A module of negative feedback regulators defines growth factor signaling

Nature Genetics

Volumn 39, Issue 4, 2007, Pages 503-512

  Amit, Ido ^a   Citri, Ami ^a,e   Shay, Tal ^a   Lu, Yiling ^b   Katz, Menachem ^a   Zhang, Fan ^b   Tarcic, Gabi ^a   Siwak, Doris ^b   Lahad, John ^b   Jacob Hirsch, Jasmine ^c   Amariglio, Ninette ^c   Vaisman, Nora ^d   Segal, Eran ^a   Rechavi, Gideon ^c   Alon, Uri ^a   Mills, Gordon B ^b   Domany, Eytan ^a   Yarden, Yosef ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

^d Sigma Aldrich Israel Ltd   (Israel)

^e STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GROWTH FACTOR;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC CORRELATION; HUMAN; HUMAN CELL; IMMEDIATE EARLY GENE; MESSENGER RNA SYNTHESIS; MOLECULAR DYNAMICS; NEGATIVE FEEDBACK; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN STABILITY; PROTEIN SYNTHESIS REGULATION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

CELLS, CULTURED; CLUSTER ANALYSIS; EPIDERMAL GROWTH FACTOR; EPITHELIAL SODIUM CHANNEL; EXTRACELLULAR SIGNAL-REGULATED MAP KINASES; FEEDBACK, BIOCHEMICAL; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; INTERCELLULAR SIGNALING PEPTIDES AND PROTEINS; KRUPPEL-LIKE TRANSCRIPTION FACTORS; MAFF TRANSCRIPTION FACTOR; MODELS, BIOLOGICAL; NERVE TISSUE PROTEINS; NUCLEAR PROTEINS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS; TRISTETRAPROLIN;

EID: 34047174559     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1987     Document Type: Article

References (50)

