Multiple transcript initiation as a mechanism for regulating gene expression

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

Volumn 9780387356402, Issue , 2007, Pages 39-66

  Farrell, Robert E ^a   Bassett, Carole L ^b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE ENCODING; MACHINERY; NUCLEIC ACIDS; PROTEINS; TRANSCRIPTION;

FUNCTIONAL PROTEINS; MESSENGER RNA; SECONDARY AND TERTIARY STRUCTURES; SEQUENCE INFORMATIONS; STRUCTURAL COMPONENT; TRANSFER RNAS;

GENE EXPRESSION REGULATION;

EID: 84920048303     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-35640-2_2     Document Type: Chapter

References (133)

1. Adam, E., Kozma-Bognar, L., Dallmann, G., and Nagy, F., 1995, Transcription of tobacco phytochrome-A genes initiates at multiple start sites and requires multiple cis-acting regulatory elements, Plant Mol. Biol. 29:983-993.
2. Anderson, S., Bankier, A.T., Barrell, B.G., deBruijin, M.H.L., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J.H., Staden, R., and Young, I.G., 1981, Sequence and organization of the human mitochondrial genome, Nature 290:457-465.
3. Antequera, F., and Bird, A.P., 1988, Unmethylated CpG islands associated with genes in higher plant DNA, EMBO J. 7:2295-2299.
4. Bag, J., 1991, mRNA and mRNP, in: Translation in Eukaryotes pp.71-79. CRC Press, Ft. Lauderdale.
5. Bai, X., Peirson, B.N., Dong, F., Xue, C., and Makaroff, C.A., 1999, Isolation and characterization of SYN1, a RAD21-like gene essential for meiosis in Arabidopsis, Plant Cell 11:417-430.
6. Bassett, C.L., Nickerson, M.L., Cohen, R.A., and Rajeevan, M.S., 2000, Alternative transcript initiation and novel post-transcriptional processing of a leucine-rich repeat receptor-like protein kinase gene that responds to short-day photoperiodic floral induction in morning glory (Ipomoea nil), Plant Mol. Biol. 43:43-58.
7. Bassett, C.L., Nickerson, M.L., Farrell Jr., R.E., and Harrison, M., 2004, Multiple transcripts of a gene for a leucine-rich repeat receptor kinase from morning glory (Ipomoea nil) originate from different TATA boxes in a tissue-specific manner, Mol. Gen. Genomics 271:752-760.
8. Binder, S., Marchfelder, A., and Brennicke, A., 1996, Regulation of gene expression in plant mitochondria, Plant Mol. Biol. 32:303-314.
9. Boeke, J.D., and Corres, V.G., 1989, transcription and reverse transcription of retrotransposons. Ann. Rev. Microbiol. 43:403-434.
10. Brown, J.W.S., Clark, G.P., Leader, D.J., Simpson, C.G., and Lowe, T., 2001, Multiple snoRNA gene clusters from Arabidopsis, RNA 7:1817-1832.
11. Brown, J.W.S., Echeverria, M., and Qu, L.-H., 2003, Plant snoRNAs: Functional evolution and new modes of gene expression, Trends in Plant Sci. 8:42-49.
12. Burke, T.W., and Kadonaga, J.T., 1996, Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters, Genes Dev. 10:711-724.
13. Cao, J.H., and Geballe, A.P., 1995, Translational inhibition by a human cytomegalovirus upstream open reading frame despite inefficient utilization of its AUG codon, J. Virol. 69:1030-1036.
14. Cheng, S.H., Cline, K., and DeLisle, A.J., 1994, An Arabidopsis chloroplast RNAbinding protein gene encodes multiple mRNAs with different 5′?ends, Plant Physiol. 106:303-311.
15. Closs, E.I., Lyons, C.R., Kelly, C., and Cunningham, J.M., 1993, Characterization of the third member of the mCAT family of cationic amino acid transporters, J. Biol. Chem. 268:20796-20800.
