Copy number variants are produced in response to low-dose ionizing radiation in cultured cells

Environmental and Molecular Mutagenesis

Volumn 55, Issue 2, 2014, Pages 103-113

  Arlt, Martin F ^a   Rajendran, Sountharia ^a   Birkeland, Shanda R ^b   Wilson, Thomas E ^a,b   Glover, Thomas W ^a,b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

CNV; Ionizing radiation; Replication stress

Indexed keywords

CNV; IONIZING RADIATION; REPLICATION STRESS;

CELL CYCLE CHECKPOINTS; CELL LINE; CHROMOSOME BREAKPOINTS; DNA COPY NUMBER VARIATIONS; DNA REPLICATION; FIBROBLASTS; GENE DELETION; GENE DUPLICATION; GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84893734050     PISSN: 08936692     EISSN: 10982280     Source Type: Journal    
DOI: 10.1002/em.21840     Document Type: Article

References (32)

1. Arlt MF, Mulle JG, Schaibley VM, Ragland RL, Durkin SG, Warren ST, Glover TW. 2009. Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants. Am J Hum Genet 84:339-350.
2. Arlt MF, Ozdemir AC, Birkeland SR, Lyons RH Jr, Glover TW, Wilson TE. 2011a. Comparison of constitutional and replication stress-induced genome structural variation by SNP array and mate-pair sequencing. Genetics 187:675-683.
3. Arlt MF, Ozdemir AC, Birkeland SR, Wilson TE, Glover TW. 2011b. Hydroxyurea induces de novo copy number variants in human cells. Proc Natl Acad Sci USA 108:17360-17365.
4. Arlt MF, Rajendran S, Birkeland SR, Wilson TE, Glover TW. 2012. De novo CNV formation in mouse embryonic stem cells occurs in the absence of Xrcc4-dependent nonhomologous end joining. PLoS Genet 8:e1002981.
5. Beunders G, Voorhoeve E, Golzio C, Pardo LM, Rosenfeld JA, Talkowski ME, Simonic I, Lionel AC, Vergult S, Pyatt RE, et al. 2013. Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus. Am J Hum Genet 92:210-220.
6. Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM, Buck G, Chen L, Beare D, Latimer C, et al. 2010. Signatures of mutation and selection in the cancer genome. Nature 463:893-898.
7. Birkeland SR, Jin N, Ozdemir AC, Lyons RH Jr, Weisman LS, Wilson TE. 2010. Discovery of mutations in Saccharomyces cerevisiae by pooled linkage analysis and whole-genome sequencing. Genetics 186:1127-1137.
8. Carvalho CM, Pehlivan D, Ramocki MB, Fang P, Alleva B, Franco LM, Belmont JW, Hastings PJ, Lupski JR. 2013. Replicative mechanisms for CNV formation are error prone. Nat Genet 45:1319-1326.
9. Di Leonardo A, Linke SP, Clarkin K, Wahl GM. 1994. DNA damage triggers a prolonged p53-dependent G1 arrest and long-term induction of Cip1 in normal human fibroblasts. Genes Dev 8:2540-2551.
10. Dimitrijevic-Bussod M, Balzaretti-Maggi VS, Gadbois DM. 1999. Extracellular matrix and radiation G1 cell cycle arrest in human fibroblasts. Cancer Res 59:4843-4847.
11. Durkin SG, Ragland RL, Arlt MF, Mulle JG, Warren ST, Glover TW. 2008. Replication stress induces tumor-like microdeletions in FHIT/FRA3B. Proc Natl Acad Sci USA 105:246-251.
12. Gadbois DM, Bradbury EM, Lehnert BE. 1997. Control of radiation-induced G1 arrest by cell-substratum interactions. Cancer Res 57:1151-1156.
13. Gadbois DM, Crissman HA, Nastasi A, Habbersett R, Wang SK, Chen D, Lehnert BE. 1996. Alterations in the progression of cells through the cell cycle after exposure to alpha particles or gamma rays. Radiat Res 146:414-424.