1. Freeman, M. Feedback control of intercellular signalling in development. Nature 408, 313-319 (2000).
2. Alon, U. An Introduction to Systems Biology: Design Principles of Biological Circuits (CRC Press, Boca Raton, Florida, 2006).
3. Kholodenko, B.N. Cell-signalling dynamics in time and space. Nat. Rev. Mol. Cell Biol. 7, 165-176 (2006).
4. Citri, A. & Yarden, Y. EGF-ERBB signalling: towards the systems level. Nat. Rev. Mol. Cell Biol. 7, 505-516 (2006).
5. Hynes, N.E. & Lane, H.A. ERBB receptors and cancer: the complexity of targeted inhibitors. Nat. Rev. Cancer 5, 341-354 (2005).
6. Shaulian, E. & Karin, M. AP-1 as a regulator of cell life and death. Nat. Cell Biol. 4, E131-E136 (2002).
7. Sun, H., Charles, C.H., Lau, L.F. & Tonks, N.K. MKP-1 (3CH134), an immediate early gene product, is a dual specificity phosphatase that dephosphorylates MAP kinase in vivo. Cell 75, 487-493 (1993).
8. Lau, L.F. & Nathans, D. Expression of a set of growth-related immediate early genes in BALB/c 3T3 cells: coordinate regulation with c-fos or c-myc. Proc. Natl. Acad. Sci. USA 84, 1182-1186 (1987).
9. Sheehan, K.M. et al. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell. Proteomics 4, 346-355 (2005).
10. Casci, T. & Freeman, M. Control of EGF receptor signalling: lessons from fruitflies. Cancer Metastasis Rev. 18, 181-201 (1999).
11. Jones, S.M. & Kazlauskas, A. Growth-factor-dependent mitogenesis requires two distinct phases of signalling. Nat. Cell Biol. 3, 165-172 (2001).
12. Klein, O.D. et al. Sprouty genes control diastema tooth development via bidirectional antagonism of epithelial-mesenchymal FGF signaling. Dev. Cell 11, 181-190 (2006).
13. Segal, E., Friedman, N., Koller, D. & Regev, A. A module map showing conditional activity of expression modules in cancer. Nat. Genet. 36, 1090-1098 (2004).
14. Iyer, V.R. et al. The transcriptional program in the response of human fibroblasts to serum. Science 283, 83-87 (1999).
15. Kalir, S. et al. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292, 2080-2083 (2001).
16. Zhang, W. et al. The functional landscape of mouse gene expression. J. Biol. 3, 21 (2004).
17. Farooq, A. & Zhou, M.M. Structure and regulation of MAPK phosphatases. Cell. Signal. 16, 769-779 (2004).
18. Qu, Z. et al. The transcriptional corepressor NAB2 inhibits NGF-induced differentiation of PC12 cells. J. Cell Biol. 142, 1075-1082 (1998).
19. Hoffmann, E. et al. MEK1-dependent delayed expression of Fos-related antigen-1 counteracts c-Fos and p65 NF-kappaB-mediated interleukin-8 transcription in response to cytokines or growth factors. J. Biol. Chem. 280, 9706-9718 (2005).
20. Szabowski, A. et al. c-Jun and JunB antagonistically control cytokine-regulated mesenchymal-epidermal interaction in skin. Cell 103, 745-755 (2000).
21. Yates, P.R., Atherton, G.T., Deed, R.W., Norton, J.D. & Sharrocks, A.D. Id helix-loop-helix proteins inhibit nucleoprotein complex formation by the TCF ETS-domain transcription factors. EMBO J. 18, 968-976 (1999).
22. Gilchrist, M. et al. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441, 173-178 (2006).
23. Fu, S., Bottoli, I., Goller, M. & Vogt, P.K. Heparin-binding epidermal growth factor-like growth factor, a v-Jun target gene, induces oncogenic transformation. Proc. Natl. Acad. Sci. USA 96, 5716-5721 (1999).
24. Barton, K. et al. Defective thymocyte proliferation and IL-2 production in transgenic mice expressing a dominant-negative form of CREB. Nature 379, 81-85 (1996).
25. Narla, G. et al. KLF6, a candidate tumor suppressor gene mutated in prostate cancer. Science 294, 2563-2566 (2001).
26. Motohashi, H., Katsuoka, F., Shavit, J.A., Engel, J.D. & Yamamoto, M. Positive or negative MARE-dependent transcriptional regulation is determined by the abundance of small Maf proteins. Cell 103, 865-875 (2000).
27. Wisdom, R. & Verma, I.M. Proto-oncogene FosB: the amino terminus encodes a regulatory function required for transformation. Mol. Cell. Biol. 13, 2635-2643 (1993).
28. Das, H. et al. Kruppel-like factor 2 (KLF2) regulates proinflammatory activation of monocytes. Proc. Natl. Acad. Sci. USA 103, 6653-6658 (2006).
29. Sassone-Corsi, P., Sisson, J.C. & Verma, I.M. Transcriptional autoregulation of the proto-oncogene fos. Nature 334, 314-319 (1988).
30. Sevetson, B.R., Svaren, J. & Milbrandt, J. A novel activation function for NAB proteins in EGR-dependent transcription of the luteinizing hormone beta gene. J. Biol. Chem. 275, 9749-9757 (2000).
31. Kaszubska, W. et al. Cyclic AMP-independent ATF family members interact with NF-kappa B and function in the activation of the E-selectin promoter in response to cytokines. Mol. Cell. Biol. 13, 7180-7190 (1993).
32. Claret, F.X., Hibi, M., Dhut, S., Toda, T. & Karin, M. A new group of conserved coactivators that increase the specificity of AP-1 transcription factors. Nature 383, 453-457 (1996).
33. Carballo, E., Lai, W.S. & Blackshear, P.J. Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin. Science 281, 1001-1005 (1998).
34. Chen, C.Y. et al. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107, 451-464 (2001).
35. Bakheet, T., Williams, B.R. & Khabar, K.S. ARED 3.0: the large and diverse AU-rich transcriptome. Nucleic Acids Res. 34, D111-D114 (2006).
36. Sharrocks, A.D. The ETS-domain transcription factor family. Nat. Rev. Mol. Cell Biol. 2, 827-837 (2001).
37. Irie, H.Y. et al. Distinct roles of Akt1 and Akt2 in regulating cell migration and epithelial-mesenchymal transition. J. Cell Biol. 171, 1023-1034 (2005).
38. Meijlink, F., Curran, T., Miller, A.D. & Verma, I.M. Removal of a 67-base-pair sequence in the noncoding region of protooncogene fos converts it to a transforming gene. Proc. Natl. Acad. Sci. USA 82, 4987-4991 (1985).
39. Mangan, S., Itzkovitz, S., Zaslaver, A. & Alon, U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J. Mol. Biol. 356, 1073-1081 (2006).
40. Lu, J.Y., Sadri, N. & Schneider, R.J. Endotoxic shock in AUF1 knockout mice mediated by failure to degrade proinflammatory cytokine mRNAs. Genes Dev. 20, 3174-3184 (2006).
41. Trotman, L.C. et al. Identification of a tumour suppressor network opposing nuclear Akt function. Nature 441, 523-527 (2006).
42. Wang, F. et al. Transcriptional repression of WEE1 by Kruppel-like factor 2 is involved in DNA damage-induced apoptosis. Oncogene 24, 3875-3885 (2005).
43. Bild, A.H. et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439, 353-357 (2006).
44. Eichenberger, P. et al. The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol. 2, e328 (2004).
45. Hoffmann, A., Leung, T.H. & Baltimore, D. Genetic analysis of NF-kappaB/Rel transcription factors defines functional specificities. EMBO J. 22, 5530-5539 (2003).
46. Murphy, L.O., Smith, S., Chen, R.H., Fingar, D.C. & Blenis, J. Molecular interpretation of ERK signal duration by immediate early gene products. Nat. Cell Biol. 4, 556-564 (2002).
47. Marshall, C.J. Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80, 179-185 (1995).
48. Werner, S.L., Barken, D. & Hoffmann, A. Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science 309, 1857-1861 (2005).
49. Levkowitz, G. et al. Ubiquitin ligase activity and tyrosine phosphorylation underlie suppression of growth factor signaling by c-Cbl/Sli-1. Mol. Cell 4, 1029-1040 (1999).
50. Stephenson, A.J. et al. Integration of gene expression profiling and clinical variables to predict prostate carcinoma recurrence after radical prostatectomy. Cancer 104, 290-298 (2005).