Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair

• Published in: Genome Research 2008-06, Vol.18 (6), p.847-858
• Main Authors: Bauters, Marijke, Van Esch, Hilde, Friez, Michael J, Boespflug-Tanguy, Odile, Zenker, Martin, Vianna-Morgante, Angela M, Rosenberg, Carla, Ignatius, Jaakko, Raynaud, Martine, Hollanders, Karen, Govaerts, Karen, Vandenreijt, Kris, Niel, Florence, Blanc, Pierre, Stevenson, Roger E, Fryns, Jean-Pierre, Marynen, Peter, Schwartz, Charles E, Froyen, Guy
• Format: Article
• Language: English
• Subjects: Base Sequence; Chromosome Breakage; Chromosome Mapping; Chromosomes, Human, X; Computational Biology; DNA Repair; DNA Replication; Gene Duplication; Genome, Human; Humans; Letter; Male; Mental Retardation, X-Linked - genetics; Methyl-CpG-Binding Protein 2 - genetics; Models, Genetic; Molecular Sequence Data; Recombination, Genetic; Sequence Analysis, DNA
• ISSN: 1088-9051; 1549-5469; 1549-5477
• DOI: 10.1101/gr.075903.107

Recurrent submicroscopic genomic copy number changes are the result of nonallelic homologous recombination (NAHR). Nonrecurrent aberrations, however, can result from different nonexclusive recombination-repair mechanisms. We previously described small microduplications at Xq28 containing MECP2 in four male patients with a severe neurological phenotype. Here, we report on the fine-mapping and breakpoint analysis of 16 unique microduplications. The size of the overlapping copy number changes varies between 0.3 and 2.3 Mb, and FISH analysis on three patients demonstrated a tandem orientation. Although eight of the 32 breakpoint regions coincide with low-copy repeats, none of the duplications are the result of NAHR. Bioinformatics analysis of the breakpoint regions demonstrated a 2.5-fold higher frequency of Alu interspersed repeats as compared with control regions, as well as a very high GC content (53%). Unexpectedly, we obtained the junction in only one patient by long-range PCR, which revealed nonhomologous end joining as the mechanism. Breakpoint analysis in two other patients by inverse PCR and subsequent array comparative genomic hybridization analysis demonstrated the presence of a second duplicated region more telomeric at Xq28, of which one copy was inserted in between the duplicated MECP2 regions. These data suggest a two-step mechanism in which part of Xq28 is first inserted near the MECP2 locus, followed by breakage-induced replication with strand invasion of the normal sister chromatid. Our results indicate that the mechanism by which copy number changes occur in regions with a complex genomic architecture can yield complex rearrangements.