Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3

Abstract

Alu repetitive elements are known to be major contributors to genome instability by generating Alu-mediated copy-number variants (CNVs). Most of the reported Alu-mediated CNVs are simple deletions and duplications, and the mechanism underlying Alu-Alu-mediated rearrangement has been attributed to non-allelic homologous recombination (NAHR). Chromosome 17 at the p13.3 genomic region lacks extensive low-copy repeat architecture; however, it is highly enriched for Alu repetitive elements, with a fraction of 30% of total sequence annotated in the human reference genome, compared with the 10% genome-wide and 18% on chromosome 17. We conducted mechanistic studies of the 17p13.3 CNVs by performing high-density oligonucleotide array comparative genomic hybridization, specifically interrogating the 17p13.3 region with ∼150 bp per probe density; CNV breakpoint junctions were mapped to nucleotide resolution by polymerase chain reaction and Sanger sequencing. Studied rearrangements include 5 interstitial deletions, 14 tandem duplications, 7 terminal deletions and 13 complex genomic rearrangements (CGRs). Within the 17p13.3 region, Alu-Alu-mediated rearrangements were identified in 80% of the interstitial deletions, 46% of the tandem duplications and 50% of the CGRs, indicating that this mechanism was a major contributor for formation of breakpoint junctions. Our studies suggest that Alu repetitive elements facilitate formation of non-recurrent CNVs, CGRs and other structural aberrations of chromosome 17 at p13.3. The common observation of Alu-mediated rearrangement in CGRs and breakpoint junction sequences analysis further demonstrates that this type of mechanism is unlikely attributed to NAHR, but rather may be due to a recombination-coupled DNA replicative repair process.

Mechanisms underlying structural variant formation in genomic disorders

“…Alu - Alu -mediated rearrangement events have been historically attributed to NAHR; however, the low nucleotide sequence identity shared between the Alu family members, which can be as low as 75%, suggests that alternative recombination mechanisms also take place 43 . A recent report of complex genomic variants such as interspersed duplications and triplications mediated by multiple iterative template switches between Alu indicates that DNA synthesis can be involved in Alu - Alu- mediated events and supports a role for DNA replication in their formation 37 .…”

“…1Ba). In some cases, the inverted repeat pair consists of small repeats such as Alu elements 37 , but the majority of DUP–TRP/INV–DUP rearrangements described thus far have been LCR-mediated. Genomic disorders such as MECP2 duplication syndrome and Pelizaeus–Merzbacher disease (PMD; OMIM 312080 ) are characterized by nonrecurrent rearrangements, mostly duplications, that present with one breakpoint grouping within an LCR-laden region 38–42 (FIG.…”

Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4

“…Repetitive DNA sequences (Cooper et al 2011), including fragile sites (Minca and Kowalski 2011;Thys et al 2015) and Alu (Gu et al 2015) have well-documented associations with genome instability via replication fork-stalling (Ozeri-Galai et al 2011) and stimulation of homology-based recombination processes (Mizuno et al 2013). Although we cannot determine the initiating DNA breakpoint for the telomere fusion events we have sequenced, we did not find any significant coincidence of inter-chromosomal (Cunningham et al 2015) and RefSeq (Pruitt et al 2014) curations-than expected by chance based on RefSeq human genome gene content estimate of 41.8%.…”

Mus81 and converging forks limit the mutagenicity of replication fork breakage

“…Alus are often found at breakpoints of copy number variants as well as complex genomic rearrangements associated with disease (27). To address whether broken fork repair stimulates template switches between diverged Alu elements, we inserted two Alus (88.2% identical) that were previously observed to mediate human disease-associated deletions (28) onto ChrII, 1.2 and 9.7 kb from the FRT site, flanking a URA3 reporter (Fig.…”