Mechanisms of change in gene copy number (original) (raw)
Iafrate, A. J. et al. Detection of large-scale variation in the human genome. Nature Genet.36, 949–951 (2004). CASPubMed Google Scholar
Kidd, J. M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature453, 56–64 (2008). CASPubMed CentralPubMed Google Scholar
Redon, R. et al. Global variation in copy number in the human genome. Nature444, 444–454 (2006). A survey of 270 individuals from the human HapMap samples using SNP arrays and comparative genomic hybridization. CASPubMed CentralPubMed Google Scholar
Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science305, 525–528 (2004). CASPubMed Google Scholar
Wong, K. K. et al. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet.80, 91–104 (2007). CASPubMed Google Scholar
Bruder, C. E. G. et al. Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am. J. Hum. Genet.82, 1–9 (2008). Google Scholar
Piotrowski, A. et al. Somatic mosaicism for copy number variation in differentiated human tissues. Hum. Mutat.29, 1118–1124 (2008). PubMed Google Scholar
Beckmann, J. S., Estivill, X. & Antonarakis, S. E. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nature Rev. Genet.8, 639–646 (2007). CASPubMed Google Scholar
Dumas, L. et al. Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res.17, 1266–1277 (2007). This paper traces the history of copy number variation through the evolution of the primate lineage. CASPubMed CentralPubMed Google Scholar
Nahon, J. L. Birth of 'human-specific' genes during primate evolution. Genetica118, 193–208 (2003). CASPubMed Google Scholar
Bailey, J. A. & Eichler, E. E. Primate segmental duplications: crucibles of evolution, diversity and disease. Nature Rev. Genet.7, 552–564 (2006). CASPubMed Google Scholar
Stankiewicz, P., Shaw, C. J., Withers, M., Inoue, K. & Lupski, J. R. Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res.14, 2209–2220 (2004). CASPubMed CentralPubMed Google Scholar
Marques-Bonet, T. et al. A burst of segmental duplications in the genome of the African great ape ancestor. Nature457, 877–881 (2009). CASPubMed CentralPubMed Google Scholar
Inoue, K. & Lupski, J. R. Molecular mechanisms for genomic disorders. Annu. Rev. Genomics Hum. Genet.3, 199–242 (2002). CASPubMed Google Scholar
Ohno, S. Evolution by Gene Duplication (Springer, Berlin, New York, 1970). Google Scholar
Rotger, M. et al. Partial deletion of CYP2B6 owing to unequal crossover with CYP2B7. Pharmacogenet. Genomics17, 885–890 (2007). CASPubMed Google Scholar
Zhang, F. et al. The DNA replication FoSTeS/MMBIR mechanism can generate human genomic, genic, and exon shuffling rearrangements. Nature Genet.41, 849–853 (2009). Studies of disease associated rearrangements in proximal chromosome 17p reveal complex rearrangements of varying size and occurrence during mitosis with potential implications for genetic counselling regarding recurrence risk. CASPubMed Google Scholar
Volik, S. et al. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res.16, 394–404 (2006). CASPubMed CentralPubMed Google Scholar
Brodeur, G. M. & Hogarty, M. D. in The Genetic Basis of Human Cancer (eds. Vogelstein, B. & Kinzler, K. W.) 161–172 (McGraw-Hill, New York, 1998). Google Scholar
Frank, B. et al. Copy number variant in the candidate tumor suppressor gene MTUS1 and familial breast cancer risk. Carcinogenesis28, 1442–1445 (2007). CASPubMed Google Scholar
Lupski, J. R. Genomic disorders: structural features of the genome can lead to DNA rearrangement and human disease traits. Trends Genet.14, 417–422 (1998). CASPubMed Google Scholar