16. Cockell, M., and Gasser, S.M., 1999, Nuclear compartments and gene regulation. Curr. Opin. Genet. Dev. 9:199-205.
17. Cohen, A.J., Lakshmi, T.R., Niu, Z., Trindade, J., Billings, P.C., and Adams, S.L., 2002, A novel noncollagenous protein encoded by an alternative transcript of the chick type III collagen gene is expressed in cartilage, bone and muscle, Mech. Dev. 114:177-180.
18. Cooper, T.A., and Mattox, W., 1997, The regulation of splice-site selection and its role in human disease. Am. J. Hum. Genet. 61:259-266.
19. Damiani Jr., R.D., and Wessler, S.R., 1993, An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators, Proc. Natl. Acad. Sci. USA 90:8244-8248.
20. Dehesh, K., Franci, C., Sharrock, R.A., Somers, D.E., Welsch, J.A., and Quail, P.H., 1994, The Arabidopsis phytochrome A gene has multiple transcription start sites and a promoter sequence motif homologous to the repressor element of monocot phytochrome A genes, Photochem. Photobiol. 59:379-384.
21. Dillon, L.S., 1987, The Gene. Its Structure, Function, and Evolution. Plenum Press, New York, pp. 896.
22. Dinesh-Kumar, S.P., and Miller, W.A., 1993, Control of start codon choice on a plant viral RNA encoding overlapping genes, Plant Cell 5:679-692.
23. Farrell Jr., R.E., 2005, RNA Methodologies: A Laboratory Guide for Isolation and Characterization, (3/e). Elsevier Academic Press, San Diego, CA, pp. 1-767.
24. Figueroa, P., Holuigue, L., Araya, A., and Jordana, X., 2000, The nuclear-encoded SDH2-RPS14 precursor is proteolytically processed between SDH2 and RPS14 to generate maize mitochondrial RPS14. Biochem. Biophys. Res. Commun. 271: 380-385.
25. Figueroa, P., Gomez, I., Holuigue, L., Araya, A., and Jordana, X., 1999, Transfer of rps14 from the mitochondrion to the nucleus in maize implied integration within a gene encoding the iron-sulphur subunit of succinate dehydrogenase and expression by alternative splicing. Plant J. 18:601-609.
26. Fra, A.M., Pasqualetto, E., Mancini, M., and Sitia, R., 2000, Genomic organization and transcriptional analysis of the human genes encoding caveolin-1 and caveolin-2, Gene 243:75-83.
27. Fujita, T., Maggio, A., Garcia-Rios, M., Bressan, R.A., and Csonka, L.N., 1998, Comparative analysis of the regulation of expression and structures of two evolutionarily divergent genes for δ1-pyrroline-5-carboxylate synthetase from tomato, Plant Physiol. 118:661-674.
28. Futterer, J., and Hohn, T., 1996, Translation in plants -rules and exceptions, Plant Mol. Biol. 32:159-189.
29. Gagliardi, D. and Leaver, C.J., 1999, Polyadenylation accelerates the degradation of the mitochondrial mRNA associated with cytoplasmic male sterility in sunflower, EMBO J. 18:3757-3766.
30. Garcia-Rios, M., Fujita, T., LaRosa, P.C., Locy, R.D., Clithero, J.M., Bressan, R.A., and Csonka, L.N., 1997, Cloning of a polycistronic cDNA from tomato encoding γ-glutamyl kinase and ?-glutamyl phosphate reductase, Proc. Natl. Acad. Sci. USA 94:8249-8254.
31. Gong, D.-W., Bi, S., Weintraub, B.D., and Reitman, M., 1998, Rat mitochondrial glycerol-3-phosphate dehydrogenase gene: multiple promoters, high levels in brown adipose tissue, and tissue-specific regulation by thyroid hormone, DNA Cell Biol. 17:301-309.
32. Gowda, S., Satyanarayana, T., Ayllon, M.A., Moreno, P., Flores, R., and Dawson, W.O., 2003, The conserved structures of the 5′?nontranslated region of Citrus tristeza virus are involved in replication and virion assembly, Virology 317:50-64.
