Genomic DNA is captured and amplified during double-strand break (DSB) repair in human cells

Little, Kevin C. E.; Chartrand, Pascal

doi:10.1038/sj.onc.1207570

Cited by 14 publications

(11 citation statements)

References 49 publications

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“…Screen for higher eukaryotic DNA sequences captured at DSBs: Although capture of mtDNA at experimentally induced DSBs had been previously reported only in S. cerevisiae, a few studies in plant and mammalian cells have reported the insertion of genomic DNA (Gorbunova and Levy 1997;Sargent et al 1997;Salomon and Puchta 1998;Little and Chartrand 2004), including microsatellite sequences (Liang et al 1998;Lin and Waldman 2001a). Using the fission yeast EC DSB repair assay, I screened for higher eukaryotic DNA sequences that may be preferentially captured at DSBs.…”

Section: Resultsmentioning

confidence: 99%

Capture of Extranuclear DNA at Fission Yeast Double-Strand Breaks

Decottignies

2005

Genetics

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Proper repair of DNA double-strand breaks (DSBs) is necessary for the maintenance of genomic integrity. Here, a new simple assay was used to study extrachromosomal DSB repair in Schizosaccharomyces pombe. Strikingly, DSB repair was associated with the capture of fission yeast mitochondrial DNA (mtDNA) at high frequency. Capture of mtDNA fragments required the Lig4p/Pku70p nonhomologous end-joining (NHEJ) machinery and its frequency was highly increased in fission yeast cells grown to stationary phase. The fission yeast Mre11 complex Rad32p/Rad50p/Nbs1p was also required for efficient capture of mtDNA at DSBs, supporting a role for the complex in promoting intermolecular ligation. Competition assays further revealed that microsatellite DNA from higher eukaryotes was preferentially captured at yeast DSBs. Finally, cotransformation experiments indicated that, in NHEJ-deficient cells, capture of extranuclear DNA at DSBs was observed if homologies-as short as 8 bp-were present between DNA substrate and DSB ends. Hence, whether driven by NHEJ, microhomology-mediated end-joining, or homologous recombination, DNA capture associated with DSB repair is a mutagenic process threatening genomic stability.

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Section: Resultsmentioning

confidence: 99%

Capture of Extranuclear DNA at Fission Yeast Double-Strand Breaks

Decottignies

2005

Genetics

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“…Each fragment is subsequently fused to an available free end, with a string of fragments sequentially extending during a single cell cycle, until a DNA segment with a telomere terminates the progression. This process, if true, may be similar to the capture of DNA fragments seen during double-strand break repair in model systems (Little and Chartrand 2004) and occasionally in balanced translocations (Reichel et al 1998).…”

Section: Genome Research 1299mentioning

confidence: 99%

Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution

Bignell¹,

Santarius²,

Pole³

et al. 2007

Genome Res.

186

177

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For decades, cytogenetic studies have demonstrated that somatically acquired structural rearrangements of the genome are a common feature of most classes of human cancer. However, the characteristics of these rearrangements at sequence-level resolution have thus far been subject to very limited description. One process that is dependent upon somatic genome rearrangement is gene amplification, a mechanism often exploited by cancer cells to increase copy number and hence expression of dominantly acting cancer genes. The mechanisms underlying gene amplification are complex but must involve chromosome breakage and rejoining. We sequenced 133 different genomic rearrangements identified within four cancer amplicons involving the frequently amplified cancer genes MYC, MYCN, and ERBB2. The observed architectures of rearrangement were diverse and highly distinctive, with evidence for sister chromatid breakage-fusion-bridge cycles, formation and reinsertion of double minutes, and the presence of bizarre clusters of small genomic fragments. There were characteristic features of sequences at the breakage-fusion junctions, indicating roles for nonhomologous end joining and homologous recombination-mediated repair mechanisms together with nontemplated DNA synthesis. Evidence was also found for sequence-dependent variation in susceptibility of the genome to somatic rearrangement. The results therefore provide insights into the DNA breakage and repair processes operative in somatic genome rearrangement and illustrate how the evolutionary histories of individual cancers can be reconstructed from large-scale cancer genome sequencing.

