Messenger RNA 3′-end formation and the regulation of gene expression

Regulation of Gene Expression in Plants: The Role of Transcript Structure and Processing

Volumn 9780387356402, Issue , 2007, Pages 101-122

  Hunt, Arthur G ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; RNA;

EXPRESSION PROFILE; MESSENGER RNA; PLANT GENOMES; POLYADENYLATION; POLYADENYLATION SIGNALS; POSTTRANSCRIPTIONAL CONTROL; UNTRANSLATED REGIONS;

GENE EXPRESSION REGULATION;

EID: 57349109725     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-35640-2_4     Document Type: Chapter

References (93)

1. Addepalli, B., Meeks, L.R., Forbes, K.P. and Hunt, A.G., 2004, Novel alternative splicing of mRNAs encoding poly(A) polymerases in Arabidopsis, Biochim. Biophys. Acta 1679:117-128.
2. Bai, C. and Tolias, P. P., 1998, Drosophila clipper/CPSF 30K is a post-transcriptionally regulated nuclear protein that binds RNA containing GC clusters, Nucl. Acids Res. 26:1597-1604.
3. Baillat, D., Hakimi, M.A., Naar, A.M., Shilatifard, A., Cooch, N. and Shiekhattar, R., 2005, Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II, Cell 123:265-276.
4. Barabino, S.M., Hubner, W., Jenny, A., Minvielle-Sebastia, L. and Keller, W., 1997, The 30-kD subunit of mammalian cleavage and polyadenylation specificity factor and its yeast homolog are RNA-binding zinc finger proteins, Genes Dev. 11: 1703-1716.
5. Barabino, S. M., Ohnacker, M. and Keller, W., 2000, Distinct roles of two Yth1p domains in 3′-end cleavage and polyadenylation of yeast pre-mRNAs, EMBO J. 19:3778-3787.
6. Bassett, C.L., Artlip, T.S., and Callahan, A.M., 2002, Characterization of the peach homologue of the ethylene receptor, PpETR1, reveals some unusual features regarding transcript processing, Planta 251:679-688.
7. Belostotsky, D.A. and Rose, A.B., 2005, Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events, Trends Plant Sci. 10:347-353.
8. Bentley, D.L., 2005, Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors, Curr. Opin. Cell Biol. 17:251-256.
9. Boisvert, F.M., Cote, J., Boulanger, M.C. and Richard, S., 2003, A proteomic analysis of arginine-methylated protein complexes, Mol. Cell. Proteomics 2:1319-1330.
10. Bond, G.L., Prives, C. and Manley, J.L., 2000, Poly(A) polymerase phosphorylation is dependent on novel interactions with cyclins, Mol. Cell Biol. 20:5310-5320.
11. Boss, P.K., Bastow, R.M., Mylne, J.S. and Dean, C., 2004, Multiple pathways in the decision to flower: Enabling, promoting, and resetting, Plant Cell 16 Suppl:S18-31.
12. Brodsky, A.S. and Silver, P.A., 2000, Pre-mRNA processing factors are required for nuclear export, RNA 6:1737-1749.
13. Brown, K.M. and Gilmartin, G.M., 2003, A mechanism for the regulation of pre-mRNA 3′?processing by human cleavage factor Im, Mol. Cell 12: 1467-1476.
14. Buratowski, S., 2005, Connections between mRNA 3′?end processing and transcription termination, Curr. Opin. Cell Biol. 17:257-261.
15. Caballero, J.J., Giron, M.D., Vargas, A.M., Sevillano, N., Suarez, M.D. and Salto, R., 2004, AU-rich elements in the mRNA 3′-untranslated region of the rat receptor for advanced glycation end products and their relevance to mRNA stability, Biochem. Biophys. Res. Commun. 319:247-255.
16. Calvo, O. and Manley, J.L., 2003, Strange bedfellows: Polyadenylation factors at the promoter, Genes Dev. 17:1321-1327.
17. Colgan, D.F., Murthy, K.G., Prives, C. and Manley, J.L., 1996, Cell-cycle related regulation of poly(A) polymerase by phosphorylation, Nature 384:282-285.
18. Delaney, K.J., Xu, R., Zhang, J., Li, Q.Q., Yun, K.-Y., Falcone, D.F., and Hunt, A.G., 2006, Calmodulin interacts with and regulates the RNA binding activity of an Arabidopsis polyadenylation factor subunit, Plant Physiol. in press.
