Genome-wide expression analysis identifies a modulator of ionizing radiation-induced p53-independent apoptosis in Drosophila melanogaster

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  van Bergeijk, Petra ^a,b   Heimiller, Joseph ^a   Uyetake, Lyle ^a   Su, Tin Tin ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GROWTH ARREST AND DNA DAMAGE INDUCIBLE PROTEIN 45; INITIATION FACTOR 1A; PROTEIN P53; STRESS ACTIVATED PROTEIN KINASE; TRANSCRIPTOME; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR 4; DROSOPHILA PROTEIN; MESSENGER RNA;

ANIMAL CELL; ANIMAL TISSUE; APOPTOSIS; ARTICLE; DNA DAMAGE; DROSOPHILA MELANOGASTER; EF1A GENE; EMBRYO; GENE EXPRESSION; IONIZING RADIATION; LARVA; MICROARRAY ANALYSIS; MUTANT; NONHUMAN; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; WILD TYPE; ANIMAL; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; GENOME; HUMAN; METABOLISM; MUTATION; RADIATION EXPOSURE;

DROSOPHILA MELANOGASTER; METAZOA;

ANIMALS; APOPTOSIS; DNA DAMAGE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GENE EXPRESSION PROFILING; GENOME, INSECT; HUMANS; LARVA; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84861533299     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036539     Document Type: Article

References (46)

