Mechanisms of gene duplication and amplification

Cold Spring Harbor Perspectives in Biology

Volumn 7, Issue 2, 2015, Pages

  Reams, Andrew B ^a   Roth, John R ^b  

^a CALIFORNIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METAZOA;

DNA; TRANSPOSON;

BACTERIAL GENE; BIOLOGICAL MODEL; CHEMISTRY; GENE AMPLIFICATION; GENE DELETION; GENE DOSAGE; GENE DUPLICATION; GENETICS; INVERTED REPEAT; MUTATION RATE; PLASMID; TRANSPOSON;

DNA; DNA TRANSPOSABLE ELEMENTS; GENE AMPLIFICATION; GENE DELETION; GENE DOSAGE; GENE DUPLICATION; GENES, BACTERIAL; INVERTED REPEAT SEQUENCES; MODELS, GENETIC; MUTATION RATE; PLASMIDS;

EID: 84922572776     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a016592     Document Type: Article

References (102)

1. Akgun E, Zahn J, Baumes S, Brown G, Liang F, Romanienko PJ, Lewis S, Jasin M. 1997. Palindrome resolution and recombination in the mammalian germ line. Mol Cell Biol 17: 5559–5570.
2. Albertson DG. 2006. Gene amplification in cancer. Trends Genet 22: 447-455.
3. Anand RP, Lovett ST, Haber JE. 2013. Break-induced DNA replication. Cold Spring Harb Perspect Biol 5: a010397.
4. Anderson RP, Roth JR. 1977. Tandem genetic duplications in phage and bacteria. Annu Rev Microbiol 31: 473–505.
5. Anderson RP, Roth JR. 1978. Tandem chromosomal duplications in Salmonella typhimurium: Fusion of histidine genes to novel promoters. J Mol Biol 119: 147–166.
6. Anderson P, Roth J. 1981. Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons. Proc Natl Acad Sci 78: 3113–3117.
7. Anderson RP, Miller CG, Roth JR. 1976. Tandem duplications of the histidine operon observed following generalized transduction in Salmonella typhimurium. J Mol Biol 105: 201–218.
8. Araya CL, Payen C, Dunham MJ, Fields S. 2010. Whole-genome sequencing of a laboratory-evolved yeast strain. BMC Genomics 11: 88.
9. Ashizawa Y, Yokochi T, Ogata Y, Shobuike Y, Kato J, Ikeda H. 1999. Mechanism of DNA gyrase-mediated illegitimate recombination: Characterization of Escherichia coli gyrA mutations that confer hyper-recombination phenotype. J Mol Biol 289: 447–458.
10. Brewer BJ, Payen C, Raghuraman MK, Dunham MJ. 2011. Origin-dependent inverted-repeat amplification: A replication-based model for generating palindromic amplicons. PLoS Genet 7: e1002016.
11. Bridges CB. 1936. The bar “gene” a duplication. Science 83: 210–211.
12. Butler DK, Yasuda LE, Yao MC. 1996. Induction of large DNA palindrome formation in yeast: Implications for gene amplification and genome stability in eukaryotes. Cell 87: 1115–1122.
13. Bzymek M, Lovett ST. 2001. Instability of repetititve DNA sequences: The role of replication in multiple mechanisms. Proc Natl Acad Sci 98: 8319–8325.
14. Cairns J, Foster PL. 1991. Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics 128: 695–701.
15. Carvalho CM, Ramocki MB, Pehlivan D, Franco LM, Gonzaga-Jauregui C, Fang P, McCall A, Pivnick EK, Hines-Dowell S, Seaver LH, et al. 2011. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. Nat Genet 43: 1074–1081.
16. Conner CP. 1993. Duplications between repetitive sequences in the chromosome of Salmonella, p. 76. University of Utah, Salt Lake City, UT.
17. Court DL, Sawitzke JA, Thomason LC. 2002. Genetic engineering using homologous recombination. Annu Rev Genet 36: 361–388.
18. Cuff LE, Elliott KT, Seaton SC, Ishaq MK, Laniohan NS, Karls AC, Neidle EL. 2012. Analysis of IS1236-mediated gene amplification events in Acinetobacter baylyi ADP1. J Bacteriol 194: 4395–4405.
