A Mechanism of Gene Amplification Driven by Small DNA Fragments

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DNA amplification is a molecular process that increases the copy number of a chromosomal tract and often causes elevated expression of the amplified gene(s). Although gene amplification is frequently observed in cancer and other degenerative disorders, the molecular mechanisms involved in the process of DNA copy number increase remain largely unknown. We hypothesized that small DNA fragments could be the trigger of DNA amplification events. Following our findings that small fragments of DNA in the form of DNA oligonucleotides can be highly recombinogenic, we have developed a system in the yeast Saccharomyces cerevisiae to capture events of chromosomal DNA amplification initiated by small DNA fragments. Here we demonstrate that small DNAs can amplify a chromosomal region, generating either tandem duplications or acentric extrachromosomal DNA circles. Small fragment-driven DNA amplification (SFDA) occurs with a frequency that increases with the length of homology between the small DNAs and the target chromosomal regions. SFDA events are triggered even by small single-stranded molecules with as little as 20-nt homology with the genomic target. A double-strand break (DSB) external to the chromosomal amplicon region stimulates the amplification event up to a factor of 20 and favors formation of extrachromosomal circles. SFDA is dependent on Rad52 and Rad59, partially dependent on Rad1, Rad10, and Pol32, and independent of Rad51, suggesting a single-strand annealing mechanism. Our results reveal a novel molecular model for gene amplification, in which small DNA fragments drive DNA amplification and define the boundaries of the amplicon region. As DNA fragments are frequently found both inside cells and in the extracellular environment, such as the serum of patients with cancer or other degenerative disorders, we propose that SFDA may be a common mechanism for DNA amplification in cancer cells, as well as a more general cause of DNA copy number variation in nature.

Vyšlo v časopise: A Mechanism of Gene Amplification Driven by Small DNA Fragments. PLoS Genet 8(12): e32767. doi:10.1371/journal.pgen.1003119
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003119

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Zdroje

1. AlbertsonDG (2006) Gene amplification in cancer. Trends Genet 22: 447–455.

2. SzerlipNJ, PedrazaA, ChakravartyD, AzimM, McGuireJ, et al. (2012) Intratumoral heterogeneity of receptor tyrosine kinases EGFR and PDGFRA amplification in glioblastoma defines subpopulations with distinct growth factor response. Proc Natl Acad Sci U S A 109: 3041–3046.

3. AlbertsonDG, CollinsC, McCormickF, GrayJW (2003) Chromosome aberrations in solid tumors. Nat Genet 34: 369–376.

4. SchimkeRT (1984) Gene amplification, drug resistance, and cancer. Cancer Res 44: 1735–1742.

5. HattingerCM, StoicoG, MichelacciF, PaselloM, SciontiI, et al. (2009) Mechanisms of gene amplification and evidence of coamplification in drug-resistant human osteosarcoma cell lines. Genes Chromosomes Cancer 48: 289–309.

6. GonzalezE, KulkarniH, BolivarH, ManganoA, SanchezR, et al. (2005) The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307: 1434–1440.

7. TomitaT, KonoY, ShimadaT (1996) Chromosomal localization of amplified esterase genes in insecticide resistant Culex mosquitoes. Insect Biochem Mol Biol 26: 853–857.

8. IafrateAJ, FeukL, RiveraMN, ListewnikML, DonahoePK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949–951.

9. KiddJM, CooperGM, DonahueWF, HaydenHS, SampasN, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56–64.

10. BruderCE, PiotrowskiA, GijsbersAA, AnderssonR, EricksonS, et al. (2008) Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet 82: 763–771.

11. PiotrowskiA, BruderCE, AnderssonR, Diaz de StahlT, MenzelU, et al. (2008) Somatic mosaicism for copy number variation in differentiated human tissues. Hum Mutat 29: 1118–1124.

12. HastingsPJ, IraG, LupskiJR (2009) A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5: e1000327 doi:10.1371/journal.pgen.1000327.

13. GazaveE, DarreF, Morcillo-SuarezC, Petit-MartyN, CarrenoA, et al. (2011) Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Res 21: 1626–1639.