19. Dichtl, B., Blank, D., Sadowski, M., Hubner, W., Weiser, S. and Keller, W., 2002, Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination, EMBO J. 21:4125-4135.
20. Dichtl, B. and Keller, W., 2001, Recognition of polyadenylation sites in yeast premRNAs by cleavage and polyadenylation factor, EMBO J. 20:3197-3209.
21. Dominski, Z., Yang, X.C. and Marzluff, W.F., 2005, The polyadenylation factor CPSF-73 is involved in histone-pre-mRNA processing, Cell 123:37-48.
22. Elliott, B.J., Dattaroy, T., Meeks-Midkiff, L.R., Forbes, K.P. and Hunt, A.G., 2003, An interaction between an Arabidopsis poly(A) polymerase and a homologue of the 100 kDa subunit of CPSF, Plant Mol. Biol. 51:373-384.
23. Flaherty, S.M., Fortes, P., Izaurralde, E., Mattaj, I.W. and Gilmartin, G.M., 1997, Participation of the nuclear cap binding complex in pre-mRNA 3′?processing, Proc. Natl. Acad. Sci. USA 94:11893-11898.
24. Forbes, K.P., Addepalli, B. and Hunt, A.G., 2006, An Arabidopsis Fip1 homolog interacts with RNA and provides conceptual links with a number of other polyadenylation factor subunits, J. Biol. Chem. 281:176-186.
25. Giranton, J.L., Ariza, M.J., Dumas, C., Cock, J.M. and Gaude, T., 1995, The S locus receptor kinase gene encodes a soluble glycoprotein corresponding to the SKR extracellular domain in Brassica oleracea, Plant J. 8: 827-834.
26. Graber, J.H., Cantor, C.R., Mohr, S.C. and Smith, T.F., 1999, In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species, Proc. Natl. Acad. Sci. USA 96:14055-14060.
27. Gross, S. and Moore, C.L., 2001, Rna15 interaction with the A-rich yeast polyadenylation signal is an essential step in mRNA 3′-end formation, Mol. Cell Biol. 21:8045-8055.
28. Gunderson, S.I., Beyer, K., Martin, G., Keller, W., Boelens, W.C. and Mattaj, L.W., 1994, The human U1A snRNP protein regulates polyadenylation via a direct interaction with poly(A) polymerase, Cell 76:531-541.
29. Gunderson, S.I., Vagner, S., Polycarpou-Schwarz, M. and Mattaj, I.W., 1997, Involvement of the carboxyl terminus of vertebrate poly(A) polymerase in U1A autoregulation and in the coupling of splicing and polyadenylation, Genes Dev. 11: 761-773.
30. Gunther, C.V. and Riddle, D.L., 2004, Alternative polyadenylation results in a truncated daf-4 BMP receptor that antagonizes DAF-7-mediated development in Caenorhabditis elegans, J. Biol. Chem. 279:39555-39564.
31. Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K. Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D., Salzberg, S.L. and White, O., 2003, Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucl. Acids Res. 31:5654-5666.
32. Hammell, C.M., Gross, S., Zenklusen, D., Heath, C.V., Stutz, F., Moore, C. and Cole, C.N., 2002, Coupling of termination, 3′?processing, and mRNA export, Mol. Cell Biol. 22:6441-6457.
33. Hansen, W.R., Barsic-Tress, N., Taylor, L. and Curthoys, N.P., 1996, The 3′-nontranslated region of rat renal glutaminase mRNA contains a pH-responsive stability element, Am. J. Physiol. 271:F126-F131.
34. Hatton, L.S., Eloranta, J.J., Figueiredo, L.M., Takagaki, Y., Manley, J.L. and O'Hare, K., 2000, The Drosophila homologue of the 64 kDa subunit of cleavage stimulation factor interacts with the 77 kDa subunit encoded by the suppressor of forked gene, " Nucl. Acids Res. 28:520-526.
35. He, X. and Moore, C., 2005, Regulation of yeast mRNA 3′?end processing by phosphorylation, Mol. Cell 19:619-629.
36. Hua, J., Sakai, H., Nourizadeh, S., Chen, Q.G., Bleeker, A.B., Ecker, J.R., and Meyerowitz, E.M., 1998, EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis, Plant Cell 10:1321-1332.
