Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE

Nucleic Acids Research

Volumn 33, Issue 9, 2005, Pages 2838-2851

  Zhang, Zhihong ^a   Dietrich, Fred S ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

5' UNTRANSLATED REGION; ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE CONTROL; GENE IDENTIFICATION; GENE MAPPING; GENETIC TRANSCRIPTION; MOLECULAR CLONING; MOLECULAR LIBRARY; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; RNA STABILITY; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE TAGGED SITE; SERIAL ANALYSIS OF GENE EXPRESSION; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; VALIDATION PROCESS; CONSENSUS SEQUENCE; FUNGAL GENE; GENE EXPRESSION PROFILING; GENETICS; GENOME; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; VALIDATION STUDY;

SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; CONSENSUS SEQUENCE; GENE EXPRESSION PROFILING; GENES, FUNGAL; GENOME, FUNGAL; OPEN READING FRAMES; SACCHAROMYCES CEREVISIAE; SEQUENCE TAGGED SITES; TRANSCRIPTION INITIATION SITE;

EID: 20144384163     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki583     Document Type: Article

References (88)

1. Dietrich,F.S., Voegeli,S., Brachat,S., Lerch,A., Gates,K., Steiner,S., Mohr,C., Pohlmann,R., Luedi,P., Choi,S. et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science, 304, 304-307.
2. Kellis,M., Birren,B.W. and Lander,E.S. (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature, 428, 617-624.
3. Cliften,P., Sudarsanam,P., Desikan,A., Fulton,L., Fulton,B., Majors,J., Waterston,R., Cohen,B.A. and Johnston,M. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, 301, 71-76.
4. Sherman,D., Durrens,P., Beyne,E., Nikolski,M. and Souciet,J.L. (2004) Genolevures: Comparative genomics and molecular evolution of hemiascomycetous yeasts. Nucleic Acids Res., 32, D315-D318.
5. Zhang,Z. and Dietrich,F.S. (2003) Verification of a new gene on Saccharomyces cerevisiae chromosome III. Yeast, 20, 731-738.
6. Brachat,S., Dietrich,F.S., Voegeli,S., Zhang,Z., Stuart,L., Lerch,A., Gates,K., Gaffney,T. and Philippsen,P. (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol., 4, R45.
7. Hannenhalli,S. and Levy,S. (2001) Promoter prediction in the human genome. Bioinformatics, 17 (Suppl. 1), S90-S96.
8. Shiraki,T., Kondo,S., Katayama,S., Waki,K., Kasukawa,T., Kawaji,H., Kodzius,R., Watahiki,A., Nakamura,M., Arakawa,T. et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad. Sci. USA, 100, 15776-15781.
9. Wei,C.L., Ng,P., Chiu,K.P., Wong,C.H., Ang,C.C., Lipovich,L., Liu,E.T. and Ruan,Y. (2004) 5′ Long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation. Proc. Natl Acad. Sci. USA, 101, 11701-11706.
10. Hashimoto,S., Suzuki,Y., Kasai,Y., Morohoshi,K., Yamada,T., Sese,J., Morishita,S., Sugano,S. and Matsushima,K. (2004) 5′-end SAGE for the analysis of transcriptional start sites. Nat. Biotechnol., 22, 1146-1149.
11. Hurowitz,E.H. and Brown,P.O. (2003) Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol., 5, R2.
12. Pesole,G., Liuni,S., Grillo,G., Licciulli,F., Mignone,F., Gissi,C. and Saccone,C., (2002) UTRdb and UTRsite: Specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res., 30, 335-340.
13. Buratowski,S., Hahn,S., Guarente,L. and Sharp,P.A. (1989) Five intermediate complexes in transcription initiation by RNA polymerase II. Cell, 56, 549-561.
