title: Repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome.
abstract: We used the I-SceI endonuclease to produce DNA double-strand breaks (DSBs) and observed that a fraction of these DSBs were repaired by insertion of sequences, which we termed "templated sequence insertions" (TSIs), derived from distant regions of the genome. These TSIs were derived from genic, retrotransposon, or telomere sequences and were not deleted from the donor site in the genome, leading to the hypothesis that they were derived from reverse-transcribed RNA. Cotransfection of RNA and an I-SceI expression vector demonstrated insertion of RNA-derived sequences at the DNA-DSB site, and TSIs were suppressed by reverse-transcriptase inhibitors. Both observations support the hypothesis that TSIs were derived from RNA templates. In addition, similar insertions were detected at sites of DNA DSBs induced by transcription activator-like effector nuclease proteins. Whole-genome sequencing of myeloma cell lines revealed additional TSIs, demonstrating that repair of DNA DSBs via insertion was not restricted to experimentally produced DNA DSBs. Analysis of publicly available databases revealed that many of these TSIs are polymorphic in the human genome. Taken together, these results indicate that insertional events should be considered as alternatives to gross chromosomal rearrangements in the interpretation of whole-genome sequence data and that this mutagenic form of DNA repair may play a role in genetic disease, exon shuffling, and mammalian evolution.
authors.affiliation: Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Onozawa
authors.affiliation: Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and.
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and.
authors.forename: Yoo Jung
authors.initials: YJ
authors.lastname: Kim
authors.affiliation: Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and.
authors.forename: Liat
authors.initials: L
authors.lastname: Goldberg
authors.affiliation: Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and.
authors.forename: Tamas
authors.initials: T
authors.lastname: Varga
authors.affiliation: Comprehensive Cancer Center, Mayo Clinic, Scottsdale, AZ 85259.
authors.forename: P Leif
authors.initials: PL
authors.lastname: Bergsagel
authors.affiliation: Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and.
authors.forename: W Michael
authors.initials: WM
authors.lastname: Kuehl
authors.affiliation: Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and aplanp@mail.nih.gov.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Aplan
mesh_terms: D045744:Cell Line, Tumor; D002934:Cinnamates; D019295:Computational Biology; D053903:DNA Breaks, Double-Stranded; D056915:DNA Copy Number Variations; D017931:DNA Primers / Q000235:genetics; D004260:DNA Repair / Q000235:genetics*; D005822:Genetic Vectors / Q000235:genetics; D006801:Humans; D006921:Hygromycin B / Q000031:analogs & derivatives; D016254:Mutagenesis, Insertional / Q000235:genetics*; D016133:Polymerase Chain Reaction; D018626:Retroelements / Q000235:genetics*; D016615:Telomere / Q000235:genetics*
chemical_list: D002934:Cinnamates; D017931:DNA Primers; D018626:Retroelements; D006921:Hygromycin B; C026273:hygromycin A
keywords: DNA patch; LINE-1; TSIP; polymorphism