Specific trans-acting proteins interact with auxiliary RNA polyadenylation elements in the COX-2 3′-UTR

RNA

Volumn 13, Issue 7, 2007, Pages 1103-1115

  Hall Pogar, Tyra ^a   Liang, Songchun ^a   Hague, Lisa K ^a   Lutz, Carol S ^a  

^a RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

Author keywords

3 untranslated region (UTR); Cyclooxygenase 2 (COX 2); Polyadenylation

Indexed keywords

CELL EXTRACT; CIS ACTING ELEMENT; COAT PROTEIN; CYCLOOXYGENASE 2; P54 NONO RELATED BINDING PROTEIN; POLYADENYLATED RNA; POLYPYRIMIDINE TRACT BINDING PROTEIN; PROTEIN; PROTEIN ASSOCIATED SPLICING FACTOR; PROTEIN U1A; UNCLASSIFIED DRUG; VIRUS FUSION PROTEIN;

3' UNTRANSLATED REGION; ARTICLE; BIOTINYLATION; CELL NUCLEUS; FEMALE; GENETIC TRANSFECTION; HELA CELL; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; MUTANT; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN RNA BINDING;

3' UNTRANSLATED REGIONS; CYCLOOXYGENASE 2; GENE DELETION; HELA CELLS; HUMANS; MEMBRANE PROTEINS; MODELS, BIOLOGICAL; NUCLEAR MATRIX-ASSOCIATED PROTEINS; OCTAMER TRANSCRIPTION FACTORS; POLYADENYLATION; POLYPYRIMIDINE TRACT-BINDING PROTEIN; PROTEIN BINDING; RIBONUCLEOPROTEIN, U1 SMALL NUCLEAR; RNA 3' POLYADENYLATION SIGNALS; RNA, MESSENGER; RNA-BINDING PROTEINS; SUBSTRATE SPECIFICITY;

EID: 34250797537     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.577707     Document Type: Article

References (65)