Stranger, B. E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science315, 848–853 (2007). CASPubMed CentralPubMed Google Scholar
Hastings, P. J., Ira, G. & Lupski, J. R. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet.5, e1000327 (2009). This review presents the MMBIR model for chromosomal rearrangement with detail of the evidence on which it is based. CASPubMed CentralPubMed Google Scholar
Friedberg, E. C. et al. DNA Repair and Mutagenesis (ASM, Washington DC, 2005). Google Scholar
Lee, J. A., Carvalho, C. M. & Lupski, J. R. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell131, 1235–1247 (2007). Description of the complex structure and microhomology of non-recurrent duplications seen in patients with a genomic disorder. CASPubMed Google Scholar
Nobile, C. et al. Analysis of 22 deletion breakpoints in dystrophin intron 49. Hum. Genet.110, 418–421 (2002). CASPubMed Google Scholar
Carvalho, C. M. et al. Complex rearrangements in patients with duplications of MECP2 can occur by Fork Stalling and Template Switching. Hum. Mol. Genet.18, 2188–2203 (2009). CASPubMed CentralPubMed Google Scholar
Chen, J. M., Chuzhanova, N., Stenson, P. D., Férec, C. & Cooper, D. N. Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions. Hum. Mutat.26, 362–373 (2005). PubMed Google Scholar
Gajecka, M. et al. Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13). Genome Res.18, 1733–1742 (2008). CASPubMed CentralPubMed Google Scholar
Sheen, C. R. et al. Double complex mutations involving F8 and FUNDC2 caused by distinct break-induced replication. Hum. Mutat.28, 1198–2006 (2007). CASPubMed Google Scholar
Vissers, L. E. et al. Complex chromosome 17p rearrangements associated with low-copy repeats in two patients with congenital anomalies. Hum. Genet.121, 697–709 (2007). CASPubMed CentralPubMed Google Scholar
Stankiewicz, P. et al. Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am. J. Hum. Genet.72, 1101–1116 (2003). CASPubMed CentralPubMed Google Scholar
Lee, J. A. et al. Role of genomic architecture in PLP1 duplication causing Pelizaeus–Merzbacher disease. Hum. Mol. Genet.15, 2250–2265 (2006). CASPubMed Google Scholar
Lee, J. A. et al. Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect. Ann. Neurol.59, 398–403 (2006). CASPubMed Google Scholar
Lovett, S. T., Hurley, R. L., Sutera, V. A. Jr, Aubuchon, R. H. & Lebedeva, M. A. Crossing over between regions of limited homology in Escherichia coli. RecA-dependent and RecA-independent pathways. Genetics160, 851–859 (2002). CASPubMed CentralPubMed Google Scholar
Liskay, R. M., Letsou, A. & Stachelek, J. L. Homology requirement for efficient gene conversion between duplicated chromosomal sequences in mammalian cells. Genetics115, 161–167 (1987). CASPubMed CentralPubMed Google Scholar
Reiter, L. T. et al. Human meiotic recombination products revealed by sequencing a hotspot for homologous strand exchange in multiple HNPP deletion patients. Am. J. Hum. Genet.62, 1023–1033 (1998). CASPubMed CentralPubMed Google Scholar
Stankiewicz, P. & Lupski, J. R. Genome architecture, rearrangements and genomic disorders. Trends Genet.18, 74–82 (2002). CASPubMed Google Scholar
Krogh, B. O. & Symington, L. S. Recombination proteins in yeast. Annu. Rev. Genet.38, 233–271 (2004). CASPubMed Google Scholar
Pâques, F. & Haber, J. E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev.63, 349–404 (1999). PubMed CentralPubMed Google Scholar
Esposito, M. S. Evidence that spontaneous mitotic recombination occurs at the two-strand stage. Proc. Natl Acad. Sci. USA75, 4436–4440 (1978). CASPubMedPubMed Central Google Scholar