19. Cunningham LA, Cote AG, Cam-Ozdemir C, Lewis SM. 2003. Rapid, stabilizing palindrome rearrangements in somatic cells by the center-break mechanism. Mol Cell Biol 23: 8740–8750.
20. Dianov GL, Kuzminov AV, Mazin AV, Salganik RI. 1991. Molecular mechanisms of deletion formation in Escherichia coli plasmids: I. Deletion formation mediated by long direct repeats. Mol Gen Genet 228: 153–159.
21. Dutra BE, Lovett ST. 2006. Cis and trans-acting effects on a mutational hotspot involving a replication template switch. J Mol Biol 356: 300–311.
22. Duval-Valentin G, Marty-Cointin B, Chandler M. 2004. Requirement of IS911 replication before integration defines a new bacterial transposition pathway. EMBO J 23: 3897–3906.
23. Elliott KT, Cuff LE, Neidle EL. 2013. Copy number change: Evolving views on gene amplification. Future Microbiol 8: 887–899.
24. Espeli O, Boccard F. 1997. In vivo cleavage of Escherichia coli BIME-2 repeats by DNA gyrase: Genetic characterization of the target and identification of the cut site. Mol Micro-biol 26: 767–777.
25. Ford M, Davies B, Griffiths M, Wilson J, Fried M. 1985. Isolation of a gene enhancer within an amplified inverted duplication after “expression selection.” Proc Natl Acad Sci 82: 3370–3374.
26. Foster PL. 2006. Methods for determining spontaneous mutation rates. Methods Enzymol 409: 195–213.
27. Galhardo RS, Hastings PJ, Rosenberg SM. 2007. Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 42: 399–435.
28. Galitski T, Roth JR. 1995. Evidence that F plasmid transfer replication underlies apparent adaptive mutation. Science 268: 421–423.
29. Galitski T, Roth JR. 1997. Pathways for homologous recombination between chromosomal direct repeats in Salmonella typhimurium. Genetics 146: 751–767.
30. Gangloff S, Zou H, Rothstein R. 1996. Gene conversion plays the major role in controlling the stability of large tandem repeats in yeast. EMBO J 15: 1715–1725.
31. Gilson E, Saurin W, Perrin D, Bachellier S, Hofnung M. 1991. The BIME family of bacterial highly repetitive sequences. Res Microbiol 142: 217–222.
32. Girirajan S, Campbell CD, Eichler EE. 2011. Human copy number variation and complex genetic disease. Annu Rev Genet 45: 203–226.
33. Green MM. 1963. Unequal crossing over and the genetical organization of the white locus of Drosophila melanogaster. Z Vererbungsl 94: 200–214.
34. Green MM. 1985. The role of mobile DNA elements in unequal and intrachromosomal crossing-over in Drosophila melanogaster. In Aneuploidy (ed. Dellarco V, Voytek P, Hollaender A), pp. 353–362. Plenum, New York.
35. Gu W, Zhang F, Lupski JR. 2008. Mechanisms for human genomic rearrangements. Pathogenetics 1: 4.
36. Haack KR, Roth JR. 1995. Recombination between chromosomal IS200 elements supports frequent duplication formation in Salmonella typhimurium. Genetics 141: 1245–1252.
37. Haber JE, Debatisse M. 2006. Gene amplification: Yeast takes a turn. Cell 125: 1237–1240.
38. Hastings PJ. 2007. Adaptive amplification. Crit Rev Biochem Mol Biol 42: 271–283.
39. Hastings PJ, Slack A, Petrosino JF, Rosenberg SM. 2004. Adaptive amplification and point mutation are independent mechanisms: Evidence for various stress-inducible mutation mechanisms. PLoS Biol 2: e399.
40. Hastings PJ, Ira G, Lupski JR. 2009a. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5: e1000327.
