• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Nov 15, 1997; 25(22): 4650–4657.
PMCID: PMC147090

Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions.


Double strand DNA breaks in plants are primarily repaired via non-homologous end joining. However, little is known about the molecular events underlying this process. We have studied non-homologous end joining of linearized plasmid DNA with different termini configurations following transformation into tobacco cells. A variety of sequences were found at novel end junctions. Joining with no sequence alterations was rare. In most cases, deletions were found at both ends, and rejoining usually occurred at short repeats. A distinct feature of plant junctions was the presence of relatively large, up to 1.2 kb long, insertions (filler DNA), in approximately 30% of the analyzed clones. The filler DNA originated either from internal regions of the plasmid or from tobacco genomic DNA. Some insertions had a complex structure consisting of several reshuffled plasmid-related regions. These data suggest that double strand break repair in plants involves extensive end degradation, DNA synthesis following invasion of ectopic templates and multiple template switches. Such a mechanism is reminiscent of the synthesis-dependent recombination in bacteriophage T4. It can also explain the frequent 'DNA scrambling' associated with illegitimate recombination in plants.

Full Text

The Full Text of this article is available as a PDF (394K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Stringer JR. DNA sequence homology and chromosomal deletion at a site of SV40 DNA integration. Nature. 1982 Mar 25;296(5855):363–366. [PubMed]
  • Shirley BW, Hanley S, Goodman HM. Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations. Plant Cell. 1992 Mar;4(3):333–347. [PMC free article] [PubMed]
  • Thacker J, Chalk J, Ganesh A, North P. A mechanism for deletion formation in DNA by human cell extracts: the involvement of short sequence repeats. Nucleic Acids Res. 1992 Dec 11;20(23):6183–6188. [PMC free article] [PubMed]
  • Roth DB, Porter TN, Wilson JH. Mechanisms of nonhomologous recombination in mammalian cells. Mol Cell Biol. 1985 Oct;5(10):2599–2607. [PMC free article] [PubMed]
  • Roth DB, Wilson JH. Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. Mol Cell Biol. 1986 Dec;6(12):4295–4304. [PMC free article] [PubMed]
  • Ruley HE, Fried M. Clustered illegitimate recombination events in mammalian cells involving very short sequence homologies. Nature. 1983 Jul 14;304(5922):181–184. [PubMed]
  • Goedecke W, Vielmetter W, Pfeiffer P. Activation of a system for the joining of nonhomologous DNA ends during Xenopus egg maturation. Mol Cell Biol. 1992 Feb;12(2):811–816. [PMC free article] [PubMed]
  • Goedecke W, Pfeiffer P, Vielmetter W. Nonhomologous DNA end joining in Schizosaccharomyces pombe efficiently eliminates DNA double-strand-breaks from haploid sequences. Nucleic Acids Res. 1994 Jun 11;22(11):2094–2101. [PMC free article] [PubMed]
  • Lehman CW, Clemens M, Worthylake DK, Trautman JK, Carroll D. Homologous and illegitimate recombination in developing Xenopus oocytes and eggs. Mol Cell Biol. 1993 Nov;13(11):6897–6906. [PMC free article] [PubMed]
  • Munz PL, Young CS. End-joining of DNA fragments in adenovirus transfection of human cells. Virology. 1991 Jul;183(1):160–169. [PubMed]
  • North P, Ganesh A, Thacker J. The rejoining of double-strand breaks in DNA by human cell extracts. Nucleic Acids Res. 1990 Nov 11;18(21):6205–6210. [PMC free article] [PubMed]
