Origin-Dependent Inverted-Repeat Amplification: A Replication-Based Model for Generating Palindromic Amplicons

1. HuangTCampbellJL 1995 Amplification of a circular episome carrying an inverted repeat of the DFR1 locus and adjacent autonomously replicating sequence element of Saccharomyces cerevisiae. J Biol Chem 270 9607 9614

2. MaCLooneyJELeuTHHamlinJL 1988 Organization and genesis of dihydrofolate reductase amplicons in the genome of a methotrexate-resistant Chinese hamster ovary cell line. Mol Cell Biol 8 2316 2327

3. GreshamDDesaiMMTuckerCMJenqHTPaiDA 2008 The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet 4 e1000303

4. HastingsPJLupskiJRRosenbergSMIraG 2009 Mechanisms of change in gene copy number. Nat Rev Genet 10 551 564

5. VialardFMignon-RavixCParainDDepetrisDPortnoiMF 2003 Mechanism of intrachromosomal triplications 15q11-q13: a new clinical report. Am J Med Genet A 118A 229 234

6. WangJReddyKSWangEHaldermanLMorganBL 1999 Intrachromosomal triplication of 2q11.2-q21 in a severely malformed infant: case report and review of triplications and their possible mechanism. Am J Med Genet 82 312 317

7. ArayaCLPayenCDunhamMJFieldsS 2010 Whole-genome sequencing of a laboratory-evolved yeast strain. BMC Genomics 11 88

8. DevriendtKMatthijsGHolvoetMSchoenmakersEFrynsJP 1999 Triplication of distal chromosome 10q. J Med Genet 36 242 245

9. EckelHWimmerRVollethMJakubiczkaSMuschkeP 2006 Intrachromosomal triplication 12p11.22-p12.3 and gonadal mosaicism of partial tetrasomy 12p. Am J Med Genet A 140 1219 1222

10. OunapKIlusTBartschO 2005 A girl with inverted triplication of chromosome 3q25.3→q29 and multiple congenital anomalies consistent with 3q duplication syndrome. Am J Med Genet A 134 434 438

11. ReddyKSLoganJJ 2000 Intrachromosomal triplications: molecular cytogenetic and clinical studies. Clin Genet 58 134 141

12. RiveraHBobadillaLRolonAKunzJCrollaJA 1998 Intrachromosomal triplication of distal 7p. J Med Genet 35 78 80

13. VerheijJBBoumanKvan LingenRAvan Lookeren CampagneJGLeegteB 1999 Tetrasomy 9p due to an intrachromosomal triplication of 9p13-p22. Am J Med Genet 86 168 173

14. UngaroPChristianSLFantesJAMutiranguraABlackS 2001 Molecular characterisation of four cases of intrachromosomal triplication of chromosome 15q11-q14. J Med Genet 38 26 34

15. MercerCLBrowneCEBarberJCMaloneyVKHuangS 2009 A complex medical phenotype in a patient with triplication of 2q12.3 to 2q13 characterized with oligonucleotide array CGH. Cytogenet Genome Res 124 179 186

16. HarrisonKJTeshimaIESilverMMJayVUngerS 1998 Partial tetrasomy with triplication of chromosome (5) (p14-p15.33) in a patient with severe multiple congenital anomalies. Am J Med Genet 79 103 107

17. McClintockB 1941 The Stability of Broken Ends of Chromosomes in Zea mays. Genetics 26 234 282

18. PayenCKoszulRDujonBFischerG 2008 Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms. PLoS Genet 4 e1000175

19. ChauvinAChenJMQuemenerSMassonEKehrer-SawatzkiH 2009 Elucidation of the complex structure and origin of the human trypsinogen locus triplication. Hum Mol Genet 18 3605 3614

20. ChenJMChuzhanovaNStensonPDFerecCCooperDN 2005 Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions. Hum Mutat 26 362 373

21. KaplanDLDaveyMJO'DonnellM 2003 Mcm4,6,7 uses a “pump in ring” mechanism to unwind DNA by steric exclusion and actively translocate along a duplex. J Biol Chem 278 49171 49182

22. OlavarrietaLMartinez-RoblesMLSogoJMStasiakAHernandezP 2002 Supercoiling, knotting and replication fork reversal in partially replicated plasmids. Nucleic Acids Res 30 656 666

23. FutcherAB 1986 Copy number amplification of the 2 micron circle plasmid of Saccharomyces cerevisiae. J Theor Biol 119 197 204

24. CadoretJCMeischFHassan-ZadehVLuytenIGuilletC 2008 Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A 105 15837 15842

25. AhmedAPodemskiL 1998 Observations on template switching during DNA replication through long inverted repeats. Gene 223 187 194

26. KugelbergEKofoidEAnderssonDILuYMellorJ 2010 The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types. Genetics 185 65 80

27. CoteAGLewisSM 2008 Mus81-dependent double-strand DNA breaks at in vivo-generated cruciform structures in S. cerevisiae. Mol Cell 31 800 812

