Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication

Abstract

Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication—inverted triplication—duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals—16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology—or homeology—driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

Double, Double, Toil and Trouble:

“…The nonrecurrent junctions in these patients were consistent with MMBIR [Beck et al, 2015]. This contention is supported by the observation of triplicated and quadruplicated segments, point mutations being associated with some of the breakpoint junctions, and the presence of intrachromosomal rearrangements [Carvalho et al, 2013;Beck et al, 2015].…”

“…Duplication of the X-linked proteolipid protein 1 (PLP1) gene is the major mutational cause for Pelizaeus-Merzbacher disease and explains ∼ 80% of the cases. This duplication occurs via a mechanism that results in a DUP-TRP/INV-DUP structure [Carvalho et al, 2011;Beck et al, 2015]. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion, a structural variation found frequently among healthy individuals.…”

“…However, since recurrent CNVs also occur in healthy individuals, they themselves are not necessarily pathogenic [Poot et al, 2010]. Indeed, in some patients, 2 recurrent CNVs were found such that concomitant changes in the dosage of genes in both CNVs may account for the clinical phenotype [Girirajan et al, paraplegia type 2 (MIM 312920), whereas triplications were detected in 6 patients [Beck et al, 2015]. STR markers for these duplicated/triplicated regions were monomorphic in 12 of the 13 patients tested.…”

Noncanonical views of homology-directed DNA repair

“…In patient samples, the PLP1 and MECP2 locus consisted of an inverted triplicated segment flanked by duplicated segments (DUP-TRP/INV-DUP). This kind of rearrangement in both genes was proposed to be facilitated by inverted repeats and was suggested to occur by a two-step process involving BIR followed by MMBIR (Carvalho et al 2013;Beck et al 2015). This hypothesis was recently proved in a pif1Δ yeast strain, where it was demonstrated that the collapse of a replication fork during BIR led to the initiation of MMBIR.…”

“…FoSTeS/MMBIR has also been used to explain the process of chromoanasynthesis, which involves a combination of chromosomal rearrangements with both losses and gains in copy number (Liu et al 2011b;Carvalho et al 2011Carvalho et al , 2013Carvalho et al , 2015Beck et al 2015). This model was proposed to explain the nonrecurrent duplications of the PLP1 gene associated with the demyelinating disorder Pelizaeus-Merzbacher disease (PMD).…”