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“…Gene amplification, a major mechanism of oncogene activation and resistance to chemotherapy, results from DNA DSBs +/+ iBMK cell line, W4-B1 (shown in green), was used as a control. (Little and Chartrand 2004). It is facilitated by the inactivation of the p53 DNA damage checkpoint (Livingstone et al 1992;White et al 1994), increased oxidative stress (in particular by H 2 O 2 ) (Mondello et al 2002), and defects in DNA repair (Lin et al 2001).…”

Section: Allelic Loss Of Beclin1 Is Associated With Gene Amplificatiomentioning

confidence: 99%

Autophagy suppresses tumor progression by limiting chromosomal instability

Mathew¹,

Kongara²,

Beaudoin³

et al. 2007

Genes Dev.

858

785

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Autophagy is a bulk degradation process that promotes survival under metabolic stress, but it can also be a means of cell death if executed to completion. Monoallelic loss of the essential autophagy gene beclin1 causes susceptibility to metabolic stress, but also promotes tumorigenesis. This raises the paradox that the loss of a survival pathway enhances tumor growth, where the exact mechanism is not known. Here, we show that compromised autophagy promoted chromosome instability. Failure to sustain metabolism through autophagy was associated with increased DNA damage, gene amplification, and aneuploidy, and this genomic instability may promote tumorigenesis. Thus, autophagy maintains metabolism and survival during metabolic stress that serves to protect the genome, providing an explanation for how the loss of a survival pathway leads to tumor progression. Identification of this novel role of autophagy may be important for rational chemotherapy and therapeutic exploitation of autophagy inducers as potential chemopreventive agents.[Keywords: Autophagy; beclin1; genomic instability; apoptosis; cancer] Received February 23, 2007; revised version accepted April 12, 2007. Autophagy is an evolutionarily conserved catabolic process involving regulated turnover and elimination of proteins and cellular organelles, such as peroxisomes, mitochondria, and endoplasmic reticulum, through the lysosomal degradation pathway (Mizushima 2005). The process of autophagy is characterized by the formation of double-membrane cytosolic vesicles, known as autophagosomes, that are essential for the lysosomal targeting of these organelles. In yeast, a number of autophagy-related genes (referred to as atg) have been identified that regulate the formation of autophagosomes and the autophagy process (Klionsky et al. 2003). Several mammalian homologs of these yeast genes have been identified (Levine and Klionsky 2004), among which the essential autophagy genes atg5 and atg7 have been most informative in demonstrating a role for autophagy in maintaining metabolism and homeostasis in mammalian development.Autophagy, constitutively active at low levels, is robustly activated under metabolic stress. Autophagy plays an important role in development, as mice deficient in autophagy due to complete deficiency of beclin1 (atg6/vps30), another essential autophagy gene, die early in embryogenesis (Yue et al. 2003). Mice lacking atg5 fail to survive the neonatal starvation period and die perinatally, suggesting that autophagy plays an important role in the maintenance of energy homeostasis (Kuma et al. 2004). Thus, autophagy functions as an alternative cellular energy source to maintain normal metabolism during development and starvation by recycling cytoplasm and macromolecules (Jin and White 2007). Furthermore, targeted deletion of atg5 and atg7 in the central nervous system results in accumulation of polyubiquitinated proteins leading to neurodegeneration, revealing a housekeeping role for autophagy in the regulation of long-lived or damaged proteins...

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Genomic DNA is captured and amplified during double-strand break (DSB) repair in human cells

Cited by 14 publications

References 49 publications

Capture of Extranuclear DNA at Fission Yeast Double-Strand Breaks

Capture of Extranuclear DNA at Fission Yeast Double-Strand Breaks

Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution

Autophagy suppresses tumor progression by limiting chromosomal instability

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