14. Marques-BonetT, KiddJM, VenturaM, GravesTA, ChengZ, et al. (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457: 877–881.

15. StarkGR (1993) Regulation and mechanisms of mammalian gene amplification. Adv Cancer Res 61: 87–113.

16. StorlazziCT, LonoceA, GuastadisegniMC, TrombettaD, D'AddabboP, et al. (2010) Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure. Genome Res 20: 1198–1206.

17. Von HoffDD, ForsethB, ClareCN, HansenKL, VanDevanterD (1990) Double minutes arise from circular extrachromosomal DNA intermediates which integrate into chromosomal sites in human HL-60 leukemia cells. J Clin Invest 85: 1887–1895.

18. MondelloC, SmirnovaA, GiulottoE (2010) Gene amplification, radiation sensitivity and DNA double-strand breaks. Mutat Res 704: 29–37.

19. CoquelleA, RozierL, DutrillauxB, DebatisseM (2002) Induction of multiple double-strand breaks within an hsr by meganucleaseI-SceI expression or fragile site activation leads to formation of double minutes and other chromosomal rearrangements. Oncogene 21: 7671–7679.

20. PipirasE, CoquelleA, BiethA, DebatisseM (1998) Interstitial deletions and intrachromosomal amplification initiated from a double-strand break targeted to a mammalian chromosome. EMBO J 17: 325–333.

21. SelvarajahS, YoshimotoM, ParkPC, MaireG, PaderovaJ, et al. (2006) The breakage-fusion-bridge (BFB) cycle as a mechanism for generating genetic heterogeneity in osteosarcoma. Chromosoma 115: 459–467.

22. McClintockB (1941) The Stability of Broken Ends of Chromosomes in Zea Mays. Genetics 26: 234–282.

23. TanakaH, BergstromDA, YaoMC, TapscottSJ (2005) Widespread and nonrandom distribution of DNA palindromes in cancer cells provides a structural platform for subsequent gene amplification. Nat Genet 37: 320–327.

24. FriedM, FeoS, HeardE (1991) The role of inverted duplication in the generation of gene amplification in mammalian cells. Biochim Biophys Acta 1090: 143–155.

25. ZhouZH, AkgunE, JasinM (2001) Repeat expansion by homologous recombination in the mouse germ line at palindromic sequences. Proc Natl Acad Sci U S A 98: 8326–8333.

26. LobachevKS, GordeninDA, ResnickMA (2002) The Mre11 complex is required for repair of hairpin-capped double-strand breaks and prevention of chromosome rearrangements. Cell 108: 183–193.

27. NarayananV, MieczkowskiPA, KimHM, PetesTD, LobachevKS (2006) The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks. Cell 125: 1283–1296.

28. HastingsPJ, LupskiJR, RosenbergSM, IraG (2009) Mechanisms of change in gene copy number. Nat Rev Genet 10: 551–564.

29. PaquesF, HaberJE (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 63: 349–404.

30. LeeJA, CarvalhoCM, LupskiJR (2007) A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131: 1235–1247.

31. ZhangF, KhajaviM, ConnollyAM, TowneCF, BatishSD, et al. (2009) The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat Genet 41: 849–853.

32. VogtN, LefevreSH, ApiouF, DutrillauxAM, CorA, et al. (2004) Molecular structure of double-minute chromosomes bearing amplified copies of the epidermal growth factor receptor gene in gliomas. Proc Natl Acad Sci U S A 101: 11368–11373.

33. AldosariN, BignerSH, BurgerPC, BeckerL, KepnerJL, et al. (2002) MYCC and MYCN oncogene amplification in medulloblastoma. A fluorescence in situ hybridization study on paraffin sections from the Children's Oncology Group. Arch Pathol Lab Med 126: 540–544.

34. TraskBJ, HamlinJL (1989) Early dihydrofolate reductase gene amplification events in CHO cells usually occur on the same chromosome arm as the original locus. Genes Dev 3: 1913–1925.

35. StoriciF, DurhamCL, GordeninDA, ResnickMA (2003) Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast. Proc Natl Acad Sci U S A 100: 14994–14999.