14. Hampsey,M. (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev., 62, 465-503.
15. Smale,S.T. and Baltimore,D. (1989) The 'initiator' as a transcription control element. Cell, 57, 103-113.
16. Weis,L. and Reinberg,D. (1992) Transcription by RNA polymerase II: initiator-directed formation of transcription-competent complexes. FASEB J., 6, 3300-3309.
17. Weis,L. and Reinberg,D. (1997) Accurate positioning of RNA polymerase II on a natural TATA-less promoter is independent of TATA-binding-protein-associated factors and initiator-binding proteins. Mol. Cell. Biol., 17, 2973-2984.
18. Bucher,P. (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol., 212, 563-578.
19. Basehoar,A.D., Zanton,S.J. and Pugh,B.F. (2004) Identification and distinct regulation of yeast TATA box-containing genes. Cell, 116, 699-709.
20. Cherry,J.M., Ball,C., Weng,S., Juvik,G., Schmidt,R., Adler,C., Dunn,B., Dwight,S., Riles,L., Mortimer,R.K. et al. (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature, 387, 67-73.
21. Burke,D., Dawson,D. and Stearns,T. (2000) Methods in Yeast Genetics; A Cold Spring Harbor Laboratory Course manual. CSHL Press, Cold Spring Harbor, NY.
22. Ewing,B., Hillier,L., Wendl,M.C. and Green,P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Rev., 8, 175-185.
23. Ewing,B. and Green,P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
24. Holstege,F.C., Jennings,E.G., Wyrick,J.J., Lee,T.I., Hengartner,C.J., Green,M.R., Golub,T.R., Lander,E.S. and Young,R.A. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell, 95, 717-728.
25. Dance,G.S., Beemiller,P., Yang,Y., Mater,D.V., Mian,I.S. and Smith,H.C. (2001) Identification of the yeast cytidine deaminase CDD1 as an orphan C → U RNA editase. Nucleic Acids Res., 29, 1772-1780.
26. Wickens,M.P., Buell,G.N. and Schimke,R.T. (1978) Synthesis of double-stranded DNA complementary to lysozyme, ovomucoid, and ovalbumin mRNAs. Optimization for full length second strand synthesis by Escherichia coli DNA polymerase I. J Biol. Chem., 253, 2483-2495.
27. Berk,A.J. and Sharp,P.A. (1977) Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell, 12, 721-732.
28. Kann,M., Najarian,R., Haslinger,A., Valenzuela,P., Welch,J. and Fogel,S. (1984) Primary structure and transcription of an amplified genetic locus: The CUP1 locus of yeast. Proc. Natl Acad. Sci. USA, 81, 337-341.
29. Liao,X.B., Clare,J.J. and Farabaugh,P.J. (1987) The upstream activation site of a Ty2 element of yeast is necessary but not sufficient to promote maximal transcription of the element. Proc. Natl Acad. Sci. USA, 84, 8520-8524.
30. Fulton,A.M., Rathjen,P.D., Kingsman,S.M. and Kingsman,A.J. (1988) Upstream and downstream transcriptional control signals in the yeast retrotransposon, TY. Nucleic Acids Res., 16, 5439-5458.
31. Nagashima,K., Kasai,M., Nagata,S. and Kaziro,Y. (1986) Structure of the two genes coding for polypeptide chain elongation factor 1 alpha (EF-1 alpha) from Saccharomyces cerevisiae. Gene, 45, 265-273.
32. Alber,T. and Kawasaki,G. (1992) Nucleotide sequence of the triose phosphate isomerase gene of Saccharomyces cerevisiae. J. Mol. Appl. Genet., 1, 419-434.
33. Strathern,J.N., Jones,E.W. and Broach,J.R. (1982) The molecular biology of the yeast Sacchromyces: Metabolism and gene expression. Cold Spring Harbor Monograph Series: 11B. Cold Spring Harbor Laboratory. Cold Spring Harbor, NY, pp. x, 680 p.
34. 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.