33. Haseloff, J., Siemering, K.R., Prasher, D.C., and Hodge, S., 1997, removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. Proc. Natl. Acad. Sci. USA 94:2122-2127.
34. Hayes, R., Kudla, J., and Gruissem, W., 1999, Degradation of chloroplast mRNA: The role of polyadenylation, Trends Biochem. Sci. 24:199-202.
35. Hoffmann, M., Dombrowski, S., Guha, C., and Binder, S., 1999, Cotranscription of the rp15-rps14-cob gene cluster in pea mitochondria. Mol. Gen. Genet. 261:537-545.
36. Holec, S., Lange, H., Kuhn, K., Alioua, M., Borner, T., and Gagliardi, D., 2006, Relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and polynucleotide phosphorylase, Mol. Cell. Biol. 26:2869-2876.
37. Hu, C.A., Delauney, A.J., and Verma, D.P.S., 1992, A bifunctional enzyme (δ1-pyrroline-5-carboxylate synthetase) catalyzes the first two steps in proline biosynthesis in plants, Proc. Natl. Acad. Sci. USA 89:9354-9358.
38. Huang, W., Wong, J.M., and Bateman, E., 1996, TATA elements direct bi-directional transcription by RNA polymerases II and III, Nucl. Acids Res. 24:1158-1163.
39. 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.
40. Ivanov, I.P., Matsufuji, S., Murakami, Y., gesteland, R.F., and Atkins, J.F., 2000, Conservation of polyamine regulation by translational frameshifting from yeast to mammals. EMBO J. 19:1907-1917.
41. Joshi, C.P., 1987, An inspection of the domain between putative TATA box and translation start site in 79 plant genes, Nucl. Acids Res. 15:6643-6652.
42. Joshi, C.P., Zhou, H., Huang, X., and Chiang, V.L., 1997, Context sequences of translation initiation codon in plants. Plant Molecular Biol. 35:993-1001.
43. Ju, B.-G., Lunyak, V.V., Perissi, V., Garcia-Bassets, I., Rose, D.W., Glass, C.K., and Rosenfeld, M.G., 2006, Estrogen-initiated gene transcription involves enzymatically driven DNA cleavage, repair and local reconfiguration of chromatin. Science 312:1798-1802.
44. Kanno, T., Huettel, B., Mette, M.F., Aufsatz, W., Jaligot, E., Daxinger, L., Kreil, D.P., Matzke, M., and Matzke, A.J.M., 2005, Atypical RNA polymerase subunits required for RNA-directed DNA methylation, Nat Genet 37:761-765.
45. Kiss, T., 2002, Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions, Cell 109:145-148.
46. Kiss, T., and Filipowicz, W., 1995, Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns, Genes Dev. 9:1411-1424.
47. Kiss, T., Marshallsay, C., and Filipowicz, W., 1991, Alteration of the RNA polymerase specificity of U3 snRNA genes during evolution and in vitro, Cell 65:517-526.
48. Kozak, M., 1978, How do eukaryotic ribosomes select initiation regions in messenger RNA? Cell 15:1109-1123.
49. Kozak, M., 1986, Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes, Cell 44:283-292.
50. Kozak, M., 1987a, An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs, Nucl. Acids Res. 15, 8125-8148.
51. Kozak, M., 1987b, At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells, J. Mol. Biol. 196:947-950.
52. Kozak, M., 1989, The scanning model for translation: An update, J. Cell Biol. 108: 229-241.
53. Kozak, M., 1990, Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes, Proc. Natl. Acad. Sci. USA 87:8301-8305.
54. Kozak, M., 1991a, An analysis of vertebrate mRNA sequences: intimations of translational control, J. Cell Biol. 115: 887-903.
55. Kozak, M., 1991b, Structural features in eukaryotic mRNAs that modulate initiation of translation, J. Biol. Chem. 266:19867-19870.
56. Kozak, M., 1997, Recognition of AUG and alternative initiator codons is augmented by G in position ?4 but is not generally affected by the nucleotides in positions ?5 and ?6, EMBO J. 16:2482-2492.