37. Hunt, A.G., 1994, Messenger RNA 3′?End Formation in Plants, Ann. Rev. Plant Physiol. Plant Mol. Biol. 45:47-60.
38. Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A. and Shinozaki, K., 2004, Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences, Nucl. Acids Res. 32: 5096-5103.
39. Imai, Y., Matsuo, N., Ogawa, S., Tohyama, M. and Takagi, T., 1998, Cloning of a gene, YT521, for a novel RNA splicing-related protein induced by hypoxia/reoxygenation, Brain Res. Mol. Brain Res. 53:33-40.
40. Ishikawa, T., Yoshimura, K., Tamoi, M., Takeda, T. and Shigeoka, S., 1997, Alternative mRNA splicing of 3′-terminal exons generates ascorbate peroxidase isoenzymes in spinach (Spinacia oleracea) chloroplasts, Biochem. J. 328:795-800.
41. Kaufmann, I., Martin, G., Friedlein, A., Langen, H. and Keller, W., 2004, Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase, EMBO J. 23:616-626.
42. Kikuchi, S., et al., 2003, Collection, mapping, and annotation of over 28, 000 cDNA clones from japonica rice, Science 301:376-379.
43. Klahre, U., Hemmings-Mieszczak, M. and Filipowicz, W., 1995, Extreme heterogeneity of polyadenylation sites in mRNAs encoding chloroplast RNA-binding proteins in Nicotiana plumbaginifolia, Plant Mol. Biol. 28:569-574.
44. Kleiman, F.E. and Manley, J.L., 2001, The BARD1-CstF-50 interaction links mRNA 3′end formation to DNA damage and tumor suppression, Cell 104:743-753.
45. Kolev, N. G. and Steitz, J.A., 2005, Symplekin and multiple other polyadenylation factors participate in 3′-end maturation of histone mRNAs, Genes Dev. 19:2583-2592.
46. Kyburz, A., Sadowski, M., Dichtl, B. and Keller, W., 2003, The role of the yeast cleavage and polyadenylation factor subunit Ydh1p/Cft2p in pre-mRNA 3′-end formation, Nucl. Acids Res. 31:3936-3945.
47. Li, Q. and Hunt, A.G., 1995, A near-upstream element in a plant polyadenylation signal consists of more than six nucleotides, Plant Mol. Biol. 28:927-934.
48. Licatalosi, D.D., Geiger, G., Minet, M., Schroeder, S., Cilli, K., McNeil, J. B. and Bentley, D.L., 2002, Functional interaction of yeast pre-mRNA 3′?end processing factors with RNA polymerase II, Mol. Cell 9:1101-1111.
49. Loke, J.C., Stahlberg, E.A., Strenski, DG., Haas, B.J., Wood, P.C. and Li, Q.Q., 2005, Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures, Plant Physiol. 138:1457-1468.
50. MacDonald, C.C., Wilusz, J. and Shenk, T., 1994, The 64-kilodalton subunit of the CstF polyadenylation factor binds to pre-mRNAs downstream of the cleavage site and influences cleavage site location, Mol. Cell Biol. 14:6647-6654.
51. MacDonald, M.H., Mogen, B.D. and Hunt, A.G., 1991, Characterization of the polyadenylation signal from the T-DNA-encoded octopine synthase gene, Nucl. Acids Res. 19:5575-5581.
52. Meeks, L.R., 2005, Isolation and Characterization of the Four Arabidopsis thaliana Poly(A) Polymerase Genes, Plant Physiology, Lexington, KY, University of Kentucky, Ph.D.
53. Meyers, B.C., Morgante, M. and Michelmore, R.W., 2002, TIR-X and TIR-NBS proteins: Two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes, Plant J. 32:77-92.
54. Meyers, B.C., Vu, T.H., Tej, S.S., Ghazal, H., Matvienko, M., Agrawal, V., Ning, J. and Haudenschild, C. D., 2004, Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing, Nat. Biotechnol. 22:1006-1011.
55. Millevoi, S., Geraghty, F., Idowu, B., Tam, J.L., Antoniou, M. and Vagner, S., 2002, A novel function for the U2AF 65 splicing factor in promoting pre-mRNA 3′-end processing, EMBO Rep. 3:869-874.