35. Martens,J.A., Laprade,L. and Winston,F. (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature, 429, 571-574.
36. Morey,C. and Avner,P. (2004) Employment opportunities for non-coding RNAs. FEBS Lett., 567, 27-34.
37. Hahn,S., Hoar,E.T. and Guarente,L. (1985) Each of three 'TATA elements' specifies a subset of the transcription initiation sites at the CYC-1 promoter of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 82, 8562-8566.
38. Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
39. Crooks,G.E., Hon,G., Chandonia,J.M. and Brenner,S.E. (2004) WebLogo: A sequence logo generator. Genome Res., 14, 1188-1190.
40. Oshiro,G., Wodicka,L.M., Washburn,M.P., Yates,J.R.,III, Lockhart,D.J. and Winzeler,E.A. (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res., 12, 1210-1220.
41. Wolfe,K.H. and Shields,D.C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387, 708-713.
42. Kellis,M., Patterson,N., Endrizzi,M., Birren,B. and Lander,E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
43. Natsoulis,G., Hilger,F. and Fink,G.R. (1986) The HTS1 gene encodes both the cytoplasmic and mitochondrial histidine tRNA synthetases of Saccaromyces cerevisiae. Cell, 46, 235-243.
44. Velculescu,V.E., Zhang,L., Zhou,W., Vogelstein,J., Basrai,M.A., Bassett,D.E.,Jr, Hieter,P., Vogelstein,B. and Kinzler,K.W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
45. Vilela,C. and McCarthy,J.E. (2003) Regulation of fungal gene expression via short open reading frames in the mRNA 5′ untranslated region. Mol. Microbiol., 49, 859-867.
46. Dujon,B., Sherman,D., Fischer,G., Durrens,P., Casaregola,S., Lafontaine,I., De Montigny,J., Marck,C., Neuveglise,C., Talla,E. et al. (2004) Genome evolution in yeasts. Nature, 430, 35-44.
47. Chenchik,A., Zhu,Y.Y., Diatchenko,L., Li,R., Jill,J. and Siebert,P.D. (1998) RT-PCR Methods for Gene Cloning and Analysis. Eaton, Natick, MA, USA.
48. Zhu,Y.Y., Machleder,E.M., Chenchik,A., Li,R. and Siebert,P.D. (2001) Reverse transcriptase template switching: A SMART approach for full-length cDNA library construction. Biotechniques, 30, 892-897.
49. Struhl,K. (1987) Promoters, activator proteins, and the mechanism of transcriptional initiation in yeast. Cell, 49, 295-297.
50. Russell,P.R. (1983) Evolutionary divergence of the mRNA transcription initiation mechanism in yeast. Nature, 301, 167-169.
51. Corden,J., Wasylyk,B., Buchwalder,A., Sassone-Corsi,P., Kedinger,C. and Chambon,P. (1980) Promoter sequences of eukaryotic protein-coding genes. Science, 209, 1406-1414.
52. Giardina,C. and Lis,J.T. (1993) DNA melting on yeast RNA polymerase II promoters. Science, 261, 759-762.
53. Choi,W.S., Yan,M., Nusinow,D. and Gralla,J.D. (2002) In vitro transcription and start site selection in Schizosaccharomyces pombe. J. Mol. Biol., 319, 1005-1013.
54. Healy,A.M., Helser,T.L. and Zitomer,R.S. (1987) Sequences required for transcriptional initiation of the Saccharomyces cerevisiae CYC7 genes. Mol. Cell. Biol., 7, 3785-3791.
55. Healy,A.M. and Zitomer,R.S. (1990) A sequence that directs transcriptional initiation in yeast. Curr. Genet., 18, 105-109.
56. Wood,V., Rutherford,K.M., Ivens,A., Rajandream,M.A. and Barrell,B. (2001) A Re-annotation of the Saccharomyces cerevisiae Genome. Comp. Funct. Genomics, 2, 143-154.
57. Magdolen,V., Oechsner,U., Muller,G. and Bandlow,W. (1988) The intron-containing gene for yeast profilin (PFY) encodes a vital function. Mol. Cell. Biol., 8, 5108-5115.