  • Pfeiffer P, Thode S, Hancke J, Vielmetter W. Mechanisms of overlap formation in nonhomologous DNA end joining. Mol Cell Biol. 1994 Feb;14(2):888–895. [PMC free article] [PubMed]
  • Pfeiffer P, Vielmetter W. Joining of nonhomologous DNA double strand breaks in vitro. Nucleic Acids Res. 1988 Feb 11;16(3):907–924. [PMC free article] [PubMed]
  • Thode S, Schäfer A, Pfeiffer P, Vielmetter W. A novel pathway of DNA end-to-end joining. Cell. 1990 Mar 23;60(6):921–928. [PubMed]
  • Winegar RA, Lutze LH, Rufer JT, Morgan WF. Spectrum of mutations produced by specific types of restriction enzyme-induced double-strand breaks. Mutagenesis. 1992 Nov;7(6):439–445. [PubMed]
  • Boulton SJ, Jackson SP. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J. 1996 Sep 16;15(18):5093–5103. [PMC free article] [PubMed]
  • Boulton SJ, Jackson SP. Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance. Nucleic Acids Res. 1996 Dec 1;24(23):4639–4648. [PMC free article] [PubMed]
  • Milne GT, Jin S, Shannon KB, Weaver DT. Mutations in two Ku homologs define a DNA end-joining repair pathway in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Aug;16(8):4189–4198. [PMC free article] [PubMed]
  • Weaver DT. What to do at an end: DNA double-strand-break repair. Trends Genet. 1995 Oct;11(10):388–392. [PubMed]
  • Teo SH, Jackson SP. Identification of Saccharomyces cerevisiae DNA ligase IV: involvement in DNA double-strand break repair. EMBO J. 1997 Aug 1;16(15):4788–4795. [PMC free article] [PubMed]
  • Landau NR, Schatz DG, Rosa M, Baltimore D. Increased frequency of N-region insertion in a murine pre-B-cell line infected with a terminal deoxynucleotidyl transferase retroviral expression vector. Mol Cell Biol. 1987 Sep;7(9):3237–3243. [PMC free article] [PubMed]
  • Concannon P, Pickering LA, Kung P, Hood L. Diversity and structure of human T-cell receptor beta-chain variable region genes. Proc Natl Acad Sci U S A. 1986 Sep;83(17):6598–6602. [PMC free article] [PubMed]
  • Alt FW, Baltimore D. Joining of immunoglobulin heavy chain gene segments: implications from a chromosome with evidence of three D-JH fusions. Proc Natl Acad Sci U S A. 1982 Jul;79(13):4118–4122. [PMC free article] [PubMed]
  • Roth DB, Chang XB, Wilson JH. Comparison of filler DNA at immune, nonimmune, and oncogenic rearrangements suggests multiple mechanisms of formation. Mol Cell Biol. 1989 Jul;9(7):3049–3057. [PMC free article] [PubMed]
  • Merrihew RV, Marburger K, Pennington SL, Roth DB, Wilson JH. High-frequency illegitimate integration of transfected DNA at preintegrated target sites in a mammalian genome. Mol Cell Biol. 1996 Jan;16(1):10–18. [PMC free article] [PubMed]
  • Anderson RA, Kato S, Camerini-Otero RD. A pattern of partially homologous recombination in mouse L cells. Proc Natl Acad Sci U S A. 1984 Jan;81(1):206–210. [PMC free article] [PubMed]
  • Nassif N, Penney J, Pal S, Engels WR, Gloor GB. Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair. Mol Cell Biol. 1994 Mar;14(3):1613–1625. [PMC free article] [PubMed]
  • Moore JK, Haber JE. Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature. 1996 Oct 17;383(6601):644–646. [PubMed]
  • Teng SC, Kim B, Gabriel A. Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature. 1996 Oct 17;383(6601):641–644. [PubMed]
  • Puchta H, Dujon B, Hohn B. Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc Natl Acad Sci U S A. 1996 May 14;93(10):5055–5060. [PMC free article] [PubMed]
  • Puchta H, Dujon B, Hohn B. Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease. Nucleic Acids Res. 1993 Nov 11;21(22):5034–5040. [PMC free article] [PubMed]
