Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

Genome Research

Volumn 18, Issue 6, 2008, Pages 939-948

  Gatta, Giusy Della ^a   Bansal, Mukesh ^a   Ambesi Impiombato, Alberto ^a,c   Antonini, Dario ^c   Missero, Caterina ^a,c,d   Di Bernardo, Diego ^a,b  

^a TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^b UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^c CEINGE BIOTECNOLOGIE AVANZATE   (Italy)

^d Institute for Cancer Genetics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR TRP63;

ALGORITHM; ANIMAL CELL; ARTICLE; BINDING SITE; CONTROLLED STUDY; DEVELOPMENT; GENE CONTROL; GENE EXPRESSION PROFILING; GENETIC ENGINEERING; GENETIC TRANSCRIPTION; GENOMICS; KERATINOCYTE; MAMMAL CELL; MATHEMATICAL COMPUTING; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; SKIN; VALIDATION PROCESS;

ALGORITHMS; ANIMALS; BINDING SITES; CELLS, CULTURED; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; KERATINOCYTES; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOSPHOPROTEINS; TRANS-ACTIVATORS; TRANSCRIPTION FACTOR AP-1;

MAMMALIA;

EID: 44849118743     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.073601.107     Document Type: Article

References (42)

1. Allison, B., Gadbury, G.L., Moonseong, H., Fernández, J.R., Lee, C-K., Prolla, T.A., and Weindruch, R. 2002. A mixture model approach for the analysis of microarray gene expression data. Computat. Stat. Data Anal. 39: 1-20.
2. Amit, I., Citri, A., Shay, T., Lu, Y., Katz, M., Zhang, F., Tarcic, G., Siwak, D., Lahad, J., Jacob-Hirsch, J., et al. 2007. A module of negative feedback regulators defines growth factor signaling. Nat. Genet. 39: 503-512.
3. Antonini, D., Rossi, B., Han, R., Minichiello, A., Di Palma, T., Corrado, M., Banfi, S., Zannini, M., Brissette, J.L., and Missero, C. 2006. An autoregulatory loop directs the tissue-specific expression of p63 through a long-range evolutionarily conserved enhancer. Mol. Cell. Biol. 26: 3308-3318.
4. Bailey, T.L. and Elkan, C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2: 28-36.
5. Baldi, P. and Long, A.D. 2001. A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509-519.
6. Bansal, M., Della-Gatta, G., and di Bernardo, D. 2006. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 22: 815-822.
7. Bansal, M., Belcastro, V., Ambesi-Impiombato, A., and di Bernardo, D. 2007. How to infer gene networks from expression profiles. Mol. Syst. Biol. 3: 78. doi: 10.1038/msb4100120.
8. Barenco, M., Tomescu, D., Brewer, D., Callard, R., Stark, J., and Hubank, M. 2006. Ranked prediction of p53 targets using hidden variable dynamic modeling. Genome Biol. 7: R25. doi: 10.1186/gb-2006-7-3-r25.
9. Basso, K., Margolin, A.A., Stolovitzky, G., Klein, U., Dalla-Favera, R., and Califano, A. 2005. Reverse engineering of regulatory networks in human B cells. Nat. Genet. 37: 382-390.
10. de Jong, H. 2002. Modeling and simulation of genetic regulatory systems: A literature review. J. Comput. Biol. 9: 67-103.
11. Dennis Jr., G., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C., and Lempicki, R.A. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4: 3. doi: 10.1186/gb-2003-4-5-p3.
12. di Bernardo, D., Thompson, M.J., Gardner, T.S., Chobot, S.E., Eastwood, E.L., Wojtovich, A.P., Elliott, S.J., Schaus, S.E., and Collins, J.J. 2005. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat. Biotechnol. 23: 377-383.
13. Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868.
14. Flores, E.R., Tsai, K.Y., Crowley, D., Sengupta, S., Yang, A., McKeon, F., and Jacks, T. 2002. p63 and p73 are required for p53-dependent apoptosis in response to DNA damage. Nature 416: 560-564.
15. Frank, S.R., Schroeder, M., Fernandez, P., Taubert, S., and Amati, B. 2001. Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation. Genes & Dev. 15: 2069-2082.
16. Gardner, T.S., di Bernardo, D., Lorenz, D., and Collins, J.J. 2003. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105.
17. Hartemink, A.J. 2005. Reverse engineering gene regulatory networks. Nat. Biotechnol. 23: 554-555.
18. Ihrie, R.A., Marques, M.R., Nguyen, B.T., Horner, J.S., Papazoglu, C., Bronson, R.T., Mills, A.A., and Attardi, L.D. 2005. Perp is a p63-regulated gene essential for epithelial integrity. Cell 120: 843-856.
19. Kel, A.E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V., and Wingender, E. 2003. MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31: 3576-3579.
20. King, O.D. and Roth, F.P. 2003. A non-parametric model for transcription factor binding sites. Nucleic Acids Res. 31: e116. doi: 10.1093/nar/gng117.