1. Brady CA, Attardi LD, (2010) p53 at a glance. J Cell Sci 123: 2527-2532.
2. Meek DW, (2004) The p53 response to DNA damage. DNA Repair (Amst) 3: 1049-1056.
3. Vogelstein B, Lane D, Levine AJ, (2000) Surfing the p53 network. Nature 408: 307-310.
4. Kaelin WG Jr, (1999) The emerging p53 gene family. J Natl Cancer Inst 91: 594-598.
5. Urist M, Tanaka T, Poyurovsky MV, Prives C, (2004) p73 induction after DNA damage is regulated by checkpoint kinases Chk1 and Chk2. Genes Dev 18: 3041-3054.
6. Wakatsuki M, Ohno T, Iwakawa M, Ishikawa H, Noda S, et al. (2008) p73 protein expression correlates with radiation-induced apoptosis in the lack of p53 response to radiation therapy for cervical cancer. Int J Radiat Oncol Biol Phys 70: 1189-1194.
7. Ahmad ZK, Altuna X, Lopez JP, An Y, Wang-Rodriguez J, et al. (2009) p73 expression and function in vestibular schwannoma. Arch Otolaryngol Head Neck Surg 135: 662-669.
8. Wichmann A, Jaklevic B, Su TT, (2006) Ionizing radiation induces caspase-dependent but Chk2- and p53-independent cell death in Drosophila melanogaster. Proc Natl Acad Sci U S A 103: 9952-9957.
9. McNamee LM, Brodsky MH, (2009) p53-independent apoptosis limits DNA damage-induced aneuploidy. Genetics 182: 423-435.
10. Wichmann A, Uyetake L, Su TT, (2010) E2F1 and E2F2 have opposite effects on radiation-induced p53-independent apoptosis in Drosophila. Dev Biol 346: 80-89.
11. Brodsky MH, Nordstrom W, Tsang G, Kwan E, Rubin GM, et al. (2000) Drosophila p53 binds a damage response element at the reaper locus. Cell 101: 103-113.
12. Jin S, Martinek S, Joo WS, Wortman JR, Mirkovic N, et al. (2000) Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc Natl Acad Sci U S A 97: 7301-7306.
13. Ollmann M, Young LM, Di Como CJ, Karim F, Belvin M, et al. (2000) Drosophila p53 is a structural and functional homolog of the tumor suppressor p53. Cell 101: 91-101.
14. Wells BS, Yoshida E, Johnston LA, (2006) Compensatory proliferation in Drosophila imaginal discs requires Dronc-dependent p53 activity. Curr Biol 16: 1606-1615.
15. Fan Y, Bergmann A, (2008) Distinct mechanisms of apoptosis-induced compensatory proliferation in proliferating and differentiating tissues in the Drosophila eye. Dev Cell 14: 399-410.
16. Ryoo HD, Gorenc T, Steller H, (2004) Apoptotic cells can induce compensatory cell proliferation through the JNK and the Wingless signaling pathways. Dev Cell 7: 491-501.
17. Brodsky MH, Weinert BT, Tsang G, Rong YS, McGinnis NM, et al. (2004) Drosophila melanogaster MNK/Chk2 and p53 regulate multiple DNA repair and apoptotic pathways following DNA damage. Mol Cell Biol 24: 1219-1231.
18. Jaklevic BR, Su TT, (2004) Relative contribution of DNA repair, cell cycle checkpoints, and cell death to survival after DNA damage in Drosophila larvae. Curr Biol 14: 23-32.
19. Wells BS, Johnston LA, (2011) Maintenance of imaginal disk plasticity and regenerative potential in Drosophila by p53. Developmental Biology in press.
20. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
21. Cha GH, Cho KS, Lee JH, Kim M, Kim E, et al. (2003) Discrete functions of TRAF1 and TRAF2 in Drosophila melanogaster mediated by c-Jun N-terminal kinase and NF-kappaB-dependent signaling pathways. Mol Cell Biol 23: 7982-7991.
22. Takekawa M, Saito H, (1998) A family of stress-inducible GADD45-like proteins mediate activation of the stress-responsive MTK1/MEKK4 MAPKKK. Cell 95: 521-530.
23. Peretz G, Bakhrat A, Abdu U, (2007) Expression of the Drosophila melanogaster GADD45 homolog (CG11086) affects egg asymmetric development that is mediated by the c-Jun N-terminal kinase pathway. Genetics 177: 1691-1702.
24. Johnston LA, (2009) Competitive interactions between cells: death, growth, and geography. Science 324: 1679-1682.
25. de la Cova C, Abril M, Bellosta P, Gallant P, Johnston LA, (2004) Drosophila myc regulates organ size by inducing cell competition. Cell 117: 107-116.
26. Li W, Baker NE, (2007) Engulfment is required for cell competition. Cell 129: 1215-1225.
27. Sokolov M, Panyutin IG, Neumann R, (2006) Genome-wide gene expression changes in normal human fibroblasts in response to low-LET gamma-radiation and high-LET-like 125IUdR exposures. Radiat Prot Dosimetry 122: 195-201.
28. Akdemir F, Christich A, Sogame N, Chapo J, Abrams JM, (2007) p53 directs focused genomic responses in Drosophila. Oncogene 26: 5184-5193.
29. Lee CY, Clough EA, Yellon P, Teslovich TM, Stephan DA, et al. (2003) Genome-wide analyses of steroid- and radiation-triggered programmed cell death in Drosophila. Curr Biol 13: 350-357.
30. Zhang Y, Lin N, Carroll PM, Chan G, Guan B, et al. (2008) Epigenetic blocking of an enhancer region controls irradiation-induced proapoptotic gene expression in Drosophila embryos. Dev Cell 14: 481-493.
31. Biedermann KA, Sun JR, Giaccia AJ, Tosto LM, Brown JM, (1991) scid mutation in mice confers hypersensitivity to ionizing radiation and a deficiency in DNA double-strand break repair. Proc Natl Acad Sci U S A 88: 1394-1397.
32. Sokolov MV, Panyutin IV, Panyutin IG, Neumann RD, (2011) Dynamics of the transcriptome response of cultured human embryonic stem cells to ionizing radiation exposure. Mutat Res 709-710: 40-48.
33. Rashi-Elkeles S, Elkon R, Shavit S, Lerenthal Y, Linhart C, et al. (2011) Transcriptional modulation induced by ionizing radiation: p53 remains a central player. Molecular oncology 5: 336-348.
34. Mehrotra S, Maqbool SB, Kolpakas A, Murnen K, Calvi BR, (2008) Endocycling cells do not apoptose in response to DNA rereplication genotoxic stress. Genes Dev 22: 3158-3171.
35. Frolov MV, Huen DS, Stevaux O, Dimova D, Balczarek-Strang K, et al. (2001) Functional antagonism between E2F family members. Genes Dev 15: 2146-2160.
36. Lu X, de la Pena L, Barker C, Camphausen K, Tofilon PJ, (2006) Radiation-induced changes in gene expression involve recruitment of existing messenger RNAs to and away from polysomes. Cancer Res 66: 1052-1061.
37. Bouwmeester T, Bauch A, Ruffner H, Angrand PO, Bergamini G, et al. (2004) A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 6: 97-105.
38. Pecorari L, Marin O, Silvestri C, Candini O, Rossi E, et al. (2009) Elongation Factor 1 alpha interacts with phospho-Akt in breast cancer cells and regulates their proliferation, survival and motility. Mol Cancer 8: 58.
39. He H, Sun Y, (2007) Ribosomal protein S27L is a direct p53 target that regulates apoptosis. Oncogene 26: 2707-2716.
40. Gladstone M, Frederick B, Zheng D, Edwards A, Yoon P, et al. (2012) A translation inhibitor identified in a Drosophila screen enhances the effect of ionizing radiation and taxol in mammalian models of cancer. Disease models & mechanisms.
41. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
42. Wu Z, Irizarry RA, Gentleman RC, Martinez-Murillo F, Spencer F, (2004) A Model-Based Background Adjustment for Oligonucleotide Expression Arrays. Journal of the American Statistical Association 99: 909-917.
43. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
44. Baldi P, Long AD, (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509-519.
45. Vardhanabhuti S, Blakemore SJ, Clark SM, Ghosh S, Stephens RJ, et al. (2006) A comparison of statistical tests for detecting differential expression using Affymetrix oligonucleotide microarrays. OMICS 10: 555-566.
46. Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS, (2005) Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 6: R16.