Stark, J. M. & Jasin, M. Extensive loss of heterozygosity is suppressed during homologous repair of chromosomal breaks. Mol. Cell. Biol.23, 733–743 (2003). CASPubMed CentralPubMed Google Scholar
Dupaigne, P. et al. The Srs2 helicase activity is stimulated by Rad51 filaments on dsDNA: implications for crossover incidence during mitotic recombination. Mol. Cell.29, 243–254 (2008). CASPubMed Google Scholar
Sun, W. et al. The FANCM ortholog Fml1 promotes recombination at stalled replication forks and limits crossing over during DNA double-strand break repair. Mol. Cell32, 118–128 (2008). CASPubMed CentralPubMed Google Scholar
Ira, G., Malkova, A., Liberi, G., Foiani, M. & Haber, J. E. Srs2 and Sgs1–Top3 suppress crossovers during double-strand break repair in yeast. Cell115, 401–411 (2003). CASPubMed CentralPubMed Google Scholar
Prakash, R. et al. Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination. Genes Dev.23, 67–79 (2009). CASPubMed CentralPubMed Google Scholar
Wu, L. & Hickson, I. D. The Bloom's syndrome helicase suppresses crossing over during homologous recombination. Nature426, 870–874 (2003). CASPubMed Google Scholar
Prado, F. & Aguilera, A. Control of cross-over by single-strand DNA resection. Trends. Genet.19, 428–431 (2003). CASPubMed Google Scholar
Smith, C. E., Llorente, B. & Symington, L. S. Template switching during break-induced replication. Nature447, 102–105 (2007). This paper shows experimental evidence from yeast on the nature of BIR. Specifically, template switching between homologous chromosomes (or sometimes non-homologous chromosomes, which causes translocation). It showed replication out to the telomere after switching. CASPubMed Google Scholar
Bauters, M. et al. Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair. Genome Res.18, 847–858 (2008). CASPubMed CentralPubMed Google Scholar
Deem, A. et al. Defective break-induced replication leads to half-crossovers in Saccharomyces cerevisiae. Genetics179, 1845–1860 (2008). CASPubMed CentralPubMed Google Scholar
Narayanan, V. & Lobachev, K. S. Intrachromosomal gene amplification triggered by hairpin-capped breaks requires homologous recombination and is independent of nonhomologous end-joining. Cell Cycle6, 1814–1818 (2007). CASPubMed Google Scholar
Payen, C., Koszul, R., Dujon, B. & Fischer, G. Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms. PLoS Genet.4, e1000175 (2008). Evidence from yeast that LCRs arise by a replicative mechanism, specifically one involving BIR. ArticlePubMedPubMed Central Google Scholar
Schmidt, K. H., Wu, J. & Kolodner, R. D. Control of translocations between highly diverged genes by Sgs1, the Saccharomyces cerevisiae homolog of the Bloom's syndrome protein. Mol. Cell. Biol.26, 5406–5420 (2006). CASPubMed CentralPubMed Google Scholar
Lin, F. L., Sperle, K. & Sternberg, N. Model for homologous recombination during transfer of DNA into mouse L cells: role for DNA ends in the recombination process. Mol. Cell. Biol.4, 1020–1034 (1984). CASPubMed CentralPubMed Google Scholar
Sweigert, S. E. & Carroll, D. Repair and recombination of X-irradiated plasmids in Xenopus laevis oocytes. Mol. Cell. Biol.10, 5849–5856 (1990). CASPubMed CentralPubMed Google Scholar
Haber, J. E. Exploring the pathways of homologous recombination. Curr. Opin. Cell Biol.4, 401–412 (1992). CASPubMed Google Scholar
Elliott, B., Richardson, C. & Jasin, M. Chromosomal translocation mechanisms at intronic Alu elements in mammalian cells. Mol. Cell17, 885–894 (2005). CASPubMed Google Scholar
