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.

Increased MECP2 gene copy number as the result of genomic duplication in neurodevelopmentally delayed males

“…associated with LCRs. 41,51 Sequencing of the actual MECP2 duplication breakpoint junctions could confirm the mechanism of nonhomologous end joining, 41,51 which has been observed for other nonrecurrent rearrangements. Such experiments are challenged by the highly complex and repetitive nature of this genomic region, and lie beyond the immediate scope of our present study.…”

“…33 Duplications within the human genome are increasingly recognized as a cause of neurodegenerative phenotypes. Such rearrangements are responsible not only for Mendelian traits such as Charcot-Marie-Tooth neuropathy type 1A 39 and Pelizaeus-Merzbacher leukodystrophy, 40,41 but also for conditions generally thought to be acquired in nature such as Parkinson 42 and Alzheimer 43 diseases. Recurrent rearrangements in Charcot-Marie-Tooth neuropathy type 1A are mediated by nonallelic homologous recombination, 44 wherein genome architectural features seem to lead to genomic instability.…”

Reduced PLP1 expression in induced pluripotent stem cells derived from a Pelizaeus–Merzbacher disease patient with a partial PLP1 duplication

“…This size is typical for PMD patients with PLP1 duplications. 8,15,16 This patient is now 43 years old and does not show any deterioration of neurological abilities. Despite being bedridden, he can verbally communicate with several words.…”

Insertion of the IL1RAPL1 gene into the duplication junction of the dystrophin gene

“…32 Especially in Pelizaeus-Merzbacher disease, an X-linked dysmyelinating disorder, nonrecurrent duplication of the dosage-sensitive PLP1 gene is known as the most common cause. 33 Recently, it was proposed that complex duplications of the proteolipid protein 1 (PLP1) gene are due to the replication-based mechanism of 'replication folk stalling and template switching (FoSTeS),' as these duplications could be explained by neither nonallelic homologous recombination nor a simple nonhomologous end joining recombination mechanism. 14 In our case, it is better to consider this possibility as the underlying mechanism for the complex genomic rearrangement ( Figure 5).…”