Functional study of zebrafish udu and its relationship to the notch signaling pathway

FUNCTIONAL STUDY OF ZEBRAFISH UDU AND ITS RELATIONSHIP TO THE NOTCH SIGNALING PATHWAY LIM CHIAW HWEE A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY INSTITUTE OF MOLECULAR AND CELL BIOLOGY DEPARTMENT OF BIOCHEMISTRY NATIONAL UNIVERSITY OF SINGAPORE 2008 Acknowledgements I sincerely thank my supervisior, Dr Yun-Jin Jiang for acting as my mentor, providing guidance, and imparting knowledge throughout my PhD program I also thank Dr Liou Yih-Cheng, Dr Alan Porter and Dr Yang Xiaohang for serving on my PhD graduate committee I owe special thanks to all members of Danio unit: the aunties, the guys and Dr You May-Su for their help in rearing and maintaining zebrafish in this study I extend my sincere appreciation to all the members of JYJ laboratory: Steven and Qi Mei for their laboratory support, especially to Li Qing for imparting valuable techniques, Shang Wei for cryostat sectioning, William and Xuehui for valuable discussion; ex-members of JYJ laboratory: Haoying, Ma Ming, Chengjin, Nguyet, Kate, Stephanine, Nick, Kenny, Kian Hong, Ashok and Rida for their assistance that helped make my experience in JYJ laboratory a memorable one Special thank to visiting scientist Dr Hsaio Chung-Der for sharing imaging technique I also thank Dr Soojin Ryu from Prof Wolfgang Driever’s laboratory for sharing expertise on flow cytometry I thank Siew Chin from BSF facility for flow cytometry analysis I thank the IMCB community of researchers and graduate students for their technical advice and friendship Funding for this project was provided by A-STAR and graduate studies was funded by IMCB Finally, I thank my family for providing the encouragement, support and their understanding, patience that made my pursuit of a graduate degree possible i Tables of Contents Page Acknowledgements i Table of Contents ii Summary viii List of Tables xi List of Figures xii List of Abbreviations xvi List of Publications xix CHAPTER Introduction 1.1 Identification of udu gene 1.2 Udu and primitive erythropoiesis 1.3 p53, a tumor suppressor 1.4 p53 isoforms 1.5 DNA damage pathway and p53 response ii 1.6 Apoptosis-the elimination of tumorigenic cells 1.7 DNA repair 10 1.8 SANT and chromatin remodeling 12 1.9 Function of SIN3/PAH domain 13 1.10 Organization of eukaryotic DNA 14 1.11 DNA replication 17 1.12 Udu counterparts in human and mouse 20 1.13 Notch signaling and its core components 22 1.14 Regulation of Notch-ligand activity 23 1.15 Notch and lateral inhibition: neurogenesis 25 1.16 Notch and midline cell fate specification 26 1.17 Notch and boundaries formation: somitogenesis 27 1.18 Notch and diseases 29 1.19 Notch and p53 30 1.20 Regulation of Notch signaling by p53 32 1.21 Zebrafish: The model system 33 1.22 Advantages of using zebrafish 34 1.23 Zebrafish mutagenic screen 35 1.24 Formation of morphologically distinct somites 36 1.25 Somite patterning 37 iii 1.26 Aims of this study 39 Materials and Methods 44 2.1 Zebrafish maintenance and embryos 44 2.2 Irradiation of zebrafish embryos with ultraviolet light 44 2.3 Total RNA extraction 44 2.4 Reverse transcription PCR 45 2.5 Quantative Real-time PCR 45 2.6 Embryos preparation 46 2.7 Antisense probe synthesis 46 2.8 Whole-mount in situ hybridization 47 2.9 Injection experiments 48 2.10 Synthesis of 5’capped mRNA 48 2.11 Brdu incorporation and staining 49 2.12 Detection of apoptotic cells in whole-mount embryos 49 2.13 Cryostat sectioning 50 2.14 FACS and cell cycle analysis 50 2.15 Comet assay 51 2.16 Immunohistochemical staining 52 CHAPTER iv 2.17 Plasmids 53 2.18 Cell culture, transfection and Immunoprecipitation 53 2.19 Cells synchronization 54 2.20 Immunofluorescence 54 2.21 Microscopy 55 udutu24 mutants were characterized by defects in somites, myotome boundaries, muscle pioneers and midline structures 59 3.1 Background 59 3.2 Summary 60 3.3 Results 61 3.31 udutu24 mutants display somite defects 61 3.32 Segmentation clock is functioning in udutu24 mutants 63 3.33 Loss of udu function affects somite boundaries and muscle pioneers 64 3.34 udutu24 mutants show defects in midline structures 66 Discussion 67 Activation of ATM-Chk2-p53 signaling pathway in udutu24 mutants 77 Background 77 CHAPTER 