Rayssiguier, C., Thaler, D. S. & Radman, M. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch repair mutants. Nature342, 396–401 (1989). CASPubMed Google Scholar
Unal, E. et al. DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain. Mol. Cell16, 991–1002 (2004). PubMed Google Scholar
Strom, L., Lindroos, H. B., Shirahige, K. & Sjogren, C. Postreplicative recruitment of cohesin to double-strand breaks is required for DNA repair. Mol. Cell16, 1003–1015 (2004). PubMed Google Scholar
Kim, J. S., Krasieva, T. B., LaMorte, V., Taylor, A. M. & Yokomori, K. Specific recruitment of human cohesin to laser-induced DNA damage. J. Biol. Chem.277, 45149–45153 (2002). CASPubMed Google Scholar
Sjogren, C. & Nasmyth, K. Sister chromatid cohesion is required for postreplicative double-strand break repair in Saccharomyces cerevisiae. Curr. Biol.11, 991–995 (2001). CASPubMed Google Scholar
Kobayashi, T., Horiuchi, T., Tongaonkar, P., Vu, L. & Nomura, M. SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast. Cell117, 441–453 (2004). CASPubMed Google Scholar
Kobayashi, T. & Ganley, A. R. Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science309, 1581–1584 (2005). CASPubMed Google Scholar
Kaye, J. A. et al. DNA breaks promote genomic instability by impeding proper chromosome segregation. Curr. Biol.14, 2096–2106 (2004). CASPubMed Google Scholar
Soutoglou, E. et al. Positional stability of single double-strand breaks in mammalian cells. Nature Cell Biol.9, 675–682 (2007). CASPubMed Google Scholar
Oh, S. D. et al. BLM ortholog, Sgs1, prevents aberrant crossing-over by suppressing formation of multichromatid joint molecules. Cell130, 259–272 (2007). CASPubMed CentralPubMed Google Scholar
Jain, S. et al. A recombination execution checkpoint regulates the choice of homologous recombination pathway during DNA double-strand break repair. Genes Dev.23, 291–303 (2009). CASPubMed CentralPubMed Google Scholar
McVey, M. & Lee, S. E. MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. Trends Genet.24, 529–538 (2008). CASPubMed CentralPubMed Google Scholar
Lieber, M. R. The mechanism of human nonhomologous DNA end joining. J. Biol. Chem.283, 1–5 (2008). CASPubMed Google Scholar
Daley, J. M., Palmbos, P. L., Wu, D. & Wilson, T. E. Nonhomologous end joining in yeast. Annu. Rev. Genet.39, 431–451 (2005). CASPubMed Google Scholar
Haviv-Chesner, A., Kobayashi, Y., Gabriel, A. & Kupiec, M. Capture of linear fragments at a double-strand break in yeast. Nucleic Acids Res.35, 5192–5202 (2007). CASPubMed CentralPubMed Google Scholar
Yu, X. & Gabriel, A. Ku-dependent and Ku-independent end-joining pathways lead to chromosomal rearrangements during double-strand break repair in Saccharomyces cerevisiae. Genetics163, 843–856 (2003). CASPubMed CentralPubMed Google Scholar
Nickoloff, J. A., De Haro, L. P., Wray, J. & Hromas, R. Mechanisms of leukemia translocations. Curr. Opin. Hematol.15, 338–345 (2008). CASPubMed CentralPubMed Google Scholar
McClintock, B. Chromosome organization and genic expression. Cold Spring Harb. Symp. Quant. Biol.16, 13–47 (1951). CASPubMed Google Scholar
Tanaka, H. & Yao, M. C. Palindromic gene amplification — an evolutionarily conserved role for DNA inverted repeats in the genome. Nature Rev. Cancer9, 216–224 (2009). CAS Google Scholar
Tanaka, H., Bergstrom, D. A., Yao, M. C. & Tapscott, S. J. Large DNA palindromes as a common form of structural chromosome aberrations in human cancers. Hum. Cell19, 17–23 (2006). PubMed Google Scholar
