DNA damage bypass operates in the S and G2 phases of the cell cycle and exhibits differential mutagenicity

Diamant, Noam; Hendel, Ayal; Vered, Ilan; Carell, Thomas; Reißner, Thomas; Wind, Niels de; Geacinov, Nicholas; Livneh, Zvi

doi:10.1093/nar/gkr596

Cited by 92 publications

(101 citation statements)

References 48 publications

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“…Some of these loci could be related to DNA repairs reported previously. 28 RFP-Killin is tightly associated with DNA throughout the cell cycle Although RFP-Killin has now been shown to exhibit punctate and mutually exclusive nuclear localization pattern with BrdU, RPA and PCNA, one would argue that RFP-Killin may have nothing to do with DNA synthesis unless RFP-Killin is really associated with DNA in vivo. To this end, we conducted the salt extraction which has been shown to disrupt GFP-PCNA signal in non-S phase nuclei, while GFP-PCNA signal associated with DNA replication forks during S phase remained unperturbed.…”

Section: Resultsmentioning

confidence: 99%

Cell cycle specific distribution of killin: evidence for negative regulation of both DNA and RNA synthesis

et al. 2015

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Section: Resultsmentioning

confidence: 99%

Cell cycle specific distribution of killin: evidence for negative regulation of both DNA and RNA synthesis

et al. 2015

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“…It is not clear what determines the labor division between TLS and HDR. Possible factors involved may include chromosomal location, the type of DNA damage, and the cell cycle, following the finding that like in S. cerevisiae cells (16,44), the TLS in mammalian cells occurs both in the S and the G2 phases (45). Interestingly, mammalian cells are very effective in tolerating BP-G, despite its bulkiness, and TT 6-4 PP, despite the significant deformation that this lesion causes.…”

Section: Discussionmentioning

confidence: 99%

Genomic assay reveals tolerance of DNA damage by both translesion DNA synthesis and homology-dependent repair in mammalian cells

Izhar

Ziv

Cohen

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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DNA lesions can block replication forks and lead to the formation of single-stranded gaps. These replication complications are mitigated by DNA damage tolerance mechanisms, which prevent deleterious outcomes such as cell death, genomic instability, and carcinogenesis. The two main tolerance strategies are translesion DNA synthesis (TLS), in which low-fidelity DNA polymerases bypass the blocking lesion, and homology-dependent repair (HDR; postreplication repair), which is based on the homologous sister chromatid. Here we describe a unique high-resolution method for the simultaneous analysis of TLS and HDR across defined DNA lesions in mammalian genomes. The method is based on insertion of plasmids carrying defined site-specific DNA lesions into mammalian chromosomes, using phage integrase-mediated integration. Using this method we show that mammalian cells use HDR to tolerate DNA damage in their genome. Moreover, analysis of the tolerance of the UV light-induced 6-4 photoproduct, the tobacco smokeinduced benzo[a]pyrene-guanine adduct, and an artificial trimethylene insert shows that each of these three lesions is tolerated by both TLS and HDR. We also determined the specificity of nucleotide insertion opposite these lesions during TLS in human genomes. This unique method will be useful in elucidating the mechanism of DNA damage tolerance in mammalian chromosomes and their connection to pathological processes such as carcinogenesis.error-prone DNA repair | homologous recombination repair | recombinational repair D NA damage is abundant, caused by both external agents such as sunlight and tobacco smoke and intracellular byproducts of metabolism, amounting to about 50,000 lesions per day per cell (1). Despite the presence of effective DNA repair mechanisms that eliminate lesions and restore the original DNA sequence, DNA replication often encounters unrepaired lesions that have escaped repair. These DNA damages may cause arrest of replication forks and the generation of postreplication gaps (2, 3). To complete replication and prevent the formation of double-strand breaks, which are highly deleterious, cells use DNA damage tolerance (DDT) mechanisms. These include translesion DNA synthesis (TLS) and homology-dependent repair (HDR), which enable bypass of the lesions and completion of replication, without removing the lesions from DNA. HDR uses the sequence from the intact sister chromatid to patch the single-stranded template region carrying the lesion. [We term HDR the pathways of DNA damage tolerance that rely on the homologous sister chromatid, also termed postreplication repair (PRR), damage avoidance, template switch, copy choice recombination, and homologous recombination repair.] This is carried out either by physical transfer of the segment complementary to the damaged template [also termed homologous recombination repair (HRR)] or by copying the complementary strand from the sister chromatid (template switch or postreplication repair). TLS employs specialized low-fidelity DNA polymerases to replicate across ...

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“…We first note that gaps are associated with single-strand breaks, which may be the form of DNA damage that is incurred at the highest rate (Vilenchik and Knudson 2003), and that they can persist from one phase of the cell cycle to another before being repaired (Diamant et al 2012); embryonic stem cells display such gaps at high frequency, possibly because of a short G1 phase (Ahuja et al 2016). A high frequency of single-strand gaps is thus not surprising.…”

Section: Duplex Deletion Disagreements Identify Single-stranded Dna Gmentioning

confidence: 95%

Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq

Taylor

Cinquin

2016

Genome Res.

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Assaying in vivo accrual of DNA damage and DNA mutations by stem cells and pinpointing sources of damage and mutations would further our understanding of aging and carcinogenesis. Two main hurdles must be overcome. First, in vivo mutation rates are orders of magnitude lower than raw sequencing error rates. Second, stem cells are vastly outnumbered by differentiated cells, which have a higher mutation rate-quantification of stem cell DNA damage and DNA mutations is thus best performed from small, well-defined cell populations. Here we report a mutation detection technique, based on the "duplex sequencing" principle, with an error rate below ∼10 −10 and that can start from as little as 50 pg DNA. We validate this technique, which we call SIP-HAVA-seq, by characterizing Caenorhabditis elegans germline stem cell mutation accrual and asking how mating affects that accrual. We find that a moderate mating-induced increase in cell cycling correlates with a dramatic increase in accrual of mutations. Intriguingly, these mutations consist chiefly of deletions in nonexpressed genes. This contrasts with results derived from mutation accumulation lines and suggests that mutation spectrum and genome distribution change with replicative age, chronological age, cell differentiation state, and/or overall worm physiological state. We also identify single-stranded gaps as plausible deletion precursors, providing a starting point to identify the molecular mechanisms of mutagenesis that are most active. SIP-HAVA-seq provides the first direct, genome-wide measurements of in vivo mutation accrual in stem cells and will enable further characterization of underlying mechanisms and their dependence on age and cell state.

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DNA damage bypass operates in the S and G2 phases of the cell cycle and exhibits differential mutagenicity

Cited by 92 publications

References 48 publications

Cell cycle specific distribution of killin: evidence for negative regulation of both DNA and RNA synthesis

Cell cycle specific distribution of killin: evidence for negative regulation of both DNA and RNA synthesis

Genomic assay reveals tolerance of DNA damage by both translesion DNA synthesis and homology-dependent repair in mammalian cells

Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq

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