3.4 CHAPTER 4.1 v 4.2 Summary 80 4.3 Results 81 4.31 Dramatic increase of apoptotic cell in udutu24 mutants 81 4.32 Elevated level of p53 mRNA transcript in udutu24 mutants 82 4.33 p53 and its downstream target genes are upregulated in udutu24 mutants 83 4.34 Loss of udu function in cell cycle defects 84 4.35 Activation of ATM-Chk2 pathway in udutu24 mutants 85 4.36 udu mutation causes DNA double stranded breaks 86 4.37 The induction of γ-H2AX after DNA damage 87 Discussion 88 PAH-L and SANT-L domains are essential for DNA replication 108 5.1 Background 108 5.2 Summary 109 5.3 Results 110 5.31 Udu counterparts in human and mouse 110 5.32 Udu is predominantly localized in the nucleus 111 5.33 PAH-L and SANT-L domains may be essential for DNA replication 112 4.4 CHAPTER vi 5.34 Interaction of PAH-L+SANT-L domains with Mcm3 and Mcm4 114 Discussion 114 Loss of functional udu up-regulates p53 and down-regulates Notch signaling during zebrafish development 130 6.1 Background 130 6.2 Summary 132 6.3 Results 133 6.31 Notch activity is down-regulated in udutu24 mutants 133 6.32 Elevated level of p53 could regulate Notch 133 6.33 Udu could regulate Notch 134 6.34 Differential level of Notch acts to regulate the elevated level of p53 in udu deficient background during zebrafish development 135 6.4 Discussion 136 CHAPTER Conclusions 145 CHAPTER References 153 5.4 CHAPTER vii Summary The zebrafish mutant, ugly duckling (udutu24) was isolated from the 1996 Tübingen Nethyl-N-nitrosourea (ENU) screen as a mutant affecting morphogenesis during gastrulation and tail formation (Hammerschmidt et al., 1996), while udusq1 mutant was isolated in a genetic screen aiming at mutants with defects in hematopoiesis (Liu et al., 2007) Udu has been shown to play an essential role during blood cell development; however, its roles in other cellular processes remain largely unexplored Both udutu24 and udusq1 embryos share similar phenotypes and the earliest observable developmental defects in udutu24 and udusq1 mutants are the somite phenotypes In this study, I have used udutu24 mutants to carry out studies to further characterize their somite phenotype The expression pattern of somite morphological markers indicated that the anterior-posterior somite identity of udutu24 embryos were affected, while the segmentation clock regulating zebrafish somitogenesis was functioning in udutu24 mutants Overall, my results showed that udutu24 mutants have defects in somite boundaries, muscle pioneers and midline structures Zebrafish embryos with mutations for Notch components have deficits of floorplate and hypochord cells, thus indicating Notch signaling is an important regulator of midline cell fate specification (Appel et al., 1999; Latimer et al., 2002; Jülich et al., 2005; Latimer and Appel, 2006; Zhang et al., 2007) Whole mount in situ hybridization (WISH) of col2a1 and her4 have provided clues to suggest that the Notch signaling pathway may be impaired in udutu24 mutants Hence, further experiments were carried out to investigate the relationship of Udu, p53 and Notch Results indicated that elevated level of p53 in viii udutu24 mutants could regulate Notch activity negatively and experimental results from mib and udu double mutants showed that differential level of Notch can function to rescue the cell death phenotype that is mediated via the p53-dependent pathway in udu embryos Finally, current data suggested that Udu may function to activate Notch only in the absence of p53, possibly due to the interference of Notch activation by p53 The main aim of this study is to find out the causes for the up-regulation of p53 Terminal deoxynucleotidyl transferase-mediated X-dUTP nick end labeling (TUNEL) assay showed that increased activation of cellular p53-apoptotic pathway correlated with regions of developmental abnormalities Experimental results showed that udutu24 mutants’ extensive p53-dependent apoptosis requires activation of the ATM-Chk2 pathway The DNA damage response pathway is a cellular surveillance system that senses the presence of damaged DNA and elicits an appropriate response to the damage The fluorescence-activated cell sorting (FACS) analysis showed that the loss of udu function resulted in defective cell cycle progression and comet