Coquelle, A., Pipiras, E., Toledo, F., Buttin, G. & Debatisse, M. Expression of fragile sites triggers intrachromosomal mammalian gene amplification and sets boundaries to early amplicons. Cell89, 215–225 (1997). CASPubMed Google Scholar
Shaw, C. J. & Lupski, J. R. Non-recurrent 17p11.2 deletions are generated by homologous and non-homologous mechanisms. Hum. Genet.116, 1–7 (2005). CASPubMed Google Scholar
Arlt, M. F. et al. Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants. Am. J. Hum. Genet.84, 339–350 (2009). CASPubMed CentralPubMed Google Scholar
Durkin, S. G. et al. Replication stress induces tumor-like microdeletions in FHIT/FRA3B. Proc. Natl Acad. Sci. USA105, 246–251 (2008). CASPubMed Google Scholar
Kuo, M. T., Vyas, R. C., Jiang, L. X. & Hittelman, W. N. Chromosome breakage at a major fragile site associated with P-glycoprotein gene amplification in multidrug-resistant CHO cells. Mol. Cell Biol.14, 5202–5211 (1994). CASPubMed CentralPubMed Google Scholar
Coquelle, A., Rozier, L., Dutrillaux, B. & Debatisse, M. 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. Oncogene21, 7671–7679 (2002). CASPubMed Google Scholar
Michel, B., Ehrlich, S. D. & Uzest, M. DNA double-strand breaks caused by replication arrest. EMBO J.16, 430–438 (1997). CASPubMed CentralPubMed Google Scholar
Albertini, A. M., Hofer, M., Calos, M. P. & Miller, J. H. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell29, 319–328 (1982). CASPubMed Google Scholar
Farabaugh, P. J., Schmeissner, U., Hofer, M. & Miller, J. H. Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli. J. Mol. Biol.126, 847–857 (1978). CASPubMed Google Scholar
Ikeda, H., Shimizu, H., Ukita, T. & Kumagai, M. A novel assay for illegitimate recombination in Escherichia coli: stimulation of lambda bio transducing phage formation by ultra-violet light and its independence from RecA function. Adv. Biophys.31, 197–208 (1995). CASPubMed Google Scholar
Shimizu, H. et al. Short-homology-independent illegitimate recombination in Escherichia coli: distinct mechanism from short-homology-dependent illegitimate recombination. J. Mol. Biol.266, 297–305 (1997). CASPubMed Google Scholar
Bi, X. & Liu, L. F. _recA_-independent and _recA_-dependent intramolecular plasmid recombination: differential homology and requirement and distance effect. J. Mol. Biol.235, 414–423 (1994). CASPubMed Google Scholar
Mazin, A. V., Kuzminov, A. V., Dianov, G. L. & Salganik, R. I. Mechanisms of deletion formation in Escherichia coli plasmids. II. Deletions mediated by short direct repeats. Mol. Gen. Genet.228, 209–214 (1991). CASPubMed Google Scholar
Chedin, F., Dervyn, E., Dervyn, R., Ehrlich, S. D. & Noirot, P. Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol. Microbiol.12, 561–569 (1994). CASPubMed Google Scholar
Lovett, S. T., Gluckman, T. J., Simon, P. J., Sutera Jr, V. A. & Drapkin, P. T. Recombination between repeats in Escherichia coli by a _recA_-independent, proximity-sensitive mechanism. Mol. Gen. Genet.254, 294–300 (1994). Google Scholar
Bierne, H., Vilette, D., Ehrlich, S. D. & Michel, B. Isolation of a dnaE mutation which enhances RecA-independent homologous recombination in the Escherichia coli chromosome. Mol. Microbiol.24, 1225–1234 (1997). CASPubMed Google Scholar
Saveson, C. J. & Lovett, S. T. Enhanced deletion formation by aberrant DNA replication in Escherichia coli. Genetics146, 457–470 (1997). CASPubMed CentralPubMed Google Scholar
Bzymek, M. & Lovett, S. T. Instability of repetitive DNA sequences: the role of replication in multiple mechanisms. Proc. Natl Acad. Sci. USA98, 8319–8325 (2001). CASPubMedPubMed Central Google Scholar
