A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
PLoS Genetics (Impact Factor: 7.53). 02/2009; 5(1):e1000327. DOI: 10.1371/journal.pgen.1000327
Source: PubMed


Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV). A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2-5 base pairs (bp). Third, endpoints occur near pre-existing low copy repeats (LCRs). Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR) for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR). Under these circumstances, single-strand 3' tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.

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    • "b The father exhibited a recent onset of central serous chorioretinopathy in the left eye with fluid and pigment epithelial detachment over the fovea in the left eye. Pigmentary changes noted in the macula are likely attributed to early, dry age-related macular degeneration These suggest fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/ MMBIR) as the potential CNV generating mechanism via three template switches (Hastings et al. 2009; Lee et al. 2007; Zhang et al. 2009). The deletion/insertion spanned from the intron upstream of exon 45 to exon 48. "
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    ABSTRACT: Over 800 mutations in the ABCA4 gene cause autosomal recessive Stargardt disease. Due to extensive genetic heterogeneity, observed variant-associated phenotypes can manifest tremendous variability of expression. Furthermore, the high carrier frequency of pathogenic ABCA4 alleles in the general population (~1:20) often results in pseudo-dominant inheritance patterns further complicating the diagnosis and characterization of affected individuals. This study describes a genotype/phenotype analysis of an unusual family with multiple macular disease phenotypes spanning across two generations and segregating four distinct ABCA4 mutant alleles. Complete sequencing of ABCA4 discovered two known missense mutations, p.C54Y and p.G1961E. Array comparative genomic hybridization revealed a large novel deletion combined with a small insertion, c.6148-698_c.6670del/insTGTGCACCTCCCTAG, and complete sequencing of the entire ABCA4 genomic locus uncovered a new deep intronic variant, c.302+68C>T. Patients with the p.G1961E mutation had the mildest, confined maculopathy phenotype with peripheral flecks while those with all other mutant allele combinations exhibited a more advanced stage of generalized retinal and choriocapillaris atrophy. This family epitomizes the clinical and genetic complexity of ABCA4-associated diseases. It contained variants from all classes of mutations, in the coding region, deep intronic, both single nucleotide variants and copy number variants that accounted for varying phenotypes segregating in an apparent dominant fashion. Unequivocally defining disease-associated alleles in the ABCA4 locus requires a multifaceted approach that includes advanced mutation detection methods and a thorough analysis of clinical phenotypes.
    Human Genetics 11/2015; DOI:10.1007/s00439-015-1605-y · 4.82 Impact Factor
    • "Six of the remaining seven events were characterized either by the absence of microhomologies at both ends or by the presence of a microhomology of 1–2 bp at only one end; the remaining event was characterized by microhomologies at both ends, one of 1 bp, the other 2 bp (see Fig. 2 in Chen et al. [2013]). In short, all seven events lacked the typical " microhomology " signature (i.e., 2 bp at both ends) of the SRS and subsequent replicationbased models [Lee et al., 2007; Sheen et al., 2007; Hastings et al., 2009; Liu et al., 2011]. This notwithstanding, these seven events can potentially be accounted for by incorporating a role for TLS DNA polymerases into the SRS model. "
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    ABSTRACT: Translesion synthesis (TLS) DNA polymerases allow the bypass of unrepaired lesions during DNA replication. Based upon mutational signatures of a subtype of multiple-nucleotide substitution (MNS) mutations causing human inherited disease, we have recently postulated two properties of TLS DNA polymerases in DNA repair: namely, the generation of neo-microhomologies potentiating strand-misalignment, and additional micro-lesions within the templated inserts when recruited to stalled replication forks. To provide further support for this postulate, we analyzed the mutational signatures of a new and complex subtype of pathogenic MNS mutation. Several mutations containing long templated inserts (8-19 bp) that are highly informative with regard to their underlying mutational mechanisms, harbor imprints of TLS DNA polymerase action. Dissecting the mechanism underlying the generation of the 19 bp-insert implicated repeated participation of TLS DNA polymerases in the conversion of a damaged base into a complex MNS lesion through a process of successive template switching and bypass repair. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Human Mutation 07/2015; 36(11). DOI:10.1002/humu.22831 · 5.14 Impact Factor
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    • "Another model achieves the same end point by template switching across two diverging replication forks (Brewer et al. 2011). The same structures can be explained by the microhomology-mediated break-induced replication (MMBIR) model described below (Hastings et al. 2009a) in which template switches are not restricted to replication fork regions. "
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    ABSTRACT: Changes in gene copy number are among the most frequent mutational events in all genomes and were among the mutations for which a physical basis was first known. Yet mechanisms of gene duplication remain uncertain because formation rates are difficult to measure and mechanisms may vary with position in a genome. Duplications are compared here to deletions, which seem formally similar but can arise at very different rates by distinct mechanisms. Methods of assessing duplication rates and dependencies are described with several proposed formation mechanisms. Emphasis is placed on duplications formed in extensively studied experimental situations. Duplications studied in microbes are compared with those observed in metazoan cells, specifically those in genomes of cancer cells. Duplications, and especially their derived amplifications, are suggested to form by multistep processes often under positive selection for increased copy number. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.
    Cold Spring Harbor perspectives in biology 02/2015; 7(2). DOI:10.1101/cshperspect.a016592 · 8.68 Impact Factor
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