Deregulated origin licensing leads to chromosomal breaks by rereplication of a gapped DNA template

Neelsen, Kai J.; Zanini, Isabella M.Y.; Mijic, Sofija; Herrador, Raquel; Zellweger, Ralph; Chaudhuri, Arnab Ray; Creavin, Kevin; Blow, J. Julian; Lopes, Massimo

doi:10.1101/gad.226373.113

Cited by 84 publications

(94 citation statements)

References 33 publications

(54 reference statements)

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“…Together, these results indicate that Pol is recruited to chromatin through mechanisms similar to TLS and that rereplication-induced ssDNA accumulation, preceding generation of DSBs, activates the Rad18-mediated monoubiquitination of PCNA. This is in agreement with previous findings obtained in other rereplication models (19,20,22).…”

Section: Rereplication Leads To the Recruitment Of Y-pols To Chromatinsupporting

confidence: 83%

“…Y-family polymerases (Y-Pols), including Pol , Pol , Pol , and REV1, are the major group of TLS polymerases. The previous observations that rereplication induces replication stress and DNA damage prompted us to investigate the roles of Y-Pols and replicative polymerases in rereplication in the present study (17)(18)(19)(20)(21)(22). We found that rereplication induced by geminin depletion causes slowing down of fork progression, inducing Rad18-mediated monoubiquitination of proliferating cell nuclear antigen (PCNA), resulting in recruitment of Y-Pols to rereplication sites, and that Y-Pols, together with replicative polymerases, contribute to rereplication.…”

mentioning

confidence: 91%

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Both High-Fidelity Replicative and Low-Fidelity Y-Family Polymerases Are Involved in DNA Rereplication

Sekimoto

Oda

Kurashima

et al. 2015

Molecular and Cellular Biology

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b DNA rereplication is a major form of aberrant replication that causes genomic instabilities, such as gene amplification. However, little is known about which DNA polymerases are involved in the process. Here, we report that low-fidelity Y-family polymerases (Y-Pols), Pol , Pol , Pol , and REV1, significantly contribute to DNA synthesis during rereplication, while the replicative polymerases, Pol ␦ and Pol , play an important role in rereplication, as expected. When rereplication was induced by depletion of geminin, these polymerases were recruited to rereplication sites in human cell lines. This finding was supported by RNA interference (RNAi)-mediated knockdown of the polymerases, which suppressed rereplication induced by geminin depletion. Interestingly, epistatic analysis indicated that Y-Pols collaborate in a common pathway, independently of replicative polymerases. We also provide evidence for a catalytic role for Pol and the involvement of Pol and Pol in cyclin E-induced rereplication. Collectively, our findings indicate that, unlike normal S-phase replication, rereplication induced by geminin depletion and oncogene activation requires significant contributions of both Y-Pols and replicative polymerases. These findings offer important mechanistic insights into cancer genomic instability. E ukaryotic cells contain regulatory mechanisms to ensure that chromosomal DNA is duplicated exactly once per cell cycle (1-3). In late mitosis and early G 1 phase, replication origins are "licensed" through the formation of the prereplicative complex by sequential recruitment of the origin recognition complex, the loading factors Cdt1 and CDC6, and the minichromosome maintenance (MCM) 2-7 replicative helicase complex (MCM complex). At the onset of S phase, cyclin-dependent kinase 2 (CDK2)-and CDC7-mediated phosphorylation activates the MCM complex to unwind DNA, followed by loading of replication machinery to initiate DNA replication. Once cells enter S phase, the MCM complex is depleted from origins, and licensing of origins is inhibited during the S and G 2 phases by multiple mechanisms, including degradation of Cdt1 and CDC6 and expression of geminin, a specific inhibitor of Cdt1.Growing evidence indicates that DNA rereplication plays a major role in genomic instability during tumor development and progression (2-4). Importantly, expression of various oncoproteins in cultured cells induces rereplication, partly through the increased expression of Cdt1 and/or CDC6, causing copy number changes and genomic rearrangements (5-7). Furthermore, a recent study documented that overexpression of KDM4A demethylase causes rereplication, resulting in site-specific gene amplification in human tumors (8). Although the molecular mechanisms for rereplication-induced genomic instability are not fully understood, it is proposed that rereplication induces double-strand breaks (DSBs) through fork collapse and collisions, leading to copy number variations and genomic rearrangements (2-4). While numerous studies have focused on the causes ...