56. Miyamoto, S., Chiorini, J.A., Urcelay, E. and Safer, B., 1996, Regulation of gene expression for translation initiation factor eIF-2 alpha: importance of the 3′ untranslated region, Biochem. J. 315 (Pt 3):791-798.
57. Mizrahi, N. and Moore, C., 2000, Posttranslational phosphorylation and ubiquitination of the Saccharomyces cerevisiae Poly(A) polymerase at the S/G(2) stage of the cell cycle, Mol. Cell Biol. 20:2794-2802.
58. Mogen, B.D., MacDonald, M.H., Leggewie, G. and Hunt, A.G., 1992, Several distinct types of sequence elements are required for efficient mRNA 3′?end formation in a pea rbcS gene, Mol. Cell Biol. 12:5406-5414.
59. Morlando, M., Greco, P., Dichtl, B., Fatica, A., Keller, W. and Bozzoni, I., 2002, Functional analysis of yeast snoRNA and snRNA 3′-end formation mediated by uncoupling of cleavage and polyadenylation, Mol. Cell Biol. 22:1379-1389.
60. Murthy, K.G. and Manley, J.L., 1995, The 160-kD subunit of human cleavagepolyadenylation specificity factor coordinates pre-mRNA 3′-end formation, Genes Dev. 9:2672-2683.
61. Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M. and Gotoh, O., 2005, Speciesspecific variation of alternative splicing and transcriptional initiation in six eukaryotes, Gene 364:53-62.
62. Nedea, E., He, X., Kim, M., Pootoolal, J., Zhong, G., Canadien, V., Hughes, T., Buratowski, S., Moore, C.L. and Greenblatt, J., 2003, Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3′-ends, J. Biol. Chem. 278: 33000-33010.
63. Niwa, M., Rose, S.D. and Berget, S.M., 1990, In vitro polyadenylation is stimulated by the presence of an upstream intron, Genes Dev. 4:1552-1559.
64. Proudfoot, N., 2004, New perspectives on connecting messenger RNA 3′?end formation to transcription, Curr. Opin. Cell Biol. 16:272-278.
65. Qu, X., Qi, Y. and Qi, B., 2002, Generation of multiple mRNA transcripts from the novel human apoptosis-inducing gene hap by alternative polyadenylation utilization and the translational activation function of 3′?untranslated region, Arch. Biochem. Biophys. 400:233-244.
66. Quesada, V., Macknight, R., Dean, C. and Simpson, G.G., 2003, Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time, EMBO J. 22: 3142-3152.
67. Razem, F.A., El-Kereamy, A., Abrams, S.R., and Hill, R.D., 2006, The RNAbinding protein FCA is an abscisic acid receptor, Nature 439:290-294.
68. Rothnie, H.M., 1996, Plant mRNA 3′-end formation, Plant Mol. Biol. 32:43-61.
69. Shell, S. A., Hesse, C., Morris, S.M. Jr. and Milcarek, C., 2005, Elevated levels of the 64-kDa cleavage stimulatory factor (CstF-64) in lipopolysaccharide-stimulated macrophages influence gene expression and induce alternative poly(A) site selection, J. Biol. Chem. 280:39950-39961.
70. Simon, P., Schott, K., Williams, R.W. and Schaeffel, F., 2004, Posttranscriptional regulation of the immediate-early gene EGR1 by light in the mouse retina, Eur. J. Neurosci. 20:3371-3377.
71. Simpson, G.G., Dijkwel, P.P., Quesada, V., Henderson, I. and Dean, C., 2003, FY is an RNA 3′?end-processing factor that interacts with FCA to control the Arabidopsis floral transition, Cell 113:777-787.
72. Skadsen, R.W. and Knauer, N.S., 1995, Alternative polyadenylation generates three low-pI alpha-amylase mRNAs with differential expression in barley, FEBS Lett. 361:220-224.
73. Stoilov, P., Rafalska, I. and Stamm, S., 2002, YTH: A new domain in nuclear proteins, Trends Biochem. Sci. 27:495-497.
74. Takagaki, Y. and Manley, J.L., 1998, Levels of polyadenylation factor CstF-64 control IgM heavy chain mRNA accumulation and other events associated with B cell differentiation, Mol. Cell 2:761-771.
75. Takagaki, Y. and Manley, J.L., 2000, Complex protein interactions within the human polyadenylation machinery identify a novel component, Mol. Cell Biol. 20: 1515-1525.