1. Appleby, S.B., Ristimaki, A., Neilson, K., Narko, K., and Hla, T. 1994. Structure of the human cyclo-oxygenase-2 gene. Biochem. J. 302: 723-727.
2. Bazan, N.G. 2001. COX-2 as a multifunctional neuronal modulator. Nat. Med. 7: 414-415.
3. Bazan, N.G., Fletcher, B.S., Herschmann, H.R., and Mukherjee, P.K. 1994. Platelet-activating factor and retinoic acid synergistically activate the inducible prostaglandin synthase gene. Proc. Natl. Acad. Sci. 91: 5252-5256.
4. Bentley, D.L. 2005. Rules of engagement: Co-transcriptional recruitment of pre-mRNA processing factors. Curr. Opin. Cell Biol. 17: 251-256.
5. Bishop-Bailey, D., Calatayud, S., Warner, T.D., Hla, T., and Mitchell, J.A. 2002. Prostaglandins and the regulation of tumor growth. J. Environ. Pathol. Toxicol. Oncol. 21: 93-101.
6. Bracken, K.E., Elger, W., Jantke, I., Nanninga, A., and Gellersen, B. 1997. Cloning of guinea pig cyclooxygenase-2 and 15-hydroxyprostaglandin dehydrogenase complementary deoxyribonucleic acids: Steroid-modulated gene expression correlates to prostaglandin F2 α secretion in cultured endometrial cells. Endocrinology 138: 237-247.
7. Brackenridge, S. and Proudfoot, N.J. 2000. Recruitment of a basal polyadenylation factor by the upstream sequence element of the human lamin B2 polyadenylation signal. Mol. Cell. Biol. 20: 2660-2669.
8. Carswell, S. and Alwine, J.C. 1989. Efficiency of utilization of the Simian Virus 40 late polyadenylation site: Effects of upstream sequences. Mol. Cell. Biol. 9: 4248-4258.
9. Castelo-Branco, P., Furger, A., Wollerton, M., Smith, C., Moreira, A., and Proudfoot, N.J. 2004. Polypyrimidine tract binding protein modulates efficiency of polyadenylation. Mol. Cell. Biol. 24: 4174-4183.
10. Cok, S.J. and Morrison, A.R. 2001. The 3′-untranslated region of murine cyclooxygenase-2 contains multiple regulatory elements that alter message stability and translational efficiency. J. Biol. Chem. 276: 23179-23185.
11. Colgan, D.F. and Manley, J.L. 1997. Mechanism and regulation of mRNA polyadenylation. Genes & Dev. 11: 2755-2766.
12. Danckwardt, S., Kaufmann, I., Gentzel, M., Foerstner, K.U., Gantzert, A.S., Gehring, N.H., Neu-Yilik, G., Bork, P., Keller, W., Wilm, M., et al. 2007. Splicing factors stimulate polyadenylation via USEs at noncanonical 3′ end formation signals. EMBO J. doi: 10.1038/sj.emboj.7601699.
13. Dixon, D.A., Kaplan, C.D., McIntyre, T.M., Zimmerman, G.A., and Prescott, S.M. 2000. Post-transcriptional control of cyclooxygenase gene expression J. Biol. Chem. 275: 11750-11757.
14. Dixon, D.A., Tolley, N.D., King, P.H., Nabors, L.B., McIntyre, T.M., Zimmerman, G.A., and Prescott, S.M. 2001. Altered expression of the mRNA stability factor HuR promotes cyclooxygenase-2 expression in colon cancer cells. J. Clin. Invest. 108: 1657-1665.
15. Dixon, D.A., Balch, G.C., Kedersha, N., Anderson, P., Zimmerman, G.A., Beauchamp, R.D., and Prescott, S.M. 2003. Regulation of cyclooxygenase-2 expression by the translational silencer TIA-1. J. Exp. Med. 198: 475-481.
16. Edmonds, M. 2002. A history of polyA sequences: From formation to factors to function. Prog. Nucleic Acid Res. Mol. Biol. 71: 285-389.
17. Edwalds-Gilbert, G., Veraldi, K.L., and Milcarek, C. 1997. Alternative poly(A) site selection in complex transcription units: Means to an end? Nucleic Acids Res. 25: 2547-2561.
18. Feng, L., Sun, W., Xia, Y., Tang, W.W., Chanmugam, P., Soyoola, E., Wilson, C.B., and Hwang, D. 1993. Cloning two isoforms of rat cyclooxygenase: Differential regulation of their expression. Arch. Biochem. Biophys. 307: 361-368.
19. Garavito, R. and Mulichak, A. 2003. The structure of mammalian cyclooxygenases. Annu. Rev. Biophys Biomol. Struct. 32: 183-206.
20. Gou, Q., Liu, C.H., Ben-Av, P., and Hla, T. 1998. Dissociation of basal turnover and cytokine-induced transcript stabilization of the human cyclooxygenase-2 mRNA by mutagenesis of the 3′-untranslated region. Biochem. Biophys. Res. Commun. 242: 508-512.
21. Gruda, M.C., Zabolotny, J.M., Xiao, J.H., Davidson, I., and Alwine, J.C. 1993. Transcriptional activation by simian virus 40 large T antigen: Interactions with multiple components of the transcription complex. Mol. Cell. Biol. 13: 961-969.