14. Gatei M, Sloper K, Sorensen C, Syljuasen R, Falck J, Hobson K, Savage K, Lukas J, Zhou BB, Bartek J, et al. 2003. Ataxia-telangiectasia-mutated (ATM) and NBS1-dependent phosphorylation of Chk1 on Ser-317 in response to ionizing radiation. J Biol Chem 278:14806-14811.
15. Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP, et al. 2009. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 459:569-573.
16. Guadagno TM, Assoian RK. 1991. G1/S control of anchorage-independent growth in the fibroblast cell cycle. J Cell Biol 115:1419-1425.
17. Harper JV, Anderson JA, O'Neill P. 2010. Radiation induced DNA DSBs: Contribution from stalled replication forks? DNA Repair (Amst) 9:907-913.
18. Hastings PJ, Ira G, Lupski JR. 2009. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 5:e1000327.
19. Helleday T, Lo J, van Gent DC, Engelward BP. 2007. DNA double-strand break repair: from mechanistic understanding to cancer treatment. DNA Repair (Amst) 6:923-935.
20. Huang HL, Hsing HW, Lai TC, Chen YW, Lee TR, Chan HT, Lyu PC, Wu CL, Lu YC, Lin ST, et al. 2010. Trypsin-induced proteome alteration during cell subculture in mammalian cells. J Biomed Sci 17:36.
21. Karlsson R, Graae L, Lekman M, Wang D, Favis R, Axelsson T, Galter D, Belin AC, Paddock S. 2012. MAGI1 copy number variation in bipolar affective disorder and schizophrenia. Biol Psychiatry 71:922-930.
22. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12:996-1006.
23. Kohno T, Yokota J. 2006. Molecular processes of chromosome 9p21 deletions causing inactivation of the p16 tumor suppressor gene in human cancer: deduction from structural analysis of breakpoints for deletions. DNA Repair (Amst) 5:1273-1281.
24. Kresse SH, Ohnstad HO, Paulsen EB, Bjerkehagen B, Szuhai K, Serra M, Schaefer KL, Myklebost O, Meza-Zepeda LA. 2009. LSAMP, a novel candidate tumor suppressor gene in human osteosarcomas, identified by array comparative genomic hybridization. Genes Chromosomes Cancer 48:679-693.
25. Krishnamoorthy K, Thomson J. 2004. A more powerful test for comparing two Poisson means. J Stat Plan Inference 119:23-35.
26. Kuzminov A. 2001. Single-strand interruptions in replicating chromosomes cause double-strand breaks. Proc Natl Acad Sci USA 98:8241-8246.
27. Ljungman M. 1999. Repair of radiation-induced DNA strand breaks does not occur preferentially in transcriptionally active DNA. Radiat Res 152:444-449.
28. Pasic I, Shlien A, Durbin AD, Stavropoulos DJ, Baskin B, Ray PN, Novokmet A, Malkin D. 2010. Recurrent focal copy-number changes and loss of heterozygosity implicate two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma. Cancer Res 70:160-171.
29. Saleh-Gohari N, Bryant HE, Schultz N, Parker KM, Cassel TN, Helleday T. 2005. Spontaneous homologous recombination is induced by collapsed replication forks that are caused by endogenous DNA single-strand breaks. Mol Cell Biol 25:7158-7169.
30. Ward JF. 1988. DNA damage produced by ionizing radiation in mammalian cells: identities, mechanisms of formation, and reparability. Prog Nucleic Acid Res Mol Biol 35:95-125.
31. Zhang F, Gu W, Hurles ME, Lupski JR. 2009. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10:451-481.
32. Zhao H, Piwnica-Worms H. 2001. ATR-mediated checkpoint pathways regulate phosphorylation and activation of human Chk1. Mol Cell Biol 21:4129-4139.