangements by promoting instability.
authors.affiliation: Clinical and Molecular Genetics, Institute of Child Health, London.
authors.forename: Karen J
authors.initials: KJ
authors.lastname: Woodward
authors.forename: Maria
authors.initials: M
authors.lastname: Cundall
authors.forename: Karen
authors.initials: K
authors.lastname: Sperle
authors.forename: Erik A
authors.initials: EA
authors.lastname: Sistermans
authors.forename: Mark
authors.initials: M
authors.lastname: Ross
authors.forename: Gareth
authors.initials: G
authors.lastname: Howell
authors.forename: Susan M
authors.initials: SM
authors.lastname: Gribble
authors.forename: Deborah C
authors.initials: DC
authors.lastname: Burford
authors.forename: Nigel P
authors.initials: NP
authors.lastname: Carter
authors.forename: Donald L
authors.initials: DL
authors.lastname: Hobson
authors.forename: James Y
authors.initials: JY
authors.lastname: Garbern
authors.forename: John
authors.initials: J
authors.lastname: Kamholz
authors.forename: Henry
authors.initials: H
authors.lastname: Heng
authors.forename: M E
authors.initials: ME
authors.lastname: Hodes
authors.forename: Sue
authors.initials: S
authors.lastname: Malcolm
authors.forename: Grace M
authors.initials: GM
authors.lastname: Hobson
mesh_terms: D001483:Base Sequence; D019457:Chromosome Breakage; D002874:Chromosome Mapping; D041321:Chromosomes, Human, X; D015331:Cohort Studies; D019295:Computational Biology; D004303:Dosage Compensation, Genetic; D020440:Gene Duplication; D018740:Genetic Heterogeneity; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008565:Membrane Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D018991:Myelin Proteolipid Protein / Q000235:genetics; D020371:Pelizaeus-Merzbacher Disease / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D020080:Tandem Repeat Sequences
chemical_list: D008565:Membrane Proteins; D018991:Myelin Proteolipid Protein; C472930:PLP1 protein, human