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Section: Rereplication Leads To the Recruitment Of Y-pols To Chromatinsupporting

confidence: 83%

mentioning

confidence: 91%

Both High-Fidelity Replicative and Low-Fidelity Y-Family Polymerases Are Involved in DNA Rereplication

Sekimoto

Oda

Kurashima

et al. 2015

Molecular and Cellular Biology

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“…The sizes of TDs resulted from BIR activated by cyclin E (CCNE1)-induced replication stress were measured to be hundreds of kb with the median around 200 kb and importantly, near one third of reported alterations were deletions (44). An increased rate of DNA double-strand breaks and release of DNA fragments consecutive to rereplicating fork collisions were shown in model systems of induced re-replication (45,46). Resolution of these breaks could result in TDs (42).…”

Section: Discussionmentioning

confidence: 99%

Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications

et al. 2016

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CDK12 is a recurrently mutated gene in serous ovarian carcinoma, whose downregulation is associated with impaired expression of DNA damage repair genes and subsequent hypersensitivity to DNA-damaging agents and PARP1/2 inhibitors. In this study, we investigated the genomic landscape associated with CDK12 inactivation in patients with serous ovarian carcinoma. We show that CDK12 loss was consistently associated with a particular genomic instability pattern characterized by hundreds of tandem duplications of up to 10 megabases (Mb) in size. Tandem duplications were characterized by a bimodal ($0.3 and $3 Mb) size distribution and overlapping microhomology at the breakpoints.This genomic instability, denoted as the CDK12 TD-plus phenotype, is remarkably distinct from other alteration patterns described in breast and ovarian cancers. The CDK12 TD-plus phenotype was associated with a greater than 10% gain in genomic content and occurred at a 3% to 4% rate in The Cancer Genome Atlas-derived and in-house cohorts of patients with serous ovarian carcinoma. Moreover, CDK12-inactivating mutations together with the TD-plus phenotype were also observed in prostate cancers. Our finding provides new insight toward deciphering the function of CDK12 in genome maintenance and oncogenesis. Cancer Res; 76(7); 1882-91. Ó2016 AACR.

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“…Increased frequency of origin firing has been implicated in genomic abnormality (22,24,(37)(38)(39)(40), and one of the indicators of genomic abnormality is micronuclei formation (41)(42)(43). Although an increase in CHK1 levels would protect collapse of replication forks stalled due to increased origin firing, it has been reported that the topological stress associated with progress of an increased number of replication forks may lead to genome abnormality by mechanisms such as fork reversal, which could be evidenced by micronuclei formation (39,40). Since GOF p53 increases origin firing, the frequency of micronuclei formation in the presence or absence of GOF p53 was determined.…”

Section: 4mentioning

confidence: 99%

Mutant p53 establishes targetable tumor dependency by promoting unscheduled replication

Singh¹,

Vaughan²,

Frum³

et al. 2017

Journal of Clinical Investigation

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Deregulated origin licensing leads to chromosomal breaks by rereplication of a gapped DNA template

Cited by 84 publications

References 33 publications

Both High-Fidelity Replicative and Low-Fidelity Y-Family Polymerases Are Involved in DNA Rereplication

Both High-Fidelity Replicative and Low-Fidelity Y-Family Polymerases Are Involved in DNA Rereplication

Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications

Mutant p53 establishes targetable tumor dependency by promoting unscheduled replication

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