Journal
HUMAN MOLECULAR GENETICS
Volume 24, Issue 14, Pages 4061-4077Publisher
OXFORD UNIV PRESS
DOI: 10.1093/hmg/ddv146
Keywords
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Funding
- Doris Duke Charitable Foundation [2013095] Funding Source: Medline
- Howard Hughes Medical Institute Funding Source: Medline
- NHGRI NIH HHS [U54 HG006542] Funding Source: Medline
- NICHD NIH HHS [1 U54 HD083092, U54 HD083092] Funding Source: Medline
- NIGMS NIH HHS [T32GM007330, R01 GM106373, T32 GM007330, R01GM106373] Funding Source: Medline
- NINDS NIH HHS [R01NS058529, F31 NS083159, R01 NS058529] Funding Source: Medline
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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 similar to 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.
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