57. Kozak, M., 1999, Initiation of translation in prokaryotes and eukaryotes, Gene 234:187-208.
58. Kozak M., 2001, Constraints on reinitiation of translation in mammals, Nucl. Acids Res. 29:5226-5232.
59. Kozak, M., 2002, Pushing the limits of the scanning mechanism for initiation of translation, Gene 299:1-34.
60. Kozak, M., 2003, Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation, Gene 318:1-23.
61. Kravchenko, J.E., Rogozin, I.B., Koonin, E.V., and Chumakov, P.M., 2005, Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin, Nature 436:735-739.
62. Kruszka, K., Barneche, F., Guyot, R., Ailhas, J., Meneau, I., Schiffer, S., Marchfelder, A., and Echeverria, M., 2003, Plant dicistronic tRNA-snoRNA genes: A new mode of expression of the small nucleolar RNAs processed by RNase Z, EMBO J. 22:621-632.
63. Kubo, N., Harada, K., Hirai, A., and Kadowaki, K., 1999, A single nuclear transcript encoding mitochondrial RPS14 and SDHB of rice is processed by alternative splicing: common use of the same mitochondrial targeting signal for different proteins. Proc. Natl. Acad. Sci. USA 96:9207-9211.
64. Kuhn, K., Weihe, A., and Borner, T., 2005, Multiple promoters are a common feature of mitochondrial genes in Arabidopsis, Nucl. Acids Res. 33:337-346.
65. Kuhn, J. and Binder, S., 2002, RT-PCR analysis of 5′?to 3′-end-ligated mRNAs identifies the extremities of cox2 transcripts in pea mitochondria, Nucl. Acids Res. 30:439-446.
66. Kurjan, J. and Herskowitz, I., 1982, Structure of a yeast pheromone gene (MF#): A putative #-factor precursor contains four tandem copies of mature #-factor, Cell 30:933-943.
67. Lagrange, T., Franzetti, B., Axelos, M., Mache, R., and Lerbs-Mache, S., 1993, Structure and expression of the nuclear gene coding for the chloroplast ribosomal protein L21: Developmental regulation of a housekeeping gene by alternative promoters, Molec. Cell. Biol. 13:2614-2622.
68. Lagrange, T., Kapanidis, A.N., Tang, H., Reinberg, D., and Ebright, R.H., 1998, New core promoter element in RNA polymerase II-dependent transcription: Sequencespecific DNA binding by transcription factor IIB, Genes Dev. 12:34-44.
69. Lambowitz, A.M., and Belfort, M., 1993, Introns as mobile genetic elements, Ann. Rev. Biochem. 62:587-622.
70. Lander, E.S., et al., 2001, Initial sequencing and analysis of the human genome, Nature 409:860-92.
71. Leader, D.J., Clark, G.P., Watters, J., Beven, A.F., Shaw, P.J., and Brown, J.W., 1997, Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-sno-RNAs, EMBO J. 16:5742-5751.
72. Leader, D.J., Clark, G.P., Watters, J., Beven, A.F., Shaw, P.J., and Brown, J.W., 1999, Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs, Plant Mol. Biol. 39:1091-1100.
73. Lee, S.W., Heinz, R., Robb, J., and Nazar, R.N., 1994, Differential utilization of alternative initiation sites in a plant defense gene responding to environmental stimuli, Eur. J. Biochem. 226:109-114.
74. Lewin, B., 2004, Genes VIII, Pearson Education, Upper Saddle River, NJ, pp. 617.
75. Liang, D., Zhou, H., Zhang, P., Chen, Y.Q., Chen, X., Chen, C.L., and Qu, L.H., 2002, A novel gene organization: intronic snoRNA gene clusters from Oryza sativa, Nuc. Acids Res. 30:3262-3272.
76. Lisitsky, I., Klaff, P., and Schuster, G., 1997, Blocking polyadenylation of mRNA in the chloroplast inhibits its degradation. Plant J. 12:1173-1178.