assay indicated the presence of increased DNA damage in udutu24 mutants Positional cloning revealed that Udu protein encodes a novel nuclear factor consisting of two PAH-L (Paired Amphipathic α-Helix like) repeats and a putative SANT-L (SW13, ADA2, N-Cor and TFIIIB like) domain and yeast-two hybrid (Y2H) screen has identified Mcm3 and Mcm4 as interacting partners of these domains Co-immunoprecipitation data indicated that PAH-L repeats and SANT-L domain of Udu interacted with Mcm3 and Mcm4 The reduction of BrdU-incorporated cells in udutu24 mutants showed that progression through the S phase is disrupted The pericentromeric heterochromatin is known to serve ix Nam Y, Weng AP, Aster JC and Blacklow SC (2003) Structural requirements for assembly of the CSL.intracellular Notch1.Mastermind-like transcriptional activation complex J Biol Chem 278:21232-21239 Nasevicius A and Ekker SC (2000) Effective targeted gene 'knockdown' in zebrafish Nat Genet 26:216-220 Nicolas M, Wolfer A, Raj K, Kummer JA, Mill P, van Noort M, Hui CC, Clevers H, Dotto GP and Radtke F (2003) Notch1 functions as a tumor suppressor in mouse skin Nat Genet 33:416-421 Nicoli S and Presta M (2007) The zebrafish/tumor xenograft angiogenesis assay Nat Protoc 2:2918-2923 Nurse P (1990) Universal control mechanism regulating onset of M-phase Nature 344:503-508 Nyberg KA, Michelson RJ, Putnam CW and Weinert TA (2002) Toward maintaining the genome: DNA damage and replication checkpoints Annu Rev Genet 36:617-656 Oates AC and Ho RK (2002) Hairy/E(spl)-related (Her) genes are central components of the segmentation oscillator and display redundancy with the Delta/Notch signaling pathway in the formation of anterior segmental boundaries in the zebrafish Development 129:2929-2946 Oda T, Elkahloun AG, Pike BL, Okajima K, Krantz ID, Genin A, Piccoli DA, Meltzer PS, Spinner NB, Collins FS and Chandrasekharappa SC (1997) Mutations in the human Jagged1 gene are responsible for Alagille syndrome Nat Genet 16:235-242 Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S and Nishimura Y (1994) Solution structure of a specific DNA complex of the Myb DNAbinding domain with cooperative recognition helices Cell 79:639-648 Oh IH and Reddy EP (1999) The myb gene family in cell growth, differentiation and apoptosis Oncogene 18:3017-3033 178 Ohishi K, Katayama N, Shiku H, Varnum-Finney B and Bernstein ID (2003) Notch signalling in hematopoiesis Semin Cell Dev Biol 14:143-150 Oka C, Nakano T, Wakeham A, de la Pompa JL, Mori C, Sakai T, Okazaki S, Kawaichi M, Shiota K, Mak TW and Honjo T (1995) Disruption of the mouse RBP-J kappa gene results in early embryonic death Development 121:3291-3301 O'Keefe RT, Henderson SC and Spector DL (1992) Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences J Cell Biol 116:1095-1110 Olive KP, Tuveson DA, Ruhe ZC, Yin B, Willis NA, Bronson RT, Crowley D and Jacks T (2004) Mutant p53 gain of function in two mouse models of Li-Fraumeni syndrome Cell 119:847-860 Ollmann, M., Young, L.M., Di Como, C.J., Karim, F., Belvin, M., Robertson, S., Whittaker, K., Demsky, M., Fisher, W.W., Buchman, A., et al 2000 Drosophila p53 is a structural and functional homolog of the tumor suppressor p53 Cell 101: 91–101 Oppenheim RW and Nunez R (1982) Electrical stimulation of hindlimb increases neuronal cell death in chick embryo Nature 295:57-59 Ostling O and Johanson KJ (1984) Microelectrophoretic study of radiation-induced DNA damages in individual mammalian cells Biochem Biophys Res Commun 123:291-298 Oswald F, Tauber B, Dobner T, Bourteele S, Kostezka U, Adler G, Liptay S and Schmid RM (2001) p300 acts as a transcriptional coactivator for mammalian Notch-1 Mol Cell Biol 21:7761-7774 Owen-Schaub LB, Angelo LS, Radinsky R, Ware CF, Gesner TG and Bartos DP (1995) Soluble Fas/APO-1 in tumor cells: a potential regulator of apoptosis? Cancer Lett 94:18 Pacek M and Walter JC (2004) A requirement for MCM7 and Cdc45 in chromosome unwinding during eukaryotic DNA replication EMBO J 23:3667-3676 179 Palmeirim I, Henrique D, Ish-Horowicz D and Pourquie O (1997) Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis Cell 91:639-648 Paques F and Haber JE (1999) Multiple pathways of recombination induced by doublestrand breaks in Saccharomyces cerevisiae Microbiol Mol