41. Hastings PJ, Lupski JR, Rosenberg SM, Ira G. 2009b. Mechanismsof change in gene copy number. Nat Rev Genet 10: 551–564.
42. Houseley J, Tollervey D. 2011. Repeat expansion in the budding yeast ribosomal DNA can occur independently of the canonical homologous recombination machinery. Nucleic Acids Res 39: 8778–8791.
43. Howarth KD, Pole JC, Beavis JC, Batty EM, Newman S, Bignell GR, Edwards PA. 2011. Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles. Genome Res 21: 525–534.
44. Hyrien O, Debatisse M, Buttin G, de Saint Vincent BR. 1987. A hotspot for novel amplification joints in a mosaic of Alu-like repeats and palindromic A+T-rich DNA. EMBO J 6: 2401–2408.
45. Hyrien O, Debatisse M, Buttin G, de Saint Vincent BR. 1988. The multicopy appearance of a large inverted duplication and the sequence at the inversion joint suggest a new model for gene amplification. EMBO J 7: 407–417.
46. Ikeda H, Shimizu H, Ukita T, Kumagai M. 1995. A novel assay for illegitimate recombination in Escherichia coli: Stimulation of λbio transducing phage formation by ultra-violet light and its independence from RecA function. Adv Biophys 31: 197–208.
47. Kitada K, Yamasaki T. 2007. The MDR1/ABCB1 regional amplification in large inverted repeats with asymmetric sequences and microhomologies at the junction sites. Cancer Genet Cytogenet 178: 120–127.
48. Kugelberg E, Kofoid E, Reams AB, Andersson DI, Roth JR. 2006. Multiple pathways of selected gene amplification during adaptive mutation. Proc Natl Acad Sci 103: 17319–17324.
49. Kugelberg E, Kofoid E, Andersson DI, Lu Y, Mellor J, Roth FP, Roth JR. 2010. The tandem inversion duplication in Salmonella enterica: Selection drives unstable precursors to final mutation types. Genetics 185: 65–80.
50. Kurth I, Georgescu RE, O’Donnell ME. 2013. A solution to release twisted DNA during chromosome replication by coupled DNA polymerases. Nature 496: 119–122.
51. Kuzminov A. 1995. Collapse and repair of replication forks in Escherichia coli. Mol Microbiol 16: 373–384.
52. Kuzminov A. 2001. DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination. Proc Natl Acad Sci 98: 8461–8468.
53. Leach DR. 1994. Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. Bioessays 16: 893–900.
54. Legouy E, Fossar N, Lhomond G, Brison O. 1989. Structure of four amplified DNA novel joints. Somat Cell Mol Genet 15: 309–320.
55. Li X, Marians KJ. 2000. Two distinct triggers for cycling of the lagging strand polymerase at the replication fork. J Biol Chem 275: 34757–34765.
56. Linskens MH, Huberman JA. 1988. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol Cell Biol 8: 4927–4935.
57. Lipinski KJ, Farslow JC, Fitzpatrick KA, Lynch M, Katju V, Bergthorsson U. 2011. High spontaneous rate of gene duplication in Caenorhabditis elegans. Curr Biol 21: 306–310.
58. Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, et al. 2011. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146: 889–903.
59. Liu P, Carvalho CM, Hastings PJ, Lupski JR. 2012. Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev 22: 211–220.
60. Lobachev KS, Shor BM, Tran HT, Taylor W, Keen JD, Resnick MA, Gordenin DA. 1998. Factors affecting inverted repeat stimulation of recombination and deletion in Saccharomyces cerevisiae. Genetics 148: 1507–1524.
