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

Abstract

Recurrent submicroscopic genomic copy number changes are the result of non-allelic homologous recombination (NAHR). Non-recurrent aberrations however, can result from different non-exclusive 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 8 of the 32 breakpoint regions coincide with low-copy repeats (LCRs), 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 to 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 non-homologous end joining (NHEJ) as the mechanism. Breakpoint analysis in two other patients by inverse PCR and subsequent array-CGH 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 (BIR) with strand invasion of the normal sister chromatid. Our results demonstrate that the mechanism by which copy number changes occur in regions with a complex genomic architecture, can yield complex rearrangements.