Biol Rev 63:349-404 Parks AL, Huppert SS and Muskavitch MA (1997) The dynamics of neurogenic signalling underlying bristle development in Drosophila melanogaster Mech Dev 63:6174 Patael-Karasik Y, Daniely M, Gotlieb WH, Ben Baruch G, Schiby J, Barakai G, Goldman B, Aviram A and Friedman E (2000) Comparative genomic hybridization in inherited and sporadic ovarian tumors in Israel Cancer Genet Cytogenet 121:26-32 Paull TT, Rogakou EP, Yamazaki V, Kirchgessner CU, Gellert M and Bonner WM (2000) A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage Curr Biol 10:886-895 Pavlopoulos E, Pitsouli C, Klueg KM, Muskavitch MA, Moschonas NK and Delidakis C (2001) neuralized Encodes a peripheral membrane protein involved in delta signaling and endocytosis Dev Cell 1:807-816 Perez-Roger I, Kim SH, Griffiths B, Sewing A and Land H (1999) Cyclins D1 and D2 mediate myc-induced proliferation via sequestration of p27(Kip1) and p21(Cip1) EMBO J 18:5310-5320 Petcherski AG and Kimble J (2000) Mastermind is a putative activator for Notch Curr Biol 10:R471-R473 Peterson CL and Laniel MA (2004) Histones and histone modifications Curr Biol 14:R546-R551 Pihan GA, Wallace J, Zhou Y and Doxsey SJ (2003) Centrosome abnormalities and chromosome instability occur together in pre-invasive carcinomas Cancer Res 63:13981404 180 Pile LA, Schlag EM and Wassarman DA (2002) The SIN3/RPD3 deacetylase complex is essential for G(2) phase cell cycle progression and regulation of SMRTER corepressor levels Mol Cell Biol 22:4965-4976 Pitsouli C and Delidakis C (2005) The interplay between DSL proteins and ubiquitin ligases in Notch signaling Development 132:4041-4050 Pourquie O (2000) Segmentation of the paraxial mesoderm and vertebrate somitogenesis Curr Top Dev Biol 47:81-105 Pourquie O (2001) The vertebrate segmentation clock J Anat 199:169-175 Pourquie O (2003) The segmentation clock: converting embryonic time into spatial pattern Science 301:328-330 Pozniak CD, Radinovic S, Yang A, McKeon F, Kaplan DR and Miller FD (2000) An anti-apoptotic role for the p53 family member, p73, during developmental neuron death Science 289:304-306 Primmett DR, Norris WE, Carlson GJ, Keynes RJ and Stern CD (1989) Periodic segmental anomalies induced by heat shock in the chick embryo are associated with the cell cycle Development 105:119-130 Primmett DR, Stern CD and Keynes RJ (1988) Heat shock causes repeated segmental anomalies in the chick embryo Development 104:331-339 Prochasson P, Neely KE, Hassan AH, Li B and Workman JL (2003) Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains Mol Cell 12:983-990 Qi R, An H, Yu Y, Zhang M, Liu S, Xu H, Guo Z, Cheng T and Cao X (2003) Notch1 signaling inhibits growth of human hepatocellular carcinoma through induction of cell cycle arrest and apoptosis Cancer Res 63:8323-8329 Radtke F and Raj K (2003) The role of Notch in tumorigenesis: oncogene or tumour suppressor? Nat Rev Cancer 3:756-767 181 Rangarajan A, Syal R, Selvarajah S, Chakrabarti O, Sarin A and Krishna S (2001) Activated Notch1 signaling cooperates with papillomavirus oncogenes in transformation and generates resistance to apoptosis on matrix withdrawal through PKB/Akt Virology 286:23-30 Rapp A and Greulich KO (2004) After double-strand break induction by UV-A, homologous recombination and nonhomologous end joining cooperate at the same DSB if both systems are available J Cell Sci 117:4935-4945 Rida PC, Le Minh N and Jiang YJ (2004) A Notch feeling of somite segmentation and beyond Dev Biol 265:2-22 Rogakou EP, Pilch DR, Orr AH, Ivanova VS and Bonner WM (1998) DNA doublestranded breaks induce histone H2AX phosphorylation on serine 139 J Biol Chem 273:5858-5868 Roperch JP, Alvaro V, Prieur S, Tuynder M, Nemani M, Lethrosne F, Piouffre L, Gendron MC, Israeli D, Dausset J, Oren M, Amson R and Telerman A (1998) Inhibition of presenilin expression is promoted by p53 and p21WAF-1 and results in apoptosis and tumor suppression Nat Med 4:835-838 Rothkamm K and Lobrich M (2003) Evidence for a lack of DNA double-strand break repair in human cells exposed to very low x-ray doses Proc Natl Acad Sci U S A 100:5057-5062 Rothkamm K, Kruger I, Thompson LH and Lobrich M (2003) Pathways of DNA doublestrand break repair during the mammalian cell cycle Mol Cell Biol 