Lovett, S. T. & Feshenko, V. V. Stabilization of diverged tandem repeats by mismatch repair: evidence for deletion formation via a misaligned replication intermediate. Proc. Natl Acad. Sci. USA93, 7120–7124 (1996). CASPubMedPubMed Central Google Scholar
Cairns, J. & Foster, P. L. Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics128, 695–701 (1991). CASPubMed CentralPubMed Google Scholar
Slack, A., Thornton, P. C., Magner, D. B., Rosenberg, S. M. & Hastings, P. J. On the mechanism of gene amplification induced under stress in Escherichia coli. PLoS Genet.2, e48 (2006). Experimental evidence fromE. colisuggesting that chromosomal structural change occurs by a replicative mechanism, and also revealing that the characteristics of amplification inE. coliare similar to those of non-recurrent changes seen in human genomic disorders. Proposes CNV formation by template switching between forks. PubMed CentralPubMed Google Scholar
Kugelberg, E., Kofoid, E., Reams AB, Andersson, D. I. & Roth, J. R. Multiple pathways of selected gene amplification during adaptive mutation. Proc. Natl Acad. Sci. USA103, 17319–17324 (2006). CASPubMedPubMed Central Google Scholar
Allgood, N. D. & Silhavy, T. J. Escherichia coli xonA (sbcB) mutants enhance illegitimate recombination. Genetics127, 671–680 (1991). CASPubMed CentralPubMed Google Scholar
Bzymek, M., Saveson, C. J., Feschenko, V. V. & Lovett, S. T. Slipped misalignment mechanisms of deletion formation: in vivo susceptibility to nucleases. J. Bacteriol.181, 477–482 (1999). CASPubMed CentralPubMed Google Scholar
Lydeard, J. R., Jain, S., Yamaguchi, M. & Haber, J. E. Break-induced replication and telomerase-independent telomere maintenance require Pol32. Nature448, 820–823 (2007). CASPubMed Google Scholar
VanHulle, K. et al. Inverted DNA repeats channel repair of distant double-strand breaks into chromatid fusions and chromosomal rearrangements. Mol. Cell. Biol.27, 2601–2614 (2007). CASPubMed CentralPubMed Google Scholar
Davis, A. P. & Symington, L. S. RAD51-dependent break-induced replication in yeast. Mol. Cell. Biol.24, 2344–2351 (2004). CASPubMed CentralPubMed Google Scholar
McVey, M., Adams, M., Staeva-Vieira, E. & Sekelsky, J. J. Evidence for multiple cycles of strand invasion during repair of double-strand gaps in Drosophila. Genetics167, 699–705 (2004). CASPubMed CentralPubMed Google Scholar
Bindra, R. S., Crosby, M. E. & Glazer, P. M. Regulation of DNA repair in hypoxic cancer cells. Cancer Metastasis Rev.26, 249–260 (2007). CASPubMed Google Scholar
Huang, L. E., Bindra, R. S., Glazer, P. M. & Harris, A. L. Hypoxia-induced genetic instability — a calculated mechanism underlying tumor progression. J. Mol. Med.85, 139–148 (2007). CASPubMed Google Scholar
Bindra, R. S. & Glazer, P. M. Repression of RAD51 gene expression by E2F4/p130 complexes in hypoxia. Oncogene.26, 2048–2057 (2007). CASPubMed Google Scholar
Coquelle, A., Toledo, F., Stern, S., Bieth, A. & Debatisse, M. A new role for hypoxia in tumor progression: induction of fragile site triggering genomic rearrangements and formation of complex DMs and HSRs. Mol. Cell2, 259–265 (1998). CASPubMed Google Scholar
Hastings, P. J., Bull, H. J., Klump, J. R. & Rosenberg, S. M. Adaptive amplification: an inducible chromosomal instability mechanism. Cell103, 723–731 (2000). CASPubMed Google Scholar
Lombardo, M.-J., Aponyi, I. & Rosenberg, S. M. General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli. Genetics166, 669–680 (2004). CASPubMed CentralPubMed Google Scholar