77. Lobo, S.M., and Hernandez, N., 1989, A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter, Cell 58:55-67.
78. Luo, M., Orsi, R., Patrucco, E., Pancaldi, S., and Cella, R., 1997, Multiple transcription start sites of the carrot dihydrofolate reductase-thymidylate synthase gene, and sub-cellular localization of the bifunctional protein, Plant Mol. Biol. 33:709-722.
79. Lupold, D.S., Caoile, A.G., and Stern, D.B., 1999, The maize mitochondrial cox2 gene has five promoters in two genomic regions, including a complex promoter consisting of seven overlapping units, J. Biol. Chem. 274:3897-3903.
80. Manley, J.L., and Proudfoot, N.J., 1994, RNA 3′?ends -Formation and function, Genes Dev. 8:259-264.
81. Mathe, C., Sagot, M.-F., Schiex, T., and Rouze, P., 2002, Current methods of gene prediction, their strengths and weaknesses, Nucl. Acids Res. 30:4103-4117.
82. Mattaj, I.W., Dathan, N.A., Parry, H.D., Carbon, P., and Krol, A., 1988, Changing the RNA polymerase specificity of U snRNA gene promoters, Cell 55:435-442.
83. Maxwell, E.S., and Fournier, M.J., 1995, The small nucleolar RNAs, Annu. Rev. Biochem. 35: 897-934.
84. Meijer, H.A., and Thomas, A.A., 2002, Control of eukaryotic protein synthesis by upstream open reading frames in the 5′-untranslated region of an mRNA, Biochem J. 367:1-11.
85. 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.
86. Mitchell, M.T., Hobson, G.M., and Benfield, P.A., 1992, TATA box-mediated polymerase III transcription in vitro, J. Biol. Chem. 267:1995-2005.
87. Misteli, T., 2000, Cell biology of transcription and pre-mRNA splicing: Nuclear architecture meets nuclear function. J. Cell Sci. 113:1841-1849.
88. Mize, G.J., Ruan, H.J., Low, J.J., and Morris, D.R., 1998, The inhibitory upstream open reading frame from mammalian S-adenosylmethionine decarboxylase mRNA has a strict sequence specificity in critical positions. J. Biol. Chem. 273, 32500-32505.
89. Mohr, G., Perlman, P.S., and Lambowitz, A.M., 1993, Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function, Nucl. Acids Res. 21:4991-4997.
90. Morris, D.R., 1995, Growth control of translation in mammalian cells, Prog. Nucl. Acid Res. Mol. Biol. 51:339-363.
91. Myers, S.J., Peters, J., Huang, Y., Comer, M.B., Barthel, F. and Dingledine, R., 1998, Transcriptional regulation of the GluR2 gene: Neural-specific expression, multiple promoters, and regulatory elements, J. Neurosci. 18:6723-6739.
92. Myers, S.J., Huang, Y., Genetta, T., and Dingledine, R., 2004, Inhibition of glutamate receptor 2 translation by a polymorphic repeat sequence in the 5′-untranslated leaders, J. Neurosci. 24:3489-3499.
93. 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.
94. Nakazono, M., Itadani, H., Wakasugi, T., Tsutsumi, N., Sugiura, M., and Hirai, A., 1995, The rps3-rpl16-nad3-rps12 gene cluster in rice mitochondrial DNA is transcribed from alternative promoters, Curr. Genet. 27:184-189.
95. Navarro-Avino, J.P., and Bennett, A.B., 2005, Role of a Ca2?-ATPase induced by ABA and IAA in the generation of specific Ca2signals, Biochem. Biophys. Res. Commun. 329:406-415.
96. Navarro-Avino, J.P., Hentzen, A.E., and Bennett, A.B., 1999, Alternative transcription initiation sites generate two LCA1 Ca-ATPase mRNA transcripts in tomato roots, Plant Mol. Biol. 40:133-140.
97. Normark, S., Bergstrom, S., Edlund, T., Grundstrom, T., Jaurin, B., Lindberg, F.P., and Olsson, O., 1983, Overlapping genes, Ann. Rev. Genet. 17:499-525.