23:5706-5715 Roy MN, Prince VE and Ho RK (1999) Heat shock produces periodic somitic disturbances in the zebrafish embryo Mech Dev 85:27-34 Ruiz-Gomez M and Ghysen A (1993) The expression and role of a proneural gene, achaete, in the development of the larval nervous system of Drosophila EMBO J 12:1121-1130 Rundlett SE, Carmen AA, Kobayashi R, Bavykin S, Turner BM and Grunstein M (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription Proc Natl Acad Sci U S A 93:14503-14508 182 Ryu S, Holzschuh J, Erhardt S, Ettl AK and Driever W (2005) Depletion of minichomosome maintenance protein in the zebrafish retina causes cell-cycle defect and apoptosis Proc Natl Acad Sci U S A 102:18467-18472 Sah VP, Attardi LD, Mulligan GJ, Williams BO, Bronson RT and Jacks T (1995) A subset of p53-deficient embryos exhibit exencephaly Nat Genet 10:175-180 Sala A and Watson R (1999) B-Myb protein in cellular proliferation, transcription control, and cancer: latest developments J Cell Physiol 179:245-250 Sasaki Y, Ishida S, Morimoto I, Yamashita T, Kojima T, Kihara C, Tanaka T, Imai K, Nakamura Y and Tokino T (2002) The p53 family member genes are involved in the Notch signal pathway J Biol Chem 277:719-724 Savitsky K, Bar-Shira A, Gilad S, Rotman G, Ziv Y, Vanagaite L, Tagle DA, Smith S, Uziel T, Sfez S, Ashkenazi M, Pecker I, Frydman M, Harnik R, Patanjali SR, Simmons A, Clines GA, Sartiel A, Gatti RA, Chessa L, Sanal O, Lavin MF, Jaspers NG, Taylor AM, Schumacher, B., Hanazawa, M., Lee, M.H., Nayak, S., Volkmann, K., Hofmann, R., Hengartner, M., Schedl, T., and Gartner, A 2005 Translational repression of C elegans p53 by GLD-1 regulates DNA damage-induced apoptosis Cell 120: 357–368 Schuurmans C and Guillemot F (2002) Molecular mechanisms underlying cell fate specification in the developing telencephalon Curr Opin Neurobiol 12:26-34 Schwartz AL and Ciechanover A (1999) The ubiquitin-proteasome pathway and pathogenesis of human diseases Annu Rev Med 50:57-74 Scott KL and Plon SE (2003) Loss of Sin3/Rpd3 histone deacetylase restores the DNA damage response in checkpoint-deficient strains of Saccharomyces cerevisiae Mol Cell Biol 23:4522-4531 Sedgwick SG and Smerdon SJ (1999) The ankyrin repeat: a diversity of interactions on a common structural framework Trends Biochem Sci 24:311-316 Selkoe D and Kopan R (2003) Notch and Presenilin: regulated intramembrane proteolysis links development and degeneration Annu Rev Neurosci 26:565-597 183 Sengupta S and Harris CC (2005) p53: traffic cop at the crossroads of DNA repair and recombination Nat Rev Mol Cell Biol 6:44-55 Shaffer CD, Wallrath LL and Elgin SC (1993) Regulating genes by packaging domains: bits of heterochromatin in euchromatin? Trends Genet 9:35-37 Shafizadeh E, Paw BH, Foott H, Liao EC, Barut BA, Cope JJ, Zon LI and Lin S (2002) Characterization of zebrafish merlot/chablis as non-mammalian vertebrate models for severe congenital anemia due to protein 4.1 deficiency Development 129:4359-4370 Shechter D, Ying CY and Gautier J (2004) DNA unwinding is an Mcm complexdependent and ATP hydrolysis-dependent process J Biol Chem 279:45586-45593 Shepard JL, Amatruda JF, Stern HM, Subramanian A, Finkelstein D, Ziai J, Finley KR, Pfaff KL, Hersey C, Zhou Y, Barut B, Freedman M, Lee C, Spitsbergen J, Neuberg D, Weber G, Golub TR, Glickman JN, Kutok JL, Aster JC and Zon LI (2005) A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility Proc Natl Acad Sci U S A 102:13194-13199 Sherr CJ (1994) G1 phase progression: cycling on cue Cell 79:551-555 Shi Y, Dodson GE, Mukhopadhyay PS, Shanware NP, Trinh AT and Tibbetts RS (2007) Identification of carboxyl-terminal MCM3 phosphorylation sites using polyreactive phosphospecific antibodies J Biol Chem 282:9236-9243 Shieh SY, Ikeda M, Taya Y and Prives C (1997) DNA damage-induced phosphorylation of p53 alleviates inhibition by MDM2 Cell 91:325-334 Shiloh Y (2001) ATM and ATR: networking cellular responses to DNA damage Curr Opin Genet Dev 11:71-77 Shiloh Y (2003) ATM and related protein kinases: safeguarding genome integrity Nat Rev Cancer 3:155-168 Shiloh Y (2006) The ATM-mediated DNA-damage response: taking shape Trends Biochem Sci 31:402-410 184 Shin J, Poling J, Park HC and Appel B (2007) Notch signaling regulates neural precursor allocation