Ponder, R. G., Fonville, N. C. & Rosenberg, S. M. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol. Cell19, 791–804 (2005). CASPubMed Google Scholar
Mullighan, C. G. et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature446, 758–764 (2007). CASPubMed Google Scholar
Shao, L. et al. Identification of chromosome abnormalities in subtelomeric regions by microarray analysis: a study of 5,380 cases. Am. J. Med. Genet. A146A, 2242–2251 (2008). PubMed CentralPubMed Google Scholar
Yatsenko, S. A. et al. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum. Mol. Genet.18, 1924–1936 (2009). CASPubMed CentralPubMed Google Scholar
Zhang, L., Lu, H. H., Chung, W. Y., Yang, J. & Li, W. H. Patterns of segmental duplication in the human genome. Mol. Biol. Evol.22, 135–141 (2005). CASPubMed Google Scholar
She, X. et al. The structure and evolution of centromeric transition regions within the human genome. Nature430, 857–864 (2004). CASPubMed Google Scholar
Nguyen, D. Q., Webber, C. & Ponting, C. P. Bias of selection on human copy-number variants. PLoS Genet.2, e20 (2006). PubMed CentralPubMed Google Scholar
Visser, R. et al. Identification of a 3.0-kb major recombination hotspot in patients with Sotos syndrome who carry a common 1.9-Mb microdeletion. Am. J. Hum. Genet.76, 52–67 (2005). CASPubMed Google Scholar
de Smith, A. J. et al. Small deletion variants have stable breakpoints commonly associated with Alu elements. PLoS ONE3, e3104 (2008). PubMed CentralPubMed Google Scholar
Bacolla, A. et al. Breakpoints of gross deletions coincide with non-B DNA conformations. Proc. Natl Acad. Sci. USA101, 14162–14167 (2004). CASPubMedPubMed Central Google Scholar
Bacolla, A., Wojciechowska, M., Kosmider, B., Larson, J. E. & Wells, R. D. The involvement of non-B DNA structures in gross chromosomal rearrangements. DNA Repair (Amst.)5, 1161–1170 (2006). CAS Google Scholar
Inagaki, H. et al. Chromosomal instability mediated by non-B DNA: cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans. Genome Res.19, 191–198 (2009). CASPubMed CentralPubMed Google Scholar
Myers, S., Freeman, C., Auton, A., Donnelly, P. & McVean, G. A common sequence motif associated with recombination hot spots and genome instability in humans. Nature Genet.40, 1124–1129 (2008). CASPubMed Google Scholar
Shaw, C. J. & Lupski, J. R. Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum. Mol. Genet.13, R57–R64 (2004). CASPubMed Google Scholar
Bi, W. et al. Increased LIS1 expression affects human and mouse brain development. Nature Genet.41, 168–177 (2009). CASPubMed Google Scholar
Galhardo, R. S., Hastings, P. J. & Rosenberg, S. M. Mutation as a stress response and the regulation of evolvability. Crit. Rev. Biochem. Mol. Biol.42, 399–435 (2007). A broad review of stress-induced mutation and its meaning for evolution. CASPubMed CentralPubMed Google Scholar
Rosenberg, S. M. Evolving responsively: adaptive mutation. Nature Rev. Genet.2, 504–515 (2001). CASPubMed Google Scholar
Cirz, R. T. et al. Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol.3, e176 (2005). PubMed CentralPubMed Google Scholar
Riesenfeld, C., Everett, M., Piddock, L. J. & Hall, B. G. Adaptive mutations produce resistance to ciprofloxacin. Antimicrob. Agents Chemother.41, 2059–2060 (1997). CASPubMed CentralPubMed Google Scholar
Bindra, R. S. S. et al. Down-regulation of Rad51 and decreased homologous recombination in hypoxic cancer cells. Mol. Cell. Biol.24, 8504–8518 (2004). This paper shows that HR enzymes are downregulated by stress in human cells, and that this is accompanied by reduction in HR. CASPubMed CentralPubMed Google Scholar