58. Nagawa,F. and Fink,G.R. (1985) The relationship between the 'TATA' sequence and transcription initiation sites at the HIS4 gene of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 82, 8557-8561.
59. van den Heuvel,J.J., Bergkamp,R.J., Planta,R.J. and Raue,H.A. (1989) Effect of deletions in the 5′-noncoding region on the translational efficiency of phosphoglycerate kinase mRNA in yeast. Gene, 79, 83-95.
60. Wright,R.M., Dircks,L.K. and Poyton,R.O. (1986) Characterization of COX9, the nuclear gene encoding the yeast mitochondrial protein cytochrome c oxidase subunit VIIa. Subunit VIIa lacks a leader peptide and is an essential component of the holoenzyme. J. Biol. Chem., 261, 17183-17191.
61. Newton,C.H., Shimmin,L.C., Yee,J. and Dennis,P.P. (1990) A family of genes encode the multiple forms of the Saccharomyces cerevisiae ribosomal proteins equivalent to the Escherichia coli L12 protein and a single form of the L1O-equivalent ribosomal protein. J. Bacteriol., 172, 579-588.
62. Paravicini,G., Braus,G. and Hutter,R. (1988) Structure of the ARO3 gene of Saccharomyces cerevisiae. Mol. Gen. Genet., 214, 165-169.
63. Dabeva,M.D. and Warner,J.R. (1987) The yeast ribosomal protein L32 and its gene. J. Biol. Chem., 262, 16055-16059.
64. Escobar-Henriques,M., Daignan-Fornier,B. and Collart,M.A. (2003) The critical cis-acting element required for IMD2 feedback regulation by GDP is a TATA box located 202 nucleotides upstream of the transcription start site. Mol. Cell. Biol., 23, 6267-6278.
65. Huet,J., Cottrelle,P., Cool,M., Vignais,M.L., Thiele,D., Marck,C., Buhler,J.M., Sentenac,A. and Fromageot,P. (1985) A general upstream binding factor for genes of the yeast translational apparatus. EMBO J., 4, 3539-3547.
66. Ogawa,N., Saitoh,H., Miura,K., Magbanua,J.P., Bun-ya,M., Harashima,S. and Oshima,Y. (1995) Structure and distribution of specific cis-elements for transcriptional regulation of PHO84 in Saccharomyces cerevisiae. Mol. Gen. Genet., 249, 406-416.
67. Cumsky,M.G., Trueblood,C.E., Ko,C. and Poyton,R.O. (1987) Structural analysis of two genes encoding divergent forms of yeast cytochrome c oxidase subunit V. Mol. Cell. Biol., 7, 3511-3519.
68. Crabeel,M., de Rijcke,M., Seneca,S., Heimberg,H., Pfeiffer,I. and Matisova,A. (1995) Further definition of the sequence and position requirements of the arginine control element that mediates repression and induction by arginine in Saccharomyces cerevisiae. Yeast, 11, 1367-1380.
69. Faitar,S.L., Brodie,S.A. and Ponticelli,A.S. (2001) Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites. Mol. Cell. Biol., 21, 4427-4440.
70. Russell,D.W., Smith,M., Williamson,V.M. and Young,E.T. (1983) Nucleotide sequence of the yeast alcohol dehydrogenase II gene. J. Biol. Chem., 258, 2674-2682.
71. Schneider,J.C. and Guarente,L. (1991) Regulation of the yeast CYT1 gene encoding cytochrome c1 by HAP1 and HAP2/3/4. Mol. Cell. Biol., 11, 4934-4942.
72. Minehart,P.L. and Magasanik,B. (1992) Sequence of the GLN1 gene of Saccharomyces cerevisiae: Role of the upstream region in regulation of glutamine synthetase expression. J. Bacteriol., 174, 1828-1836.
73. Freeman,K.B., Karns,L.R., Lutz,K.A. and Smith,M.M. (1992) Histone H3 transcription in Saccharomyces cerevisiae is controlled by multiple cell cycle activation sites and a constitutive negative regulatory element. Mol. Cell Biol., 12, 5455-5463.
