Gene repair in mammalian cells is stimulated by the elongation of S phase and transient stalling of replication forks

Brachman, Erin E.; Kmiec, Eric B.

doi:10.1016/j.dnarep.2004.11.007

Cited by 66 publications

(76 citation statements)

References 53 publications

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“…The finding that DNA replication has a crucial role in the coordination of the targeting reaction in bacteria, 20,21 yeast 23,24 and various mammalian cell lines including ESCs, 16,25,26 has been a major breakthrough. However, ssODN-mediated gene targeting may also occur through other mechanisms.…”

Section: Discussionmentioning

confidence: 99%

“…19 Over the past few years, it has become evident that DNA replication is the predominant cellular process underlying ssODN-mediated gene targeting in bacteria, [20][21][22] yeast 23,24 and various mammalian cell lines including ESCs. 16,25,26 According to this model, the ssODN anneals to its chromosomal complement when this becomes exposed as singlestranded DNA within the context of a replication fork. Upon annealing, the ssODN can serve as a primer for DNA synthesis to form a 'pseudo' Okazaki fragment, resulting in physical incorporation of the ssODN into the nascent DNA strand.…”

Section: Mechanistic Models For Ssodn-mediated Gene Targetingmentioning

confidence: 99%

“…Increasing the number of cells that progressed through S phase or slowing down replication fork progression during ssODN exposure resulted in elevated targeting frequencies in various mammalian cell lines. [25][26][27] The discontinuous nature of lagging strand DNA synthesis may expose more ssDNA regions and thus facilitate ssODN annealing. Indeed, studies in E. coli demonstrated that ssODNs corresponding in sequence to the lagging strand consistently performed better, irrespective of the direction of transcription, thereby establishing a direct link between ssODN polarity and the direction of replication through the target locus.…”

Section: Mechanistic Models For Ssodn-mediated Gene Targetingmentioning

confidence: 99%

See 2 more Smart Citations

Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application

Aarts

Riele

2010

Gene Ther

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Gene targeting by single-stranded oligodeoxyribonucleotides (ssODNs) is a promising technique for introducing site-specific sequence alterations without affecting the genomic organization of the target locus. Here, we discuss the significant progress that has been made over the last 5 years in unraveling the mechanisms and reaction parameters underlying ssODN-mediated gene targeting. We will specifically focus on ssODN-mediated gene targeting in murine embryonic stem cells (ESCs) and the impact of the DNA mismatch repair (MMR) system on the targeting process. Implications of novel findings for routine application of ssODN-mediated gene targeting and challenges that need to be overcome for future therapeutic applications are highlighted.

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Section: Discussionmentioning

confidence: 99%

Section: Mechanistic Models For Ssodn-mediated Gene Targetingmentioning

confidence: 99%

Section: Mechanistic Models For Ssodn-mediated Gene Targetingmentioning

confidence: 99%

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Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application

Aarts

Riele

2010

Gene Ther

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“…Clearly, the level of transcriptional activity 34 and/or the movement of DNA replication forks 35,36 could influence the route taken by the oligonucleotide. One pathway (Figure 1a) involves a direct nucleotide exchange reaction that could be catalyzed by mismatch repair or nucleotide excision repair activities.…”

Section: Prospects: Regulatory Pathways Will Guide Experimental Desigmentioning

confidence: 99%

Gene therapy progress and prospects: targeted gene repair

et al. 2005

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The capacity to correct a mutant gene within the context of the chromosome holds great promise as a therapy for inherited disorders but fulfilling this promise has proven to be challenging. However, steady progress is being made and the development of gene repair as a viable and robust approach is underway. Here, we present some of the recent advances that are helping to shape our thinking about the feasibility and the limitations of this technique. For the most part, these advances center on understanding the regulation of the reaction and validating its application in animal models. Gene Therapy (2005) 12, 639-646.

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“…11,12 Furthermore, the efficacy could be improved by slowing down progression of replication forks again suggesting that also in mammalian cells at least one mechanism of oligonucleotide-mediated gene modification involves replication of DNA. 13,14 We have previously identified another parameter affecting the frequency of oligonucleotide-mediated gene modification: DNA mismatch repair (MMR). We found that single-stranded synthetic oligonucleotide sequences consisting of 20-60 non-chemically modified deoxyribonucleotides can be used to site-specifically delete, insert or substitute one or a few base pairs in the genome of murine ES cells.…”

Section: Introductionmentioning

confidence: 99%

Effective oligonucleotide-mediated gene disruption in ES cells lacking the mismatch repair protein MSH3

et al. 2006

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We have previously demonstrated that site-specific insertion, deletion or substitution of one or two nucleotides in mouse embryonic stem cells (ES cells) by single-stranded deoxyribo-oligonucleotides is several hundred-fold suppressed by DNA mismatch repair (MMR) activity. Here, we have investigated whether compound mismatches and larger insertions escape detection by the MMR machinery and can be effectively introduced in MMR-proficient cells. We identified several compound mismatches that escaped detection by the MMR machinery to some extent, but could not define general rules predicting the efficacy of complex base-pair substitutions. In contrast, we found that fournucleotide insertions were largely subject to suppression by the MSH2/MSH3 branch of MMR and could be effectively introduced in Msh3-deficient cells. As these cells have no overt mutator phenotype and Msh3-deficient mice do not develop cancer, Msh3-deficient ES cells can be used for oligonucleotide-mediated gene disruption. As an example, we present disruption of the Fanconi anemia gene Fancf. Gene Therapy (2006) 13, 686-694.

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Gene repair in mammalian cells is stimulated by the elongation of S phase and transient stalling of replication forks

Cited by 66 publications

References 53 publications

Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application

Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application

Gene therapy progress and prospects: targeted gene repair

Effective oligonucleotide-mediated gene disruption in ES cells lacking the mismatch repair protein MSH3

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