Simultaneous gene expression analysis of steady-state and actively translated mRNA populations form osteosarcoma MG-63 cells in response to IL-1α via an open expression analysis platform

Nucleic Acids Research

Volumn 31, Issue 17, 2003, Pages 5157-5166

  Ju, Jingfang ^a   Huang, Chunli ^a   Minskoff, Stacey A ^a   Mayotte, Jane E ^a   Taillon, Bruce E ^a   Simons, Jan F ^a  

^a CURAGEN CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; INTERLEUKIN 1ALPHA; MESSENGER RNA;

BONE DISEASE; CELL ADHESION; CONTROLLED STUDY; DRUG TARGETING; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE ISOLATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; INFLAMMATION; MARKER GENE; METABOLIC BONE DISEASE; METHODOLOGY; OSTEOPENIA; OSTEOPOROSIS; OSTEOSARCOMA CELL; POLYSOME; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; REVIEW; RNA SEQUENCE; RNA TRANSLATION; STEADY STATE;

CELL LINE, TUMOR; DATABASES, NUCLEIC ACID; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; INTERLEUKIN-1; OSTEOSARCOMA; PROTEIN BIOSYNTHESIS; RNA, MESSENGER;

EUKARYOTA;

EID: 0344875236     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg702     Document Type: Review

References (46)