74. Kunzler,M., Paravicini,G., Egli,C.M., Irniger,S. and Braus,G.H. (1992) Cloning, primary structure and regulation of the ARO4 gene, encoding the tyrosine-inhibited 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae. Gene, 113, 67-74.
75. Zagoree,M., Buhler,J.M., Treich,I., Keng,T., Guarente,L. and Labbe-Bois,R. (1988) Isolation, sequence, and regulation by oxygen of the yeast HEM13 gene coding for coproporphyrinogen oxidase. J. Biol. Chem., 263, 9718-9724.
76. Schneider,J.C. and Guarente,L. (1987) The untranslated leader of nuclear COX4 gene of Saccharomyces cerevisiae contains an intron. Nucleic Acids Res., 15, 3515-3529.
77. Pavlovic,B. and Horz,W. (1988) The chromatin structure at the promoter of a glyceraldehyde phosphate dehydrogenase gene from Saccharomyces cerevisiae reflects its functional state. Mol. Cell. Biol., 8, 5513-5520.
78. Brindle,P.K., Holland,J.P., Willett,C.E., Innis,M.A. and Holland,M.J. (1990) Multiple factors bind the upstream activation sites of the yeast enolase genes ENO1 and ENO2: ABFI protein, like repressor activator protein RAP1, binds cis-acting sequences which modulate repression or activation of transcription. Mol. Cell. Biol., 10, 4872-4885.
79. Beacham,I.R., Schweitzer,B.W., Warrick,H.M. and Carbon,J. (1984) The nucleotide sequence of the yeast ARG4 gene. Gene, 29, 271-279.
80. Repetto,B. and Tzagoloff,A. (1989) Structure and regulation of KGD1, the structural gene for yeast alpha-ketoglutarate dehydrogenase. Mol. Cell. Biol., 9, 2695-2705.
81. Sarokin,L. and Carlson,M. (1985) Comparison of two yeast invertase genes: Conservation of the upstream regulatory region. Nucleic Acids Res., 13, 6089-6103.
82. Dohrmann,P.R., Voth,W.P. and Stillman,D.J. (1996) Role of negative regulation in promoter specificity of the homologous transcriptional activators Ace2p and Swi5p. Mol. Cell. Biol., 16, 1746-1758.
83. Nouraini,S., Hu,J., McBroom,L.D. and Friesen,J.D. (1996) Mutations in an Abf1p binding site in the promoter of yeast RPO26 shift the transcription start sites and reduce the level of RPO26 mRNA. Yeast, 12, 1339-1350.
84. Hahn,S., Pinkham,J., Wei,R., Miller,R. and Guarente,L. (1988) The HAP3 regulatory locus of Saccharomyces cerevisiae encodes divergent overlapping transcripts. Mol. Cell. Biol., 8, 655-663.
85. Urban-Grimal, D., Volland, C., Garnier, T., Dehoux, P. and Labbe-Bois, R. (1986) The nucleotide sequence of the HEM1 gene and evidence for a precursor form of the mitochondrial 5-aminolevulinate synthase in Saccharomyces cerevisiae. Eur. J. Biochem., 156, 511-519.
86. Losson,R., Fuchs,R.P. and Lacroute,F. (1985) Yeast promoters URA1 and URA3. Examples of positive control. J. Mol. Biol., 185, 65-81.
87. Kim,G.J., Park,J.H., Lee,D.C., Ro,H.S. and Kim,H.S. (1997) Primary structure, sequence analysis, and expression of the thermostable D-hydantoinase from Bacillus stearothermophilus SD1. Mol. Gen. Genet., 255, 152-156.
88. Erkine,A.M., Adams,C.C., Gao,M. and Gross,D.S. (1995) Multiple protein-DNA interactions over the yeast HSC82 heat shock gene promoter. Nucleic Acids Res., 23, 1822-1829.