61. Lovett ST, Drapkin PT, Sutera VA Jr, Gluckman-Peskind TJ. 1993. A sister-strand exchange mechanism for recA-in-dependent deletion of repeated DNA sequences in Escherichia coli. Genetics 135: 631–642.
62. Luria SE. 1951. The frequency distribution of spontaneous bacteriophage mutants as evidence for the exponential rate of phage reproduction. Cold Spring Harb Symp Quant Biol 16: 463–470.
63. Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, et al. 2008. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci 105: 9272-9277.
64. Mazin AV, Kuzminov AV, Dianov GL, Salganik RI. 1991. Mechanisms of deletion formation in Escherichia coli plasmids: II. Deletions mediated by short direct repeats. Mol Gen Genet 228: 209-214.
65. McClintock B. 1941. The stability of broken ends of chromosomes in Zea Mays. Genetics 26: 234–282.
66. Mehta A, Haber JE. 2014. Sources of DNA double-strand breaks and models for recombinational DNA repair. Cold Spring Harb Perspect Biol 6: a016428.
67. Mishmar D, Rahat A, Scherer SW, Nyakatura G, Hinzmann B, Kohwi Y, Mandel-Gutfroind Y, Lee JR, Drescher B, Sas DE, et al. 1998. Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site. Proc Natl Acad Sci 95: 8141-8146.
68. Morgan LV. 1925. Polyploidy in Drosophila melanogaster with two attached X chromosomes. Genetics 10: 148-178.
69. MorricalSW. 2015. DNA pairing and annealing processes in homologous recombination and homology-directed repair. Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a016444.
70. Muller HJ. 1936. Bar duplication. Science 83: 528–530.
71. Naito A, Naito S, Ikeda H. 1984. Homology is not required for recombination mediated by DNA gyrase of Escherichia coli. Mol Gen Genet 193: 238-243.
72. Narayanan V, Lobachev KS. 2007. Intrachromosomal gene amplification triggered by hairpin-capped breaks requires homologous recombination and is independent of nonhomologous end-joining. Cell Cycle 6:1814–1818.
73. Okuno Y, Hahn PJ, Gilbert DM. 2004. Structure of a palindromic amplicon junction implicates microhomology-mediated end joining as a mechanism of sister chromatid fusion during gene amplification. Nucleic Acids Res 32: 749–756.
74. Papanicolaou C, Ripley LS. 1991. An in vitro approach to identifying specificity determinants of mutagenesis mediated by DNA misalignments. J Mol Biol 221: 805–821.
75. Peterson BC, Rownd RH. 1985. Recombination sites in plasmid drug resistance gene amplification. J Bacteriol 164: 1359–1361.
76. Petes TD, Hill CW. 1988. Recombination between repeated genes in microorganisms. Annu Rev Genet 22: 147–168.
77. Rattray AJ, Shafer BK, Neelam B, Strathern JN. 2005. A mechanism of palindromic gene amplification in Saccharomyces cerevisiae. Genes Dev 19: 1390-1399.
78. Reams AB, Neidle EL. 2003. Genome plasticity in Acinetobacter: New degradative capabilities acquired by the spontaneous amplification of large chromosomal segments. Mol Microbiol 47: 1291-1304.
79. Reams AB, Neidle EL. 2004. Gene amplification involves site-specific short homology-independent illegitimate recombination in Acinetobacter sp. strain ADP1. J Mol Biol 338: 643-656.
80. Reams AB, Kofoid E, Savageau M, Roth JR. 2010. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics 184: 1077–1094.
81. Reams AB, Kofoid E, Kugelberg E, Roth JR. 2012. Multiple pathways of duplication formation with and without recombination (RecA) in Salmonella enterica. Genetics 192: 397–415.