22. Hall-Pogar, T., Zhang, H., Tian, B., and Lutz, C.S. 2005. Alternative polyadenylation of cyclooxygenase-2. Nucleic Acids Res. 33: 2565-2579.
23. Hla, T. and Maciag, T. 1991. Cyclooxygenase gene expression is downregulated by heparin-binding (acidic fibroblast) growth factor-1 in human endothelial cells. J. Biol. Chem. 266: 24059-24063.
24. Hla, T. and Neilson, K. 1992. Human cyclooxygenase-2 cDNA. Proc. Natl. Acad. Sci. 89: 7384-7388.
25. Hla, T., Bishop-Bailey, D., Liu, C.H., Schaefers, H.J., and Trifan, O.C. 1999. Cyclooxygenase-1 and -2 isoenzymes. Int. J. Biochem. Cell Biol. 31: 551-557.
26. Hu, J., Lutz, C.S., Wilusz, J., and Tian, B. 2005. Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11: 1485-1493.
27. Hwang, D., Scollard, D., Byrne, J., and Levine, E. 1998. Expression of cyclooxygenase-1 and cyclooxygenase-2 in human breast cancer. J. Natl. Cancer Inst. 90: 455-460.
28. Kutchera, W., Jones, D.A., Matsunami, N., Groden, J., McIntyre, T.M., Zimmerman, G.A., White, R.L., and Prescott, S.M. 1996. Prostaglandin synthase 2 is abnormally expressed in human colon cancer: Evidence for a transcriptional effect. Proc. Natl. Acad. Sci. 93: 4816-4820.
29. Landen, C.N., Marthur, S.P., Richardson, M.S., and Creasman, W.T. 2003. Expression of cyclooxygenase-2 in cervical, endometrial, and ovarian malignancies. Am. J. Obstet. Gynecol. 188: 1174-1176.
30. nrb is a component of the snRNP free U1A (SF-A) complex that promotes pre-mRNA cleavage during polyadenylation. RNA 12: 111-121.
31. Lukiw, W.J. and Bazan, N.G. 1997. Cyclooxygenase 2 RNA message abundance, stability and hypervariability in sporadic Alzheimer neocortex. J. Neurosci. Res. 50: 937-945.
32. Lutz, C.S. and Alwine, J.C. 1994. Direct interaction of the U1snRNP-A protein with the upstream efficiency element of the SV40 late polyadenylation signal. Genes & Dev. 8: 576-586.
33. Lutz, C.S., Murthy, K.G.K., Schek, N., O'Connor, J.P., Manley, J.L., and Alwine, J.C. 1996. Interaction between the U1snRNP-A protein and the 160-kDa subunit of cleavage-polyadenylation specificity factor increases polyadenylation efficiency in vitro. Genes & Dev. 10: 325-337.
34. Lutz, C.S., Cooke, C., O'Connor, J.P., Kobayashi, R., and Alwine, J.C. 1998. The snRNP-free U1A (SF-A) complex(es): Identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. RNA 4: 1493-1499.
35. Lutz-Freyermuth, C., Query, C.C., and Keene, J.D. 1990. Quantitative determination that one of two potential RNA-binding domains of the A protein component of the U1 small nuclear ribonucleoprotein complex binds with high affinity to stem-loop II of U1 RNA. Proc. Natl. Acad. Sci. 87: 6393-6397.
36. Lykke-Andersen, J., Shu, M.D., and Steitz, J.A. 2000. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell 103: 1121-1131.
37. Maniatis, T. and Reed, R. 2002. An extensive network of coupling among gene expression machines. Nature 416: 499-506.
38. Moreira, A., Wollerton, M., Monks, J., and Proudfoot, N.J. 1995. Upstream sequence elements enhance poly(A) site efficiency of the C2 complement gene and are phylogenetically conserved. EMBO J. 14: 3809-3819.
39. Moreira, A., Takagaki, Y., Brackenridge, S., Wollerton, M., Manley, J.L., and Proudfoot, N.J. 1998. The upstream sequence element of the C2 complement poly(A) signal activates mRNA 3′-end formation by two distinct mechanisms. Genes & Dev. 12: 2522-2534.
40. Natalizio, B.J., Muniz, L.C., Arhin, G.K., Wilusz, J., and Lutz, C.S. 2002. Upstream elements present in the 3′-UTR of collagen gene influence the processing efficiency of overlapping polyadenylation signals. J. Biol. Chem. 277: 42733-42740.
41. Newton, R., Seybold, J., Liu, S.F., and Barnes, P.J. 1997. Alternate COX-2 transcripts are differentially regulated: Implications for post-transcriptional control. Biochem. Biophys. Res. Commun. 234: 85-89.
42. Newton, R., Seybold, J., Kuitert, L.M.E., Bergmann, M., and Barnes, P.J. 1998. Repression of cyclooxygenase-2 and prostaglandin E2 release by dexamethasone occurs by transcriptional and post-transcriptional mechanisms involving loss of polyadenylated mRNA. J. Biol. Chem. 273: 32312-32321.
