Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination

Abstract

Background: Recurrent rearrangements of the human genome resulting in disease or variation are mainly mediated by non-allelic homologous recombination (NAHR) between low-copy repeats. However, other genomic structures, including AT-rich palindromes and retroviruses, have also been reported to underlie recurrent structural rearrangements. Notably, recurrent deletions of Yq12 conveying azoospermia, as well as non-pathogenic reciprocal duplications, are mediated by human endogenous retroviral elements (HERVs). We hypothesized that HERV elements throughout the genome can serve as substrates for genomic instability and result in human copy-number variation (CNV).

Results: We developed parameters to identify HERV elements similar to those that mediate Yq12 rearrangements as well as recurrent deletions of 3q13.2q13.31. We used these parameters to identify HERV pairs genome-wide that may cause instability. Our analysis highlighted 170 pairs, flanking 12.1% of the genome. We cross-referenced these predicted susceptibility regions with CNVs from our clinical databases for potentially HERV-mediated rearrangements and identified 78 CNVs. We subsequently molecularly confirmed recurrent deletion and duplication rearrangements at four loci in ten individuals, including reciprocal rearrangements at two loci. Breakpoint sequencing revealed clustering in regions of high sequence identity enriched in PRDM9-mediated recombination hotspot motifs.

Conclusions: The presence of deletions and reciprocal duplications suggests NAHR as the causative mechanism of HERV-mediated CNV, even though the length and the sequence homology of the HERV elements are less than currently thought to be required for NAHR. We propose that in addition to HERVs, other repetitive elements, such as long interspersed elements, may also be responsible for the formation of recurrent CNVs via NAHR.

Figure 1

Genome-wide map of HERV-mediated genome instability. Chromosome ideograms with 70 predicted HERV susceptibility regions indicated in purple flanked by individual HERV elements indicated in red. Potentially HERV-mediated CNVs identified in the Baylor College of Medicine or Signature Genomics clinical databases are shown below the chromosome ideograms in cyan. HERV-mediated CNVs that have been molecularly confirmed in this study or the literature are indicated in yellow. CNV, copy-number variation; HERV, human endogenous retrovirus.

Figure 2

Distribution of HERV susceptibility regions. Percentage of each chromosome consisting of potential HERV susceptibility regions. HERV, human endogenous retrovirus.

Figure 3

Breakpoint analysis of HERV-mediated CNVs. (A) Representative Sanger sequencing trace of the deletion breakpoint region of patient 8. The patient’s breakpoint sequence is presented between the proximal and distal chromosome 11 reference sequences. The informative cis-morphisms that define the breakpoint uncertainty region are highlighted in yellow. (B) An analogous presentation of a deletion breakpoint for patient 9. Chr, chromosome; CNV, copy-number variation; HERV, human endogenous retrovirus.

Figure 4

HERV structure and breakpoint distribution of HERV-mediated CNVs. Structures of the HERV elements involved at each locus are presented compared to the consensus HERV-H sequence from RepBase. Gaps in the consensus represent insertions in the genomic HERV elements mediating the CNVs. Gaps in the genomic HERVs represent deletions compared to the reference. The color of the genomic HERV elements denotes identity at that position when aligned with its partner element over a 50-bp window. Blue represents 0% sequence identity (i.e. caused by a large insertion or deletion) while orange represents perfect identity. The region of the crossover for each patient is presented as a colored X with the size of the X representing the uncertainty bounded by informative cis-morphisms. Red X’s indicate deletions; green X’s indicate duplications; the purple X represents breakpoints for two patients that occurred between the same two cis-morphisms. Recombination hotspot motifs in each HERV element are annotated along the HERV sequences as black H’s. The relative positions of the genes encoded in the HERV genome are annotated along the top of the first consensus. * Previously published locus. CNV, copy-number variation; HERV, human endogenous retrovirus; LTR, long tandem repeat.