98. Ojala, D., Montoya, J., and Attardi, G., 1981, tRNA punctuation model of RNA processing in human mitochondria, Nature 290:470-474.
99. Onodera, Y., J.R. Haag, T. Ream, P.C. Nunes, O. Pontes, and C.S. Pikaard. 2005. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylationdependent heterochromatin formation. Cell 120:613-622.
100. Pain, V., 1996, Initiation of protein synthesis in eukaryotic cells, Eur. J. Biochem. 236:747-771.
101. Pan, S., Czarnecka-Verner, E., and Gurley, W.B., 2000, Role of the TATA binding protein-transcription factor IIB interaction in supporting basal and activated transcription in plant cells, Plant Cell 12:125-135.
102. Pennisi, E., 1999, Keeping genome databases clean and up to date. Science 286:447-450.
103. Pradhan, S. and Adams, R.L.P., 1995, Distinct CG and CNG DNA methyltransferases in Pisum sativum, Plant J. 7:471-481.
104. Prasanth, K.V., Prasanth, S.G., Xuan, Z., Hearn, S., Freier, S.M., Bennett, C.F., Zhang, M.Q., and Spector, D.L., 2005, Regulating gene expression through RNA nuclear retention, Cell 123:249-263.
105. Quesada, V., Ponce, M.R., and Micol, J.L., 1999, OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana, FEBS Lett. 461:101-106.
106. Richter, D., 1983, Vasopressin and oxytocin are expressed as polyproteins, Trends Biochem. Sci. 8:278-291.
107. Rom, E., and Kahana, C., 1994, Polyamines regulate the expression of ornithine decarboxylase antizyme in vitro by inducing ribosomal frame-shifting. Proc. Natl. Acad. Sci. USA 91:3959-3963.
108. Ruiz-Echevarria, M.J., Czaplinski, K., and Peltz, S.W., 1996, Making sense of nonsense in yeast, Trends Biochem. Sci. 21:433-438.
109. Ruiz-Echevarria, M., and Peltz, S.W., 2000, The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames, Cell 101:741-751.
110. Ryabova, L.A., Pooggin, M.M., Dominguez, D.I., and Hohn, T., 2000, Continuous and discontinuous ribosome scanning on the cauliflower mosaic virus 35S RNA leader is controlled by short open reading frames, J. Biol. Chem. 275:37278-37284.
111. Saldanha, R., Mohr, G., Belfort, M., and Lambowitz, A.M., 1993, Group I and group II introns, Fed. Amer. Soc. Exp. Biol. (FASEB) J. 7:15-24.
112. Savoure, A., Jaoua, S., Hua, X.-J., Ardiles, W., Van Montagu, M., and Vergruggen, N., 1995, Isolation, characterization, and chromosomal location of a gene encoding the δ1-pyrroline-5-carboxylate synthetase in Arabidopsis thaliana, FEBS Lett. 372:13-19.
113. Schul, W., van Der Kraan, I., Matera, A.G., van Driel, R., and de Jong, L., 1999, Nuclear domains enriched in RNA 3′-processing factors associate with coiled bodies and histone genes in a cell cycle-dependent manner. Mol. Biol. Cell 10:3815-3824.
114. Schuster, G., Lisitsky, I., and Klaff, P., 1999, Update on chloroplast molecular biology: Polyadenylation and degradation of mRNA is the chloroplast, Plant Physiol. 120:937-944.
115. Sheen, J., 1991, Molecular mechanism underlying the differential expression of maize pyruvate, orthophosphate dikinase genes, Plant Cell 3:225-245.
116. Smale, S.T., and Baltimore, D., 1989, The "initiator" as a transcription control element, Cell 57:103-113.
117. Souciet, G., Menand, B., Ovesna, J., Cosset, A., Dietrich, A., and Wintz, H., 1999, Characterization of two bifunctional Arabidopsis thaliana genes coding for mitochondrial and cytosolic forms of valyl-tRNA synthetase and threonyltRNA synthetase by alternative use of two in-frame AUGs, Eur. J. Biochem. 266:848-854.