  • Shalev G, Levy AA. The maize transposable element Ac induces recombination between the donor site and an homologous ectopic sequence. Genetics. 1997 Jul;146(3):1143–1151. [PMC free article] [PubMed]
  • Chiurazzi M, Ray A, Viret JF, Perera R, Wang XH, Lloyd AM, Signer ER. Enhancement of somatic intrachromosomal homologous recombination in Arabidopsis by the HO endonuclease. Plant Cell. 1996 Nov;8(11):2057–2066. [PMC free article] [PubMed]
  • Baran G, Echt C, Bureau T, Wessler S. Molecular analysis of the maize wx-B3 allele indicates that precise excision of the transposable Ac element is rare. Genetics. 1992 Feb;130(2):377–384. [PMC free article] [PubMed]
  • Scott L, LaFoe D, Weil CF. Adjacent sequences influence DNA repair accompanying transposon excision in maize. Genetics. 1996 Jan;142(1):237–246. [PMC free article] [PubMed]
  • Saedler H, Nevers P. Transposition in plants: a molecular model. EMBO J. 1985 Mar;4(3):585–590. [PMC free article] [PubMed]
  • Wessler S, Tarpley A, Purugganan M, Spell M, Okagaki R. Filler DNA is associated with spontaneous deletions in maize. Proc Natl Acad Sci U S A. 1990 Nov;87(22):8731–8735. [PMC free article] [PubMed]
  • Ralston EJ, English JJ, Dooner HK. Sequence of three bronze alleles of maize and correlation with the genetic fine structure. Genetics. 1988 May;119(1):185–197. [PMC free article] [PubMed]
  • Gheysen G, Villarroel R, Van Montagu M. Illegitimate recombination in plants: a model for T-DNA integration. Genes Dev. 1991 Feb;5(2):287–297. [PubMed]
  • Feinberg AP, Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. [PubMed]
  • Lehman CW, Trautman JK, Carroll D. Illegitimate recombination in Xenopus: characterization of end-joined junctions. Nucleic Acids Res. 1994 Feb 11;22(3):434–442. [PMC free article] [PubMed]
  • Lehman CW, Carroll D. Homologous recombination catalyzed by a nuclear extract from Xenopus oocytes. Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10840–10844. [PMC free article] [PubMed]
  • Anderson OD, Litts JC, Gautier MF, Greene FC. Nucleic acid sequence and chromosome assignment of a wheat storage protein gene. Nucleic Acids Res. 1984 Nov 12;12(21):8129–8144. [PMC free article] [PubMed]
  • Goldberg SZ, Kuebbing D, Trauber D, Schafer MP, Lewis SE, Popp RA, Anderson WF. A 66-base pair insert bridges the deletion responsible for a mouse model of beta-thalassemia. J Biol Chem. 1986 Sep 15;261(26):12368–12374. [PubMed]
  • Doseff A, Martienssen R, Sundaresan V. Somatic excision of the Mu1 transposable element of maize. Nucleic Acids Res. 1991 Feb 11;19(3):579–584. [PMC free article] [PubMed]
  • Nicholls RD, Fischel-Ghodsian N, Higgs DR. Recombination at the human alpha-globin gene cluster: sequence features and topological constraints. Cell. 1987 May 8;49(3):369–378. [PubMed]
  • Pulak RA, Anderson P. Structures of spontaneous deletions in Caenorhabditis elegans. Mol Cell Biol. 1988 Sep;8(9):3748–3754. [PMC free article] [PubMed]
  • Spritz RA, Orkin SH. Duplication followed by deletion accounts for the structure of an Indian deletion beta (0)-thalassemia gene. Nucleic Acids Res. 1982 Dec 20;10(24):8025–8029. [PMC free article] [PubMed]
  • Formosa T, Alberts BM. DNA synthesis dependent on genetic recombination: characterization of a reaction catalyzed by purified bacteriophage T4 proteins. Cell. 1986 Dec 5;47(5):793–806. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • MedGen
    Related information in MedGen
  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...