82. Reams AB, Kofoid E, Duleba N, Roth JR. 2014. Recombination and annealing pathways compete for substrates in making rrn duplications in Salmonella enterica. Genetics 196: 119–135.
83. Ripley LS. 1982. Model for the participation of quasi-palindromic DNA sequencesin frameshift mutation. Proc Natl Acad Sci 79: 4128–4132.
84. Romero D, Palacios R. 1997. Gene amplification and genomic plasticity in prokaryotes. Annu Rev Genet 31:91–111.
85. Sano E, Maisnier-Patin S, Aboubechara J, Quiñones-Soto S, Roth JR. 2014. Plasmid copy number underlies adaptive mutability in bacteria. Genetics 198: 919–933.
86. Sawitzke JA, Thomason LC, Costantino N, Bubunenko M, Datta S,Court DL. 2007. Recombineering:Invivo genetic engineering in E. coli, S. enterica, and beyond. Methods Enzymol 421: 171–199.
87. Shiraishi K, Imai Y, Yoshizaki S, Tadaki T, Ogata Y, Ikeda H. 2006. The role of UvrD in RecET-mediated illegitimate recombination in Escherichia coli. Genes Genet Syst 81: 291–297.
88. Shyamala V, Schneider E, Ames GF. 1990. Tandem chromosomal duplications: Role of REP sequences in the recombination event at the join-point. EMBO J 9: 939–946.
89. Sinden RR, Zheng GX, Brankamp RG, Allen KN. 1991. On the deletion of inverted repeated DNA in Escherichia coli: Effects of length, thermal stability, and cruciform formation in vivo. Genetics 129: 991–1005.
90. Slack A, Thornton PC, Magner DB, Rosenberg SM, Hastings PJ. 2006. On the mechanism of gene amplification induced under stress in Escherichia coli. PLoS Genet 2: e48.
91. Spies M, Kowalczykowski SC. 2005. Homologous recombination by the RecBCD and RecF pathways. In The bacterial chromosome (ed. Higgins N), pp. 389–404. ASM, Washington, D.C.
92. Stark GR, Debatisse M, Giulotto E, Wahl GM. 1989. Recent progress in understanding mechanisms of mammalian DNA amplification. Cell 57: 901–908.
93. Tanaka H, Yao MC. 2009. Palindromic gene amplification— An evolutionarily conserved role for DNA inverted repeats in the genome. Nat Rev Cancer 9: 216–224.
94. Tice SC. 1914.Anew sex-linked characterin Drosophila. Biol Bull 26: 221–230.
95. Tlsty TD. 1990. Normal diploid human and rodent cells lack a detectable frequency of gene amplification. Proc Natl Acad Sci 87: 3132–3136.
96. Tlsty TD, Margolin BH, Lum K. 1989. Differences in the rates of gene amplification in nontumorigenic and tumorigenic cell lines as measured by Luria-Delbruck fluctuation analysis. Proc Natl Acad Sci 86: 9441–9445.
97. Tsubota SI, Rosenberg D, Szostak H, Rubin D, Schedl P. 1989. The cloning of the Bar region and the B breakpoint in Drosophila melanogaster: Evidence for a transposon-induced rearrangement. Genetics 122: 881–890.
98. Watanabe T, Horiuchi T. 2005. A novel gene amplification system in yeast based on double rolling-circle replication. EMBO J 24: 190–198.
99. Wright JA, Smith HS, Watt FM, Hancock MC, Hudson DL, Stark GR. 1990. DNA amplification is rare in normal human cells. Proc Natl Acad Sci 87: 1791–1795.
100. Yamamoto K, Kusano K, Takahashi NK, Yoshikura H, Kobayashi I. 1992. Gene conversion in the Escherichia coli RecF pathway: A successive half crossing-over model. Mol Gen Genet 234: 1–13.
101. Yang Y, Ames GF. 1988. DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences. Proc Natl Acad Sci 85: 8850–8854.
102. Zlotorynski E, Rahat A, Skaug J, Ben-Porat N, Ozeri E, Hershberg R, Levi A, Scherer SW, Margalit H, Kerem B. 2003. Molecular basis for expression of common and rare fragile sites. Mol Cell Biol 23: 7143–7151.