1. Silvennoinen, J.A., Karttunen, T.J., Niemela, S.E., Manelius, J.J. et al. (1995) A controlled study of bone mineral density in patients with inflammatory bowel disease. Gut, 37, 71-76.
2. Priante, G., Bordin, L, Musacchio, E., Clari, G. et al. (2002) Fatty acids and cytokine mRNA expression in human osteoblastic cells: a specific effect of arachidonic acid. Clin. Sci., 102, 403-409.
3. Birch, M.A. and Skerry, T.M. (1999) Differential regulation of syndecan expression by osteosarcoma cell lines in response to cytokines but not osteotropic hormones. Bone, 24, 571-578.
4. Yayon, A.M., Klagsbrun, M., Esko, J.D., Leder, P. et al. (1991) Cell surface heparin-like molecules are required for binding of basic fibroblast growth factor. Cell, 64, 841-848.
5. Billiau, A., Edy, V.G., Heremans, H., Van Damme, J., Desmyter, J. et al. (1977) Human interferon: mass production in a newly established cell line, MG-63. Antimicrobial Agents Chemother., 12, 11-15.
6. Stein, G.S., Kian, J.B., Stein, J.L., Van Wijnen, A.J. et al. (1996) Transcriptional control of osteoblast growth and differentiation. Physiol. Rev., 76, 593-629.
7. Panagakos, F.S., Hinojosa, L.P. and Kumar, S. (1994) Formation and mineralization of extra-cellular matrix secreted by an immortal human osteoblastic cell line: modulation by tumor necrosis factor-alpha. Inflammation, 18, 267-283.
8. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P.O. and Davis, R.W. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl Acad. Sci. USA, 93, 10614-10619.
9. Zhang, L., Zhou, W., Velculescu, V.E., Kern, S.E., Hruban, R.H., Hamilton, S.R., Vogelstein, B. and Kinzler, K.W. (1997) Gene expression profiles in normal and cancer cells. Science, 276, 1268-1272.
10. Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D. and Lockhart, D.J. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
11. Mikulits, W., Berengere, P., Habermann, B., Beug, H., Garcia-Sanz, J.A. and Mullner, E.W. (2000) Isolation of translationally controlled mRNAs by differential screening. FASEB J., 14, 1641-1652.
12. Derrigo, M., Cestelli, A., Savettieri, G. and Di Liegro, I. (2000) RNA-protein interactions in the control of stability and localization of messenger RNA. Int. J. Mol. Med., 5, 111-123.
13. Sheikh, M.S. and Fornace, A.J., Jr (1999) Regulation of translation initiation following stress. Oncogene, 18, 6121-6128.
14. Hershey, J., Mathews, M.B. and Sonenberg, N.S. (1996) Origins and targets of translational control. In Translational Control. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Vol. 30, pp. 1-29.
15. Zong, Q., Schummer, M., Hood, L. and Morris, D.R. (1999) Messenger RNA translation state: the second dimension of high-throughput expression screening. Proc. Natl Acad. Sci. USA, 96, 10632-10636.
16. Johannes, G., Carter, M.S., Eisen, M.B., Brown, P.O. and Sarnow, P. (1999) Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl Acad. Sci. USA, 96, 13118-13123.
17. Sachs, A.B., Sarnow, P. and Hentze, M.W. (1997) Starting at the beginning, middle and end: translation initiation in eukaryotes. Cell, 89, 831-838.
18. Chu, E., Grem, J.L., Johnston, P.G. and Allegra, C.J. (1996) New concepts for the development and use of antifolates. Stem Cells, 14, 41-46.
19. Shimkets, R.A., Lowe, D.G., Tsu-Ning Tai, J., Sehl, P., Jin, H. et. al. (1999) Gene expression analysis by transcript profiling coupled to a gene database query. Nat. Biotechnol., 17, 798-803.
20. Rogers, J.T., Leiter, L.M., McPhee, J., Cahill, C.M., Zhan, S.S. et. al. (1999) Translation of the alzheimer amyloid precursor protein mRNA is up-regulated by interleukin-1 through 5′-untranslated region sequences. J. Biol. Chem., 274, 6421-6431.
21. Rousseau, D., Kaspar, R., Rosenwald, I., Gehrke, L. and Sonenberg, N. (1996) Translation initiation of ornithine decarboxylase and nucleocytoplasmic transport of cyclin D1 mRNA are increased in cells overexpressing eukaryotic initiation factor 4E. Proc. Natl Acad. Sci. USA, 93, 1065-1070.
22. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227, 680-685.
23. Morris, D.R. (1995) Growth control of translation in mammalian cells. Prog. Nucleic Acid Res. Mol. Biol., 51, 339-363.
24. Rudland, P.S., Weil, S. and Hunter, A.R. (1975) Changes in RNA metabolism and accumulation of presumptive messenger RNA during transition from the growing to the quiescent state of cultured mouse fibroblasts. J. Mol. Biol., 96, 745-766.
25. Spedding, G. and Draper, D.E. (1993) Allosteric mechanism for translational repression in the Escherichia coli alpha operon. Proc. Natl Acad. Sci. USA, 90, 4399-4403.
26. Tang, C.K. and Draper, D.E. (1990) Evidence for allosteric coupling between the ribosome and repressor binding sites of a translationally regulated mRNA. Biochemistry, 29, 4434-4439.
27. McDonald, P.P., Fadok, V.A., Bratton, D. and Henson, P.M. (1999) Transcriptional and translational regulation of inflammatory mediator production by endogenous TGF-beta in macrophages that have ingested apoptotic cells. J. Immunol., 163, 6164-6172.
28. Gaugler, M.H., Squiban, C., Claraz, M., Schweitzer, K., Weksler, B., Gourmelon, P. and Van der Meeren, A. (1998) Characterization of the response of human bone marrow endothelial cells to in vitro irradiation. Br. J. Haematol., 103, 980-989.
29. Mamdouh, Z., Chen, X., Pierini, L.M., Maxfield, F.R. et al. (2003) Targeted recycling of PECAM from endothelial surface-connected compartments during diapedesis. Nature, 421, 748-753.
30. Dufner, A. and Thomas, G. (1999) Ribosomal S6 kinase signaling and the control of translation. Exp. Cell Res., 253, 100-109.
31. Chu, E., Koeller, D.M., Casey, J.L., Drake, J.C., Chabner, B.A. et. al. (1991) Autoregulation of human thymidylate synthase messenger RNA translation by thymidylate synthase. Proc. Natl Acad. Sci. USA, 88, 8977-8981.
32. Ju, J., Pedersen-Lane, J., Maley, F. and Chu, E. (1999) Regulation of p53 expression by thymidylate synthase. Proc. Natl Acad. Sci. USA, 96, 3769-3774.
33. Baharians, Z. and Schonthal, A.H. (1998) Autoregulation of protein phosphatase type 2A expression. J. Biol. Chem., 273, 19019-19024.
34. Choi, I., Lee, M.J., Kim, E.J., Kang, H.S. and Pyun, K.H. (1998) Roles of protein phosphatase 2A in IL-6 signal transduction in Hep3B cells. Immunol. Lett., 61, 103-107.
35. Nazian, S.J., Brewer, L.D. and Ness, G.C. (1991) Pituitary regulation of the expression of the farnesyl pyrophosphate synthetase gene in the testes of the sexually maturing rat. J. Androl., 12, 264-272.
36. Puls, A., Eliopoulos, A.G., Nobes, C.D., Bridges, T., Young, L.S. and Hall, A. (1999) Activation of the small GTPase Cdc42 by the inflammatory cytokines TNF(alpha) and IL-1 and by the Epstein-Barr virus transforming protein LMP1. J. Cell Sci., 112, 2983-2992.
37. Moncrieff, C.L., Bailey, M.E.S., Morrison, N. and Johnson, K.J. (1999) Cloning and chromosomal localization of human cdc-42 binding protein kinase beta. Genomics, 57, 297-300.
38. Igaki, T., Kanda, H., Yamamato-Goto, Y., Kanuka, H. et al. (2002) Eiger, a TNF superfamily ligand that triggers the Drophila JNK pathway. EMBO J., 21, 3009-3018.
39. Deveraux, Q.L. and Reed, J.C. (1999) IAP family proteins - suppressors of apoptosis. Genes Dev., 13, 239-252.
40. Chu, E., Takimoto, C.H., Voeller, D., Grem, J.L. and Allegra, C.J. (1993) Specific binding of human dihydrofolate reductase protein to dihydrofolate reductase messenger RNA in vitro. Biochemistry, 32, 4756-4760.
41. Ercikan-Abali, E.A., Banerjee, D., Waltham, M.C., Skacel, N., Scotto, K.W. and Bertino, J.R. (1997) Dihydrofolate reductase protein inhibits its own translation by binding to dihydrofolate reductase mRNA sequences within the coding region. Biochemistry, 36, 12317-12322.
42. Abid, M.R., Li, Y., Anthony, C. and De Benedetti, A. (1999) Translational regulation of ribonucleotide reductase by eukaryotic initiation factor 4E links protein synthesis to the control of DNA replication. J. Biol. Chem., 274, 35991-35998.
43. Gingras, A.C., Raught, B. and Sonenberg, N. (2001) Regulation of translation initiation by FRAP/mTOR. Genes Dev., 15, 807-826.
44. 2+-modulating cyclophilin ligand modulates calcium influx signaling in T lymphocytes. J. Biol. Chem., 271, 8549-8552.
45. Holloway, M.P. and Bram, R.J. (1998) Co-localization of calcium-modulating cyclophilin ligand with intracellular calcium pools. J. Biol. Chem., 273, 16346-16350.
46. Wang, H., Marsters, S.A., Baker, T., Chan, B. et al. (2001) TACI-ligand interactions are required for T cells activation and collagen-induced arthritis in mice. Nature Immunol., 2, 632-637.