Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration

Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.
Nature Genetics (Impact Factor: 29.35). 03/2012; 44(4):390-7, S1. DOI: 10.1038/ng.2202
Source: PubMed


We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.

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    • "Replication fork stalling and template switching has been hypothesized to underpin some of the complex genomic rearrangements found in constitutional genomic disorders (Liu et al. 2011b). One study, for example, showed that 19% of individuals with chromosomal abnormalities had evidence for complexity of genomic rearrangements at the breakpoints (Chiang et al. 2012). In many cases, these complexes of structural variation are driven by clustered rearrangements with a striking resemblance to those described here, and cause severe developmental disorders (Liu et al. 2011b). "
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    ABSTRACT: Mutation is associated with developmental and hereditary disorders, aging and cancer. While we understand some mutational processes operative in human disease, most remain mysterious. We used C. elegans whole genome sequencing to model mutational signatures, analyzing 183 worm populations across 17 DNA repair-deficient backgrounds, propagated for 20 generations or exposed to carcinogens. The baseline mutation rate in C. elegans was ~1/genome/generation, not overtly altered across several DNA repair deficiencies over 20 generations. Telomere erosion led to complex chromosomal rearrangements initiated by breakage-fusion-bridge cycles and completed by simultaneously acquired, localized clusters of breakpoints. Aflatoxin-B1 induced substitutions of guanines in GpC context, as observed in aflatoxin-induced liver cancers. Mutational burden increased with impaired nucleotide excision repair. Cisplatin and mechlorethamine, DNA crosslinking agents, caused dose- and genotype-dependent signatures among indels, substitutions and rearrangements. Strikingly, both agents induced clustered rearrangements resembling 'chromoanasynthesis,' a replication-based mutational signature seen in constitutional genomic disorders, suggesting interstrand crosslinks may play a pathogenic role in such events. Cisplatin mutagenicity was most pronounced in xpf-1 mutants, suggesting this gene critically protects cells against platinum chemotherapy. Thus, experimental model systems combined with genome sequencing can recapture and mechanistically explain mutational signatures associated with human disease.
    Full-text · Article · Jul 2014 · Genome Research
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    • "This mechanism generates complex rearrangements formed by the incorrect ligation of ends with little or no sequence of homology and the insertion of some nucleotides, with the further loss of some fragments to generate deletions (Kloosterman et al. 2011; Holland and Cleveland 2012). The other mechanism that can be involved in the formation of complex rearrangements is chromoanasynthesis, which is generally involved in constitutional rearrangements that show complexity, microhomology at breakpoints , and occasionally the fusions of distant sequences and is indicative of a DNA replication-based mechanism as the causative agent, including fork stalling and template switching (FoSTeS) and/or microhomology-mediated break-induced replication (MMBIR) (Zhang et al. 2009; Liu et al. 2011; Chiang et al. 2012; Holland and Cleveland 2012). FoSTeS occurs when the DNA replication forks stall due to a DNA lesion or an error, allowing the replication fork to invade another fork through an area of microhomology. "
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    ABSTRACT: Genome rearrangements are caused by the erroneous repair of DNA double-strand breaks, leading to several alterations that result in loss or gain of the structural genomic of a dosage-sensitive genes. However, the mechanisms that promote the complexity of rearrangements of congenital or developmental defects in human disease are unclear. The investigation of complex genomic abnormalities could help to elucidate the mechanisms and causes for the formation and facilitate the understanding of congenital or developmental defects in human disease. We here report one case of a patient with atypical clinical features of the 1p36 syndrome and the use of cytogenomic techniques to characterize the genomic alterations. Analysis by multiplex ligation-dependent probe amplification and array revealed a complex rearrangement in the 1p36.3 region with deletions and duplication interspaced by normal sequences. We also suggest that chromoanagenesis could be a possible mechanism involved in the repair and stabilization of this rearrangement.
    Full-text · Article · Jul 2014 · MGG Molecular & General Genetics
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    • "This discovery has generated excitement and ongoing investigation. Subsequent studies have found evidence for chromothripsis in multiple myeloma (2), medulloblastoma (3,4), neuroblastoma (5) and colorectal cancers (6) as well as the germline (7,8). Moreover in some studies, chromothripsis has been associated with more aggressive cancers. "
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    ABSTRACT: The chromothripsis hypothesis suggests an extraordinary one-step catastrophic genomic event allowing a chromosome to 'shatter into many pieces' and reassemble into a functioning chromosome. Recent efforts have aimed to detect chromothripsis by looking for a genomic signature, characterized by a large number of breakpoints (50-250), but a limited number of oscillating copy number states (2-3) confined to a few chromosomes. The chromothripsis phenomenon has become widely reported in different cancers, but using inconsistent and sometimes relaxed criteria for determining rearrangements occur simultaneously rather than progressively. We revisit the original simulation approach and show that the signature is not clearly exceptional, and can be explained using only progressive rearrangements. For example, 3.9% of progressively simulated chromosomes with 50-55 breakpoints were dominated by two or three copy number states. In addition, by adjusting the parameters of the simulation, the proposed footprint appears more frequently. Lastly, we provide an algorithm to find a sequence of progressive rearrangements that explains all observed breakpoints from a proposed chromothripsis chromosome. Thus, the proposed signature cannot be considered a sufficient proof for this extraordinary hypothesis. Great caution should be exercised when labeling complex rearrangements as chromothripsis from genome hybridization and sequencing experiments.
    Full-text · Article · Jun 2014 · Nucleic Acids Research
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