and binary neuronal fate decisions in zebrafish Development 134:1911-1920 Shroff R, Arbel-Eden A, Pilch D, Ira G, Bonner WM, Petrini JH, Haber JE and Lichten M (2004) Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break Curr Biol 14:1703-1711 Sieger D, Tautz D and Gajewski M (2003) The role of Suppressor of Hairless in Notch mediated signalling during zebrafish somitogenesis Mech Dev 120:1083-1094 Siekmann AF and Lawson ND (2007) Notch signalling limits angiogenic cell behaviour in developing zebrafish arteries Nature 445:781-784 Siekmann AF, Covassin L and Lawson ND (2008) Modulation of VEGF signalling output by the Notch pathway Bioessays 30:303-313 Silverstein RA and Ekwall K (2005) Sin3: a flexible regulator of global gene expression and genome stability Curr Genet 47:1-17 Singh B, Reddy PG, Goberdhan A, Walsh C, Dao S, Ngai I, Chou TC, Charoenrat P, Levine AJ, Rao PH and Stoffel A (2002) p53 regulates cell survival by inhibiting PIK3CA in squamous cell carcinomas Genes Dev 16:984-993 Smerdon MJ and Conconi A (1999) Modulation of DNA damage and DNA repair in chromatin Prog Nucleic Acid Res Mol Biol 62:227-255 Smithers L, Haddon C, Jiang YJ and Lewis J (2000) Sequence and embryonic expression of deltaC in the zebrafish Mech Dev 90:119-123 Spronk CA, Tessari M, Kaan AM, Jansen JF, Vermeulen M, Stunnenberg HG et al (2000) The Mad1-Sin3B interaction involves a novel helical fold Nat Struct Biol 7:1100-1104 Stickney HL, Barresi MJ and Devoto SH (2000) Somite development in zebrafish Dev Dyn 219:287-303 185 Strano S, Munarriz E, Rossi M, Cristofanelli B, Shaul Y, Castagnoli L, Levine AJ, Sacchi A, Cesareni G, Oren M and Blandino G (2000) Physical and functional interaction between p53 mutants and different isoforms of p73 J Biol Chem 275:29503-29512 Streisinger G, Walker C, Dower N, Knauber D and Singer F (1981) Production of clones of homozygous diploid zebra fish (Brachydanio rerio) Nature 291:293-296 Taddei A, Maison C, Roche D and Almouzni G (2001) Reversible disruption of pericentric heterochromatin and centromere function by inhibiting deacetylases Nat Cell Biol 3:114-120 Taghert PH, Doe CQ and Goodman CS (1984) Cell determination and regulation during development of neuroblasts and neurones in grasshopper embryo Nature 307:163-165 Takeuchi T, Adachi Y and Ohtsuki Y (2005) Skeletrophin, a novel ubiquitin ligase to the intracellular region of Jagged-2, is aberrantly expressed in multiple myeloma Am J Pathol 166:1817-1826 Takke C and Campos-Ortega JA (1999) her1, a zebrafish pair-rule like gene, acts downstream of notch signalling to control somite development Development 126:30053014 Takke C, Dornseifer P, Weizsacker E and Campos-Ortega JA (1999) her4, a zebrafish homologue of the Drosophila neurogenic gene E(spl), is a target of NOTCH signalling Development 126:1811-1821 Talbot WS and Schier AF (1999) Positional cloning of mutated zebrafish genes Methods Cell Biol 60:259-286 Talora C, Cialfi S, Segatto O, Morrone S, Kim CJ, Frati L, Paolo DG, Gulino A and Screpanti I (2005) Constitutively active Notch1 induces growth arrest of HPV-positive cervical cancer cells via separate signaling pathways Exp Cell Res 305:343-354 Tamura K, Taniguchi Y, Minoguchi S, Sakai T, Tun T, Furukawa T and Honjo T (1995) Physical interaction between a novel domain of the receptor Notch and the transcription factor RBP-J kappa/Su(H) Curr Biol 5:1416-1423 186 Tanabe Y and Jessell TM (1996) Diversity and pattern in the developing spinal cord Science 274:1115-1123 Tani S, Kurooka H, Aoki T, Hashimoto N and Honjo T (2001) The N- and C-terminal regions of RBP-J interact with the ankyrin repeats of Notch1 RAMIC to activate transcription Nucleic Acids Res 29:1373-1380 Teng SC, Wu KJ, Tseng SF, Wong CW and Kao L (2006) Importin KPNA2, NBS1, DNA repair and tumorigenesis J Mol Histol 37:293-299 Thornberry NA and Lazebnik Y (1998) Caspases: enemies within Science 281:13121316 Tripathi V, Ali A, Bhat R and Pati U (2007) CHIP chaperones wild type p53 tumor suppressor protein J Biol Chem 282:28441-28454 Truman JW and Schwartz LM (1984) Steroid regulation of neuronal death in the moth nervous system J Neurosci 4:274-280 Trump BF and Berezesky IK (1995) Calcium-mediated cell injury and cell death FASEB J 9:219-228 Tsukiyama T (2002) The