36. StoriciF, ResnickMA (2003) Delitto perfetto targeted mutagenesis in yeast with oligonucleotides. Genet Eng (N Y) 25: 189–207.

37. StuckeyS, MukherjeeK, StoriciF (2011) In vivo site-specific mutagenesis and gene collage using the delitto perfetto system in yeast Saccharomyces cerevisiae. Methods Mol Biol 745: 173–191.

38. Orr-WeaverTL, SzostakJW (1983) Yeast recombination: the association between double-strand gap repair and crossing-over. Proc Natl Acad Sci U S A 80: 4417–4421.

39. StoriciF, SnipeJR, ChanGK, GordeninDA, ResnickMA (2006) Conservative repair of a chromosomal double-strand break by single-strand DNA through two steps of annealing. Mol Cell Biol 26: 7645–7657.

40. SymingtonLS (2002) Role of RAD52 epistasis group genes in homologous recombination and double-strand break repair. Microbiol Mol Biol Rev 66: 630–670.

41. DaleyJM, PalmbosPL, WuD, WilsonTE (2005) Nonhomologous end joining in yeast. Annu Rev Genet 39: 431–451.

42. LydeardJR, JainS, YamaguchiM, HaberJE (2007) Break-induced replication and telomerase-independent telomere maintenance require Pol32. Nature 448: 820–823.

43. PrakashR, SatoryD, DrayE, PapushaA, SchellerJ, et al. (2009) Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination. Genes Dev 23: 67–79.

44. BartschS, KangLE, SymingtonLS (2000) RAD51 is required for the repair of plasmid double-stranded DNA gaps from either plasmid or chromosomal templates. Mol Cell Biol 20: 1194–1205.

45. HubscherU, NasheuerHP, SyvaojaJE (2000) Eukaryotic DNA polymerases, a growing family. Trends Biochem Sci 25: 143–147.

46. IraG, MalkovaA, LiberiG, FoianiM, HaberJE (2003) Srs2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast. Cell 115: 401–411.

47. MyungK, DattaA, ChenC, KolodnerRD (2001) SGS1, the Saccharomyces cerevisiae homologue of BLM and WRN, suppresses genome instability and homeologous recombination. Nat Genet 27: 113–116.

48. OnodaF, SekiM, MiyajimaA, EnomotoT (2000) Elevation of sister chromatid exchange in Saccharomyces cerevisiae sgs1 disruptants and the relevance of the disruptants as a system to evaluate mutations in Bloom's syndrome gene. Mutat Res 459: 203–209.

49. ZhuZ, ChungWH, ShimEY, LeeSE, IraG (2008) Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134: 981–994.

50. ToledoF, ButtinG, DebatisseM (1993) The origin of chromosome rearrangements at early stages of AMPD2 gene amplification in Chinese hamster cells. Curr Biol 3: 255–264.

51. AmlerLC, SchwabM (1989) Amplified N-myc in human neuroblastoma cells is often arranged as clustered tandem repeats of differently recombined DNA. Mol Cell Biol 9: 4903–4913.

52. JonesDT, KocialkowskiS, LiuL, PearsonDM, BacklundLM, et al. (2008) Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Cancer Res 68: 8673–8677.

53. BaseckeJ, WhelanJT, GriesingerF, BertrandFE (2006) The MLL partial tandem duplication in acute myeloid leukaemia. Br J Haematol 135: 438–449.

54. StephensPJ, McBrideDJ, LinML, VarelaI, PleasanceED, et al. (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462: 1005–1010.

55. McBrideDJ, EtemadmoghadamD, CookeSL, AlsopK, GeorgeJ, et al. (2012) Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes. J Pathol 227: 446–455.

56. NgCK, CookeSL, HoweK, NewmanS, XianJ, et al. (2012) The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer. J Pathol 226: 703–712.

57. BurgersPM (2009) Polymerase dynamics at the eukaryotic DNA replication fork. J Biol Chem 284: 4041–4045.

58. SymingtonLS, GautierJ (2011) Double-strand break end resection and repair pathway choice. Annu Rev Genet 45: 247–271.

59. MooreJK, HaberJE (1996) Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature 383: 644–646.

60. ShibataY, KumarP, LayerR, WillcoxS, GaganJR, et al. (2012) Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science 336: 82–86.