Mihaylova, V. T. et al. Decreased expression of the DNA mismatch repair gene Mlh1 under hypoxic stress in mammalian cells. Mol. Cell. Biol.23, 3265–3273 (2003). CASPubMed CentralPubMed Google Scholar
Kolodner, R. D. et al. Germ-line msh6 mutations in colorectal cancer families. Cancer Res.59, 5068–5074 (1999). CASPubMed Google Scholar
Loeb, L. A. Mutator phenotype may be required for multistage carcinogenesis. Cancer Res.51, 3075–3079 (1991). CASPubMed Google Scholar
Modrich, P. Mismatch repair, genetic stability and tumour avoidance. Phil. Trans. R. Soc. Lond. B347, 89–95 (1995). CAS Google Scholar
Nguyen, D. Q. et al. Reduced purifying selection prevails over positive selection in human copy number variant evolution. Genome Res.18, 1711–1723 (2008). CASPubMed CentralPubMed Google Scholar
Perry, G. H. et al. Diet and the evolution of human amylase gene copy number variation. Nature Genet.39, 1256–1260 (2007). CASPubMed Google Scholar
Gonzalez, E. et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science307, 1434–1440 (2005). CASPubMed Google Scholar
Higgs, D. R. et al. A review of the molecular genetics of the human alpha-globin gene cluster. Blood73, 1081–1104 (1989). CASPubMed Google Scholar
Nozawa, M., Kawahara, Y. & Nei, M. Genomic drift and copy number variation of sensory receptor genes in humans. Proc. Natl Acad. Sci. USA104, 20421–20426 (2007). CASPubMedPubMed Central Google Scholar
Jakobsson, M. et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature451, 998–1003 (2008). CASPubMed Google Scholar
Locke, D. P. et al. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet.79, 275–290 (2006). CASPubMed CentralPubMed Google Scholar
Sharp, A. J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet.77, 78–88 (2005). CASPubMed CentralPubMed Google Scholar
Fortna, A. et al. Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol.2, E207 (2004). PubMed CentralPubMed Google Scholar
McCarroll, S. A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genet.40, 1166–1174 (2008). CASPubMed Google Scholar
Turner, D. J. et al. Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nature Genet.40, 90–95 (2008). CASPubMed Google Scholar
Lam, K. W. & Jeffreys, A. J. Processes of copy-number change in human DNA: the dynamics of α-globin gene deletion. Proc. Natl Acad. Sci. USA103, 8921–8927 (2006). CASPubMedPubMed Central Google Scholar
Lam, K. W. & Jeffreys, A. J. Processes of de novo duplication of human α-globin genes. Proc. Natl Acad. Sci. USA104, 10950–10955 (2007). CASPubMedPubMed Central Google Scholar
Flores, M. et al. Recurrent DNA inversion rearrangements in the human genome. Proc. Natl Acad. Sci. USA104, 6099–6106 (2007). CASPubMedPubMed Central Google Scholar
Liang, Q., Conte, N., Skarnes, W. C. & Bradley, A. Extensive genomic copy number variation in embryonic stem cells. Proc. Natl Acad. Sci. USA105, 17453–17456 (2008). CASPubMedPubMed Central Google Scholar
Lupski, J. R. Genomic rearrangements and sporadic disease. Nature Genet.39, S43–47 (2007). CASPubMed Google Scholar
van Ommen G. J. Frequency of new copy number variation in humans. Nature Genet.37, 333–334 (2005). CASPubMed Google Scholar
Tuzun, E., Bailey, J. A. & Eichler, E. E. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res.14, 493–506 (2004). CASPubMed CentralPubMed Google Scholar
Graubert, T. A. et al. A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet.3, e3 (2007). PubMed CentralPubMed Google Scholar
Lovett, S. T. Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences. Mol. Microbiol.52, 1243–1253 (2004). CASPubMed Google Scholar