in vivo functions of ATP-dependent chromatin-remodelling factors Nat Rev Mol Cell Biol 3:422-429 Tye BK (1999) MCM proteins in DNA replication Annu Rev Biochem 68:649-686 Unsal-Kacmaz K, Makhov AM, Griffith JD and Sancar A (2002) Preferential binding of ATR protein to UV-damaged DNA Proc Natl Acad Sci U S A 99:6673-6678 Vairapandi M, Balliet AG, Fornace AJ, Jr., Hoffman B and Liebermann DA (1996) The differentiation primary response gene MyD118, related to GADD45, encodes for a nuclear protein which interacts with PCNA and p21WAF1/CIP1 Oncogene 12:25792594 187 van Attikum H, Fritsch O, Hohn B and Gasser SM (2004) Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair Cell 119:777-788 van Eeden FJ, Granato M, Schach U, Brand M, Furutani-Seiki M, Haffter P, Hammerschmidt M, Heisenberg CP, Jiang YJ, Kane DA, Kelsh RN, Mullins MC, Odenthal J, Warga RM, Allende ML, Weinberg ES and Nusslein-Volhard C (1996) Mutations affecting somite formation and patterning in the zebrafish, Danio rerio Development 123:153-164 Vaux DL, Haecker G and Strasser A (1994) An evolutionary perspective on apoptosis Cell 76:777-779 Vo N and Goodman RH (2001) CREB-binding protein and p300 in transcriptional regulation J Biol Chem 276:13505-13508 Vogelstein B, Lane D and Levine AJ (2000) Surfing the p53 network Nature 408:307310 Waldman T, Kinzler KW and Vogelstein B (1995) p21 is necessary for the p53-mediated G1 arrest in human cancer cells Cancer Res 55:5187-5190 Wallberg AE, Pedersen K, Lendahl U and Roeder RG (2002) p300 and PCAF act cooperatively to mediate transcriptional activation from chromatin templates by notch intracellular domains in vitro Mol Cell Biol 22:7812-7819 Wallrath LL (1998) Unfolding the mysteries of heterochromatin Curr Opin Genet Dev 8:147-153 Wang H, Clark I, Nicholson PR, Herskowitz I and Stillman DJ (1990) The Saccharomyces cerevisiae SIN3 gene, a negative regulator of HO, contains four paired amphipathic helix motifs Mol Cell Biol 10:5927-5936 Wang L, Cui Y, Lord BI, Roberts SA, Potten CS, Hendry JH and Scott D (1996) Gamma-ray-induced cell killing and chromosome abnormalities in the bone marrow of p53-deficient mice Radiat Res 146:259-266 188 Wang W and Struhl G (2005) Distinct roles for Mind bomb, Neuralized and Epsin in mediating DSL endocytosis and signaling in Drosophila Development 132:2883-2894 Wang XW, Zhan Q, Coursen JD, Khan MA, Kontny HU, Yu L, Hollander MC, O'Connor PM, Fornace AJ, Jr and Harris CC (1999) GADD45 induction of a G2/M cell cycle checkpoint Proc Natl Acad Sci U S A 96:3706-3711 Weijzen S, Velders MP, Elmishad AG, Bacon PE, Panella JR, Nickoloff BJ, Miele L and Kast WM (2002) The Notch ligand Jagged-1 is able to induce maturation of monocytederived human dendritic cells J Immunol 169:4273-4278 Weinberg ES, Allende ML, Kelly CS, Abdelhamid A, Murakami T, Andermann P, Doerre OG, Grunwald DJ and Riggleman B (1996) Developmental regulation of zebrafish MyoD in wild-type, no tail and spadetail embryos Development 122:271-280 Weissman AM (2001) Themes and variations on ubiquitylation Nat Rev Mol Cell Biol 2:169-178 Wienholds E and Plasterk RH (2004) Target-selected gene inactivation in zebrafish Methods Cell Biol 77:69-90 Wienholds E, Schulte-Merker S, Walderich B and Plasterk RH (2002) Target-selected inactivation of the zebrafish rag1 gene Science 297:99-102 Williams CK, Li JL, Murga M, Harris AL and Tosato G (2006) Up-regulation of the Notch ligand Delta-like inhibits VEGF-induced endothelial cell function Blood 107:931-939 Williams GT and Smith CA (1993) Molecular regulation of apoptosis: genetic controls on cell death Cell 74:777-779 Williams SD and David SS (1998) Evidence that MutY is a monofunctional glycosylase capable of forming a covalent Schiff base intermediate with substrate DNA Nucleic Acids Res 26:5123-5133 Wilson SH (1998) Mammalian base excision repair and DNA polymerase beta Mutat Res 407:203-215 189 Wilson SH and Kunkel TA (2000) Passing the baton in base excision repair Nat Struct Biol 7:176-178 Wong LY, Recht J and Laurent BC (2006) Chromatin remodeling and repair of DNA double-strand breaks J Mol Histol 37:261-269 Wong N, Lai P, Lee SW, Fan S, Pang E, Liew CT et al (1999) Assessment of genetic changes in hepatocellular carcinoma by comparative genomic hybridization