61. LehmannMJ, SczakielG (2005) Spontaneous uptake of biologically active recombinant DNA by mammalian cells via a selected DNA segment. Gene Ther 12: 446–451.

62. VlassovVV, LaktionovPP, RykovaEY (2007) Extracellular nucleic acids. Bioessays 29: 654–667.

63. NagataS (2000) Apoptotic DNA fragmentation. Exp Cell Res 256: 12–18.

64. HemmiH, TakeuchiO, KawaiT, KaishoT, SatoS, et al. (2000) A Toll-like receptor recognizes bacterial DNA. Nature 408: 740–745.

65. HolmgrenL, SzelesA, RajnavolgyiE, FolkmanJ, KleinG, et al. (1999) Horizontal transfer of DNA by the uptake of apoptotic bodies. Blood 93: 3956–3963.

66. MorozkinES, LaktionovPP, RykovaEY, VlassovVV (2004) Extracellular nucleic acids in cultures of long-term cultivated eukaryotic cells. Ann N Y Acad Sci 1022: 244–249.

67. TsangJC, LoYM (2007) Circulating nucleic acids in plasma/serum. Pathology 39: 197–207.

68. JahrS, HentzeH, EnglischS, HardtD, FackelmayerFO, et al. (2001) DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res 61: 1659–1665.

69. LeonSA, ShapiroB, SklaroffDM, YarosMJ (1977) Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res 37: 646–650.

70. TongYK, LoYM (2006) Diagnostic developments involving cell-free (circulating) nucleic acids. Clin Chim Acta 363: 187–196.

71. SpetzAL, PattersonBK, LoreK, AnderssonJ, HolmgrenL (1999) Functional gene transfer of HIV DNA by an HIV receptor-independent mechanism. J Immunol 163: 736–742.

72. Garcia-OlmoD, Garcia-OlmoDC, Dominguez-BerzosaC, GuadalajaraH, VegaL, et al. (2012) Oncogenic transformation induced by cell-free nucleic acids circulating in plasma (genometastasis) remains after the surgical resection of the primary tumor: a pilot study. Expert Opin Biol Ther 12: S61–S68.

73. BergsmedhA, SzelesA, HenrikssonM, BrattA, FolkmanMJ, et al. (2001) Horizontal transfer of oncogenes by uptake of apoptotic bodies. Proc Natl Acad Sci U S A 98: 6407–6411.

74. ShenY, NandiP, TaylorMB, StuckeyS, BhadsavleHP, et al. (2011) RNA-driven genetic changes in bacteria and in human cells. Mutat Res 717: 91–98.

75. StoriciF, BebenekK, KunkelTA, GordeninDA, ResnickMA (2007) RNA-templated DNA repair. Nature 447: 338–341.

76. YangY, SterlingJ, StoriciF, ResnickMA, GordeninDA (2008) Hypermutability of damaged single-strand DNA formed at double-strand breaks and uncapped telomeres in yeast Saccharomyces cerevisiae. PLoS Genet 4: e1000264 doi:10.1371/journal.pgen.1000264.

77. KozeretskaIA, DemydovSV, OstapchenkoLI (2011) Mobile genetic elements and cancer. From mutations to gene therapy. Exp Oncol 33: 198–205.

78. TanakaH, CaoY, BergstromDA, KooperbergC, TapscottSJ, et al. (2007) Intrastrand annealing leads to the formation of a large DNA palindrome and determines the boundaries of genomic amplification in human cancer. Mol Cell Biol 27: 1993–2002.

79. RoseMD, NovickP, ThomasJH, BotsteinD, FinkGR (1987) A Saccharomyces cerevisiae genomic plasmid bank based on a centromere-containing shuttle vector. Gene 60: 237–243.

80. Sokal RR, Rohlf FJ (1981) Biometry: The Principles and Practice of Statistics in Biological Research. 2nd ed W H Freeman and Company, San Francisco.

81. Sherman F, Fink GR, Hicks JB (1986) Methods in Yeast Genetics. Cold Spring Harbor NY: Cold Spring Harbor Laboratory Press.