21. King, K.E., Ponnamperuma, R.M., Yamashita, T., Tokino, T., Lee, L.A., Young, M.F., and Weinberg, W.C. 2003. ΔNp63α functions as both a positive and a negative transcriptional regulator and blocks in vitro differentiation of murine keratinocytes. Oncogene 22: 3635-3644.
22. Koster, M.I., Kim, S., Mills, A.A., DeMayo, F.J., and Roop, D.R. 2004. p63 is the molecular switch for initiation of an epithelial stratification program. Genes & Dev. 18: 126-131.
23. Lee, H. and Kimelman, D. 2002. A dominant-negative form of p63 is required for epidermal proliferation in zebrafish. Dev. Cell 2: 607-616.
24. Littlewood, T.D., Hancock, D.C., Danielian, P.S., Parker, M.G., and Evan, G.I. 1995. A modified oestrogen receptor ligand-binding domain as an improved switch for the regulation of heterologous proteins. Nucleic Acids Res. 23: 1686-1690.
25. Mills, A.A., Zheng, B., Wang, X.J., Vogel, H., Roop, D.R., and Bradley, A. 1999. p63 is a p53 homologue required for limb and epidermal morphogenesis. Nature 398: 708-713.
26. Montgomery, D.C., Peck, E.A., and Vining, G.G. 2001. Introduction to linear regression analysis. Wiley, New York.
27. Nguyen, B.C., Lefort, K., Mandinova, A., Antonini, D., Devgan, V., Della Gatta, G., Koster, M.I., Zhang, Z., Wang, J., Tommasi di Vignano, A., et al. 2006. Cross-regulation between Notch and p63 in keratinocyte commitment to differentiation. Genes & Dev. 20: 1028-1042.
28. Oettgen, P., Alani, R.M., Barcinski, M.A., Brown, L., Akbarali, Y., Boltax, J., Kunsch, C., Munger, K., and Libermann, T.A. 1997. Isolation and characterization of a novel epithelium-specific transcription factor, ESE-1, a member of the ets family. Mol. Cell. Biol. 17: 4419-4433.
29. Pellegrini, G., Dellambra, E., Golisano, O., Martinelli, E., Fantozzi, I., Bondanza, S., Ponzin, D., McKeon, F., and De Luca, M. 2001. p63 identifies keratinocyte stem cells. Proc. Natl. Acad. Sci. 98: 3156-3161.
30. Sbisa, E., Mastropasqua, G., Lefkimmiatis, K., Caratozzolo, M.F., D'Erchia, A.M., and Tullo, A. 2006. Connecting p63 to cellular proliferation: The example of the adenosine deaminase target gene. Cell Cycle 5: 205-212.
31. Senoo, M., Pinto, F., Crum, C.P., and McKeon, F. 2007. p63 Is essential for the proliferative potential of stem cells in stratified epithelia. Cell 129: 523-536.
32. Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., et al. 2005. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. 102: 15545-15550.
33. Testoni, B., Borrelli, S., Tenedini, E., Alotto, D., Castagnoli, C., Piccolo, S., Tagliafico, E., Ferrari, S., Vigano, M.A., and Mantovani, R. 2006. Identification of new p63 targets in human keratinocytes. Cell Cycle 5: 2805-2811.
34. Truong, A.B., Kretz, M., Ridky, T.W., Kimmel, R., and Khavari, P.A. 2006. p63 regulates proliferation and differentiation of developmentally mature keratinocytes. Genes & Dev. 20: 3185-3197.
35. van Someren, E.P., Vaes, B.L., Steegenga, W.T., Sijbers, A.M., Dechering, K.J., and Reinders, M.J. 2005. Least Absolute Regression Network Analysis of the murine osteoblast differentiation network. Bioinformatics 22: 477-484.
36. Vastrik, I., Kaipainen, A., Penttila, T.L., Lymboussakis, A., Alitalo, R., Parvinen, M., and Alitalo, K. 1995. Expression of the mad gene during cell differentiation in vivo and its inhibition of cell growth in vitro. J. Cell Biol. 128: 1197-1208.
37. Vigano, M.A., Lamartine, J., Testoni, B., Merico, D., Alotto, D., Castagnoli, C., Robert, A., Candi, E., Melino, G., Gidrol, X., et al. 2006. New p63 targets in keratinocytes identified by a genome-wide approach. EMBO J. 25: 5105-5116.
38. Workman, C.T., Mak, H.C., McCuine, S., Tagne, J.B., Agarwal, M., Ozier, O., Begley, T.J., Samson, L.D., and Ideker, T. 2006. A systems approach to mapping DNA damage response pathways. Science 312: 1054-1059.
39. Yang, A., Kaghad, M., Wang, Y., Gillett, E., Fleming, M.D., Dotsch, V., Andrews, N.C., 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.
40. Yang, A., Schweitzer, R., Sun, D., Kaghad, M., Walker, N., Bronson, R.T., Tabin, C., Sharpe, A., Caput, D., Crum, C., et al. 1999. p63 is essential for regenerative proliferation in limb, craniofacial and epithelial development. Nature 398: 714-718.
41. Yang, A., Zhu, Z., Kapranov, P., McKeon, F., Church, G.M., Gingeras, T.R., and Struhl, K. 2006. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol. Cell 24: 593-602.
42. Zenz, R. and Wagner, E.F. 2006. Jun signalling in the epidermis: From developmental defects to psoriasis and skin tumors. Int. J. Biochem. Cell Biol. 38: 1043-1049.