analysis: relationship to disease stage, tumor size, and cirrhosis Am J Pathol 154:37-43 Wood KA and Youle RJ (1995) The role of free radicals and p53 in neuron apoptosis in vivo J Neurosci 15:5851-5857 Wreggett KA, Hill F, James PS, Hutchings A, Butcher GW and Singh PB (1994) A mammalian homologue of Drosophila heterochromatin protein (HP1) is a component of constitutive heterochromatin Cytogenet Cell Genet 66:99-103 Wu L, Aster JC, Blacklow SC, Lake R, Artavanis-Tsakonas S and Griffin JD (2000) MAML1, a human homologue of Drosophila mastermind, is a transcriptional co-activator for NOTCH receptors Nat Genet 26:484-489 Xu X, Meiler SE, Zhong TP, Mohideen M, Crossley DA, Burggren WW and Fishman MC (2002) Cardiomyopathy in zebrafish due to mutation in an alternatively spliced exon of titin Nat Genet 30:205-209 Yamaguchi M, Fujimori-Tonou N, Yoshimura Y, Kishi T, Okamoto H and Masai I (2008) Mutation of DNA primase causes extensive apoptosis of retinal neurons through the activation of DNA damage checkpoint and tumor suppressor p53 Development 135:1247-1257 Yamamoto A, Amacher SL, Kim SH, Geissert D, Kimmel CB and De Robertis EM (1998) Zebrafish paraxial protocadherin is a downstream target of spadetail involved in morphogenesis of gastrula mesoderm Development 125:3389-3397 Yan YL, Hatta K, Riggleman B and Postlethwait JH (1995) Expression of a type II collagen gene in the zebrafish embryonic axis Dev Dyn 203:363-376 190 Yang A, Kaghad M, Wang Y, Gillett E, Fleming MD, Dotsch V, Andrews NC, Caput D and McKeon F (1998) p63, a p53 homolog at 3q27-29, encodes multiple products with transactivating, death-inducing, and dominant-negative activities Mol Cell 2:305-316 Yang A, Walker N, Bronson R, Kaghad M, Oosterwegel M, Bonnin J, Vagner C, Bonnet H, Dikkes P, Sharpe A, McKeon F and Caput D (2000) p73-deficient mice have neurological, pheromonal and inflammatory defects but lack spontaneous tumours Nature 404:99-103 Yang X, Klein R, Tian X, Cheng HT, Kopan R and Shen J (2004) Notch activation induces apoptosis in neural progenitor cells through a p53-dependent pathway Dev Biol 269:81-94 Yin Y, Stephen CW, Luciani MG and Fahraeus R (2002) p53 Stability and activity is regulated by Mdm2-mediated induction of alternative p53 translation products Nat Cell Biol 4:462-467 Yoo HY, Shevchenko A, Shevchenko A and Dunphy WG (2004) Mcm2 is a direct substrate of ATM and ATR during DNA damage and DNA replication checkpoint responses J Biol Chem 279:53353-53364 Zhang C, Li Q, Lim CH, Qiu X and Jiang YJ (2007) The characterization of zebrafish antimorphic mib alleles reveals that Mib and Mind bomb-2 (Mib2) function redundantly Dev Biol 305:14-27 Zhang L, Kendrick C, Julich D and Holley SA (2008) Cell cycle progression is required for zebrafish somite morphogenesis but not segmentation clock function Development 135:2065-2070 Zhong J, Zhang H, Stanyon CA, Tromp G and Finley RL, Jr (2003) A strategy for constructing large protein interaction maps using the yeast two-hybrid system: regulated expression arrays and two-phase mating Genome Res 13:2691-2699 Zhou BB and Elledge SJ (2000) The DNA damage response: putting checkpoints in perspective Nature 408:433-439 191 Zhou S, Fujimuro M, Hsieh JJ, Chen L, Miyamoto A, Weinmaster G and Hayward SD (2000) SKIP, a CBF1-associated protein, interacts with the ankyrin repeat domain of NotchIC To facilitate NotchIC function Mol Cell Biol 20:2400-2410 Zudaire I, Odero MD, Caballero C, Valenti C, Martinez-Penuela JM, Isola J and Calasanz MJ (2002) Genomic imbalances detected by comparative genomic hybridization are prognostic markers in invasive ductal breast carcinomas Histopathology 40:547-555 192 ... between the Notch and p53 pathway During mammalian neural development, activation of the Notch signaling pathway is known to be involved in the maintenance of neural progenitor identity and the suppression... Hence, the aim of this study is to investigate what causes the up-regulation of p53 and to further characterize other developmental defects that are associated with the loss of udu function in the. .. 2005) The intrinsic apoptotic pathway can also be activated by p53 involving the pro-apoptotic Bcl-2 family members The translocation of p53 to the mitochondria provoke the release of cytochrome