28. HaradaSUchidaMShimizuN 2009 Episomal high copy number maintenance of hairpin-capped DNA bearing a replication initiation region in human cells. J Biol Chem 284 24320 24327

29. KunesSBotsteinDFoxMS 1990 Synapsis-mediated fusion of free DNA ends forms inverted dimer plasmids in yeast. Genetics 124 67 80

30. DorseyMPetersonCBrayKPaquinCE 1992 Spontaneous amplification of the ADH4 gene in Saccharomyces cerevisiae. Genetics 132 943 950

31. WaltonJDPaquinCEKanekoKWilliamsonVM 1986 Resistance to antimycin A in yeast by amplification of ADH4 on a linear, 42 kb palindromic plasmid. Cell 46 857 863

32. NarayananVMieczkowskiPAKimHMPetesTDLobachevKS 2006 The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks. Cell 125 1283 1296

33. WahlGM 1989 The importance of circular DNA in mammalian gene amplification. Cancer Res 49 1333 1340

34. ItalianoAAttiasRAuriasAPerotGBurel-VandenbosF 2006 Molecular cytogenetic characterization of a metastatic lung sarcomatoid carcinoma: 9p23 neocentromere and 9p23-p24 amplification including JAK2 and JMJD2C. Cancer Genet Cytogenet 167 122 130

35. NonetGHCarrollSMDeRoseMLWahlGM 1993 Molecular dissection of an extrachromosomal amplicon reveals a circular structure consisting of an imperfect inverted duplication. Genomics 15 543 558

36. SchreinerBGretenFRBaurDMFingerleAAZechnerU 2003 Murine pancreatic tumor cell line TD2 bears the characteristic pattern of genetic changes with two independently amplified gene loci. Oncogene 22 6802 6809

37. BarboutiAStankiewiczPNusbaumCCuomoCCookA 2004 The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. Am J Hum Genet 74 1 10

38. LangeJSkaletskyHvan DaalenSKEmbrySLKorverCM 2009 Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes. Cell 138 855 869

39. ScottSACohenNBrandtTWarburtonPEEdelmannL 2010 Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome. Hum Mol Genet 19 3383 3393

40. YuSGrafWD 2010 Telomere capture as a frequent mechanism for stabilization of the terminal chromosomal deletion associated with inverted duplication. Cytogenet Genome Res 129 265 274

41. ZuffardiOBonagliaMCicconeRGiordaR 2009 Inverted duplications deletions: underdiagnosed rearrangements?? Clin Genet 75 505 513

42. VoineaguINarayananVLobachevKSMirkinSM 2008 Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Proc Natl Acad Sci U S A 105 9936 9941

43. MizunoKLambertSBaldacciGMurrayJMCarrAM 2009 Nearby inverted repeats fuse to generate acentric and dicentric palindromic chromosomes by a replication template exchange mechanism. Genes Dev 23 2876 2886

44. PaekALKaocharSJonesHElezabyAShanksL 2009 Fusion of nearby inverted repeats by a replication-based mechanism leads to formation of dicentric and acentric chromosomes that cause genome instability in budding yeast. Genes Dev 23 2861 2875

45. CohenSHassinDKarbySLaviS 1994 Hairpin structures are the primary amplification products: a novel mechanism for generation of inverted repeats during gene amplification. Mol Cell Biol 14 7782 7791

46. CohenSLaviS 1996 Induction of circles of heterogeneous sizes in carcinogen-treated cells: two-dimensional gel analysis of circular DNA molecules. Mol Cell Biol 16 2002 2014

47. TanakaHBergstromDAYaoMCTapscottSJ 2005 Widespread and nonrandom distribution of DNA palindromes in cancer cells provides a structural platform for subsequent gene amplification. Nat Genet 37 320 327

48. TanakaHCaoYBergstromDAKooperbergCTapscottSJ 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

49. LlorenteBSmithCESymingtonLS 2008 Break-induced replication: what is it and what is it for? Cell Cycle 7 859 864

50. MalkovaAIvanovELHaberJE 1996 Double-strand break repair in the absence of RAD51 in yeast: a possible role for break-induced DNA replication. Proc Natl Acad Sci U S A 93 7131 7136

51. SonodaEHocheggerHSaberiATaniguchiYTakedaS 2006 Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair (Amst) 5 1021 1029

52. MurmannAEConradDFMashekHCurtisCANicolaeRI 2009 Inverted duplications on acentric markers: mechanism of formation. Hum Mol Genet 18 2241 2256

53. KandaTOtterMWahlGM 2001 Mitotic segregation of viral and cellular acentric extrachromosomal molecules by chromosome tethering. J Cell Sci 114 49 58

54. KandaTWahlGM 2000 The dynamics of acentric chromosomes in cancer cells revealed by GFP-based chromosome labeling strategies. J Cell Biochem  Suppl Suppl 35 107 114