76. Takagaki, Y., Seipelt, R.L., Peterson, M.L. and Manley, J.L., 1996, The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation, Cell 87:941-952.
77. Tang, G., Zhu, X., Gakiere, B., Levanony, H., Kahana, A. and Galili, G., 2002, The bifunctional LKR/SDH locus of plants also encodes a highly active monofunctional lysine-ketoglutarate reductase using a polyadenylation signal located within an intron, 2002, Plant Physiol. 130:147-154.
78. Tantikanjana, T., Nasrallah, M.E., Stein, J.C., Chen, C.H. and Nasrallah, J.B., 1993, An alternative transcript of the S locus glycoprotein gene in a class II pollen-recessive self-incompatibility haplotype of Brassica oleracea encodes a membraneanchored protein, Plant Cell 5:657-666.
79. Tian, B., Hu, J., Zhang, H. and Lutz, C.S., 2005, A large-scale analysis of mRNA polyadenylation of human and mouse genes, Nucl. Acids Res. 33:201-212.
80. Touriol, C., Morillon, A., Gensac, M.C., Prats, H. and Prats, A.C., 1999, Expression of human fibroblast growth factor 2 mRNA is post-transcriptionally controlled by a unique destabilizing element present in the 3′-untranslated region between alternative polyadenylation sites, J. Biol. Chem. 274:21402-21408.
81. Touriol, C., Roussigne, M., Gensac, M.C., Prats, H. and Prats, A.C., 2000, Alternative translation initiation of human fibroblast growth factor 2 mRNA controlled by its 3′-untranslated region involves a Poly(A) switch and a translational enhancer, J. Biol. Chem. 275:19361-19367.
82. Valentini, S.R., Weiss, V.H. and Silver, P.A., 1999, Arginine methylation and binding of Hrp1p to the efficiency element for mRNA 3′-end formation, RNA 5:272-280.
83. Venkataraman, K., Brown, K.M. and Gilmartin, G.M., 2005, Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition, Genes Dev. 19:1315-1327.
84. Wahle, E., 1991, A novel poly(A)-binding protein acts as a specificity factor in the second phase of messenger RNA polyadenylation, Cell 66:759-768.
85. Wahle, E. and Ruegsegger, U., 1999, 3′-End processing of pre-mRNA in eukaryotes, FEMS Microbiol. Rev. 23:277-295.
86. Wallace, A.M., Dass, B., Ravnik, S.E., Tonk, V., Jenkins, N.A., Gilbert, D. J., Copeland, N.G. and MacDonald, C.C., 1999, Two distinct forms of the 64, 000 Mr protein of the cleavage stimulation factor are expressed in mouse male germ cells, Proc. Natl. Acad. Sci. USA 96:6763-6768.
87. Wallace, A.M., Denison, T.L., Attaya, E.N. and MacDonald, C.C., 2004, Developmental distribution of the polyadenylation protein CstF-64 and the variant tauCstF-64 in mouse and rat testis, Biol. Reprod. 70:1080-1087.
88. Wang, S.W., Asakawa, K., Win, T.Z., Toda, T. and Norbury, C.J., 2005, Inactivation of the pre-mRNA cleavage and polyadenylation factor Pfs2 in fission yeast causes lethal cell cycle defects, Mol. Cell Biol. 25:2288-2296.
89. Xiao, Y.L., Smith, S.R., Ishmael, N., Redman, J.C., Kumar, N., Monaghan, E.L., Ayele, M., Haas, B.J., Wu, H.C. and Town, C.D., 2005, Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants, Plant Physiol. 139:1323-1337.
90. Xu, R., Ye, X. and Quinn Li, Q., 2004, AtCPSF73-II gene encoding an Arabidopsis homolog of CPSF 73 kDa subunit is critical for early embryo development, Gene 324:35-45.
91. Yan, J. and Marr, T.G., 2005, Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat, Genome Res. 15:369-375.
92. Yao, Y., Song, L., Katz, Y. and Galili, G., 2002, Cloning and characterization of Arabidopsis homologues of the animal CstF complex that regulates 3′?mRNA cleavage and polyadenylation, J. Exp. Bot. 53:2277-2278.
93. Zhao, J., Hyman, L. and Moore, C., 1999, Formation of mRNA 3′?ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis, Microbiol. Mol. Biol. Rev. 63:405-44.