43. O'Banion, M.K., Winn, V.D., and Yong, D.A. 1992. cDNA cloning and functional activity of a glucocorticoid-regulated inflammatory cyclooxygenase. Proc. Natl. Acad. Sci. 89: 4888-4892.
44. O'Banion, M.K., Miller, J.C., Chang, J.W., Kaplan, M.D., and Coleman, P.D. 1996. Interleukin-1 b induces prostaglandin G/H synthase-2 (cyclooxygenase-2) in primary murine astrocyte cultures. J. Neurochem. 66: 2532-2540.
45. O'Connor, J.P., Alwine, J.C., and Lutz, C.S. 1997. Identification of non-snRNP associated U1A protein in human cell nucleoplasm. RNA 3: 1444-1455.
46. Peng, R., Hawkins, I., Link, A.J., and Patton, J.G. 2006. The splicing factor PSF is part of a large complex that assembles in the absence of pre-mRNA and contains all five snRNPs. RNA Biol. 3: 69-76.
47. Prescott, S.M. 2000. Is cyclooxygenase-2 the α and ω in cancer? J. Clin. Invest. 105: 1511-1513.
48. Prescott, S.M. and Fitzpatrick, F.A. 2000. Cyclooxygenase-2 and carcinogenesis. Biochim. Biophys. Acta 1470: 69-78.
49. Proudfoot, N. 2000. Connecting transcription to messenger RNA processing. Trends Biochem. Sci. 25: 290-293.
50. Proudfoot, N.J., Furger, A., and Dye, M.J. 2002. Integrating mRNA processing with transcription. Cell 108: 501-512.
51. Ristimaki, A., Garfinkel, S., Wessendorf, J., Maciag, T., and Hla, T. 1994. Induction of cyclooxygenase-2 by interleukin-1 α. Evidence for post-transcriptional regulation. J. Biol. Chem. 269: 11769-11775.
52. Ristimaki, A., Narko, K., and Hla, T. 1996. Down-regulation of cytokine-induced cyclooxygenase 2 transcript isoforms by dexamethasone: Evidence for post-transcriptional regulation. Biochem. J. 318: 325-331.
53. Ryan, K., Calvo, O., and Manley, J.L. 2004. Evidence that polyadenylation factor CPSF-73 is the mRNA 3′ processing endonuclease. RNA 10: 565-573.
54. San, H., Kawahito, Y., Wilder, R.L., Hasiramoto, A., Mukai, S., Asai, K., Kimura, S., Kato, H., Kondo, M., and Hla, T. 1995. Expression of cyclooxygenase-1 and -2 in human colorectal cancer. Cancer Res. 55: 3785-3789.
55. Schmidt, C.M., Wang, Y., and Wiesenauer, C. 2003. Novel combination of cyclooxygenase-2 and MEK inhibition in human hepatocellular carcinoma provides a synergistic increase in apoptosis. J. Gastrointest. Surg. 7: 1024-1033.
56. Tian, B., Hu, J., Zhang, H., and Lutz, C.S. 2005. A large scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33: 201-212.
57. Wahle, E. and Kuhn, U. 1997. The mechanism of 3′ cleavage and polyadenylation of eukaryotic pre-mRNA. Prog. Nucleic Acid Res. Mol. Biol. 57: 41-71.
58. Wickens, M., Anderson, P., and Jackson, R.J. 1997. Life and death in the cytoplasm: Messages from the 3′ end. Curr. Opin. Genet. Dev. 7: 220-232.
59. Williams, C.S., Mann, M., and DuBois, R.N. 1999. The role of cyclooxygenases in inflammation, cancer and development. Oncogene 18: 7908-7916.
60. Wilusz, J., Shenk, T., Takagaki, Y., and Manley, J.L. 1990. A multicomponent complex is required for the AAUAAA-dependent cross-linking of a 64-kilodalton protein to polyadenylation substrates. Mol. Cell. Biol. 10: 1244-1248.
61. Xie, W., Cipman, J.G., Robertson, D.L., Eirkson, R.L., and Simmons, D.L. 1991. Expression of a mitogen-responsive gene encoding prostaglandin synthase is regulated by mRNA splicing. Proc. Natl. Acad. Sci. 88: 2692-2696.
62. Young, T.M., Wang, Q., Pe'ery, T., and Mathews, M.B. 2003. The human I-mfa domain-containing protein, HIC, interacts with cyclin T1 and modulates P-TEFb-dependent transcription. Mol. Cell. Biol. 23: 6373-6384.
63. Zhang, H., Lee, J.Y., and Tian, B. 2005. Biased alternative polyadenylation in human tissues. Genome Biol. 6: 1-13.
64. Zhao, J., Hyman, L., and Moore, C. 1999. Formation of mRNA 3′ ends in eukaryotes: Mechanism, regulationm and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63: 405-445.
65. Zhao, X., Oberg, D., Rush, M., Fay, J., Lambkin, H., and Schwartz, S. 2005. A 57-nucleotide upstream early polyadenylation element in human papilloma virus type 16 interacts with hFip1, CstF64, hnRNP C1/C2, and polypyrimidine tract binding protein. J. Virol. 79: 4270-4288.