118. Spector, D.L., 1993, Macromolecular domains within the cell nucleus. Ann. Rev. Cell Biol. 9:265-315.
119. Tamaoki, M., Tsugawa, H., Minami, E., Kayano, T., Yamamoto, N., Kano-Murakami, Y., and Matsuoka, M., 1995, Alternative RNA products form a rice homeobox gene. Plant J. 7:927-938.
120. Thimmapuram, J., Duan, H., Liu, L., and Schuler, M.A., 2005, Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome, RNA 11:128-138.
121. Tracy, R.L., and Stern, D.B., 1995, Mitochondrial transcription initiation: Promoter structures and RNA polymerases, Curr. Genet. 28:205-216.
122. Venter, J.C., et al., 2001, The sequence of the human genome, Science 291:1304-1351.
123. Vera, A., Hirose, T., and Sugiura, M., 1996, A ribosomal protein gene (rpl32) from tobacco chloroplast DNA is transcribed from alternative promoters: Similarities in promoter region organization in plastid housekeeping genes, Mol. Gen. Genet. 251:518-525.
124. Wahleithner, J.A., and Wolstenholme, D.R., 1988, A sequence encoding a maturaserelated protein in a group II intron of a plant mitochondrial nad1 gene. Nucl. Acids Res. 16:6897-6913.
125. Wang, L., and Wessler, S.R., 2001, Role of mRNA secondary structure in translational repression of the maize transcriptional activator Lc, Plant Physiol. 125:1380-1387.
126. Wang, Z., and Sachs, M.S., 1997, Ribosome stalling is responsible for arginine-specific translational attenuation in Neurospora crassa, Mol. Cell. Biol. 17:4904-4913.
127. Weitzel, J.M., Grott, S., Radtke, C., Kutz, S., and Steitz, H.J., 2000, Multiple promoters direct the tissue-specific expression of rat mitochondrial glycerol-3-phosphate dehydrogenase, Biol. Chem. 381:611-614.
128. Wetizel, J.M., Kutz, S., Radtke, C., Grott, S., and Steitz, H.J., 2001, Hormonal regulation of multiple promoters of the rat mitochondrial glycerol-3-phosphate dehydrogenase gene, Eur. J. Biochem. 268:4095-4103.
129. Wisniewski, M.E., Bassett, C.L., Renaut, J., Farrell Jr., R.E., Tworkoski, T., and Artlip, T.S., 2006, Differential regulation of two dehydrin genes from peach (Prunus persica L. Batsch) by photoperiod, low temperature, and water deficit, Tree Physiol. 26:575-584.
130. Wray, G.A., Hahn, M.W., Abouheif, E., Balhoff, J.P., Pizer, M., Rockman, M.V., and Romano, L.A., 2003, The evolution of transcriptional regulation in eukaryotes, Mol. Biol. Evol. 20:1377-1419.
131. Yamada, M., Ozawa, A., Ishii, S., Shibusawa, N., Hashida, T., Ishizuka, T., Hosoya, T., Monden, T., Satoh, T., and Mori, M., 2001, Isolation and characterization of the rat prolactin-releasing peptide gene: multiple TATA boxes in the promoter region, Biochem. Biophys. Res. Comm. 281:53-56.
132. Yoshiba, Y., Kiyosue, T., Katagiri, T., Ueda, H., Mizoguchi, T., Yamaguchi-Shinozaki, K., Wada, K., Harada, Y., and Shinozaki, K., 1995, Correlation between the induction of a gene for δ1-pyrroline-5-carboxylate synthetase and the accumulation of proline in Arabidopsis thaliana under osmotic stress, Plant J. 7:751-760.
133. Zhang, Y., Niu, Z., Cohen, A.J., Nah, H.-D., and Adams, S.L., 1997, The chick type III collagen gene contains two promoters that are preferentially expressed in different cell types and are separated over 20 kb by DNA containing 23 exons, Nucl. Acids Res. 25:2470-2477.