Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae

Genome Research

Volumn 12, Issue 11, 2002, Pages 1723-1731

  Sudarsanam, Priya ^a,b   Pilpel, Yitzhak ^a   Church, George M ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

ARTICLE; CONTROLLED STUDY; DOWNSTREAM PROCESSING; EUKARYOTIC CELL; GENE CASSETTE; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENOME ANALYSIS; METHODOLOGY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; REGULATORY MECHANISM; RNA PROCESSING; RNA TRANSCRIPTION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION;

BASE COMPOSITION; COMPUTATIONAL BIOLOGY; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENES, RRNA; GENOME, FUNGAL; PROMOTER REGIONS (GENETICS); RNA, FUNGAL; SACCHAROMYCES CEREVISIAE;

EUKARYOTA; FUNGI; MYXOGASTRIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0036851309     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.301202     Document Type: Article

References (34)

1. Arnone, M.I. and Davidson, E.H. 1997. The hardwiring of development: Organization and function of genomic regulatory systems. Development 124: 1851-1864.
2. Berman, B.P., Nibu, Y., Pfeiffer, B.D., Tomancak, P., Celniker, S.E., Levine, M., Rubin, G.M., and Eisen, M.B. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. 99: 757-762.
3. Bussemaker, H.J., Li, H., and Siggia, E.D. 2001. Regulatory element detection using correlation with expression. Nat. Genet. 27: 167-171.
4. Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., et al. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 2: 65-73.
5. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O., and Herskowitz, I. 1998. The transcriptional program of sporulation in budding yeast. Science 282: 699-705.
6. Dequard-Chablat, M., Riva, M., Carles, C., and Sentenac, A. 1991. RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III). J. Biol. Chem. 266: 15300-15307.
7. DeRisi, J.L., Iyer, V.R., and Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
8. Fessele, S., Maier, H., Zischek, C., Nelson, P.J., and Werner, T. 2002. Regulatory context is a crucial part of gene function. Trends Genet. 18: 60-63.
9. Frith, M.C., Hansen, U., and Weng, Z. 2001. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 17: 878-889.
10. Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., Botstein, D., and Brown, P.O. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11: 4241-4257.
11. GuhaThakurta, D. and Stormo, G.D. 2001. Identifying target sites for cooperatively binding factors. Bioinformatics 17: 608-621.
12. Halton, M.S., Grad, Y., Church, G.M., and Michelson, A.M. 2002. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12: 1019-1028.
13. Hughes, J.D., Estep, P.W., Tavazoie, S., and Church, G.M. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296: 1205-1214.
14. Inokuchi, K. and Nakayama, A. 1991. Lack of a requirement for strict rotational alignment among transcription factor binding sites in yeast. Nucleic Acids Res. 19: 3099-3103.
15. Jelinsky, S.A., Estep, P., Church, G.M., and Samson, L.D. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol. Cell. Biol. 20: 8157-8167.
16. Jensen, L.J. and Knudsen, S. 2000. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics 16: 326-333.
17. Kel, A., Kel-Margoulis, O., Babenko, V., and Wingender, E. 1999. Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells. J. Mol. Biol. 288: 353-376.
18. Kel, O.V., Romaschenko, A.G., Kel, A.E., Wingender, E., and Kolchanov, N.A. 1995. A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res. 23: 4097-4103.
19. Lavorgna, G., Boncinelli, E., Wagner, A., and Werner, T. 1998. Detection of potential target genes in silico? Trends Genet. 14: 375-376.
20. Lopez, M.C., Smerage, J.B., and Baker, H.V. 1998. Multiple domains of repressor activator protein 1 contribute to facilitated binding of glycolysis regulatory protein 1. Proc. Natl. Acad. Sci. 95: 14112-14117.
21. Mai, B., Miles, S., and Breeden, L.L. 2002. Characterization of the ECB binding complex responsible for the M/G(1)-specific transcription of CLN3 and SW14. Mol. Cell. Biol. 22: 430-441.
22. Markstein, M., Markstein, P., Markstein, V., and Levine, M.S. 2002. Genome-wide analysis of clustered dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. 99: 763-768.
23. McInerny, C.J., Partridge, J.F., Mikesell, G.E., Creemer, D.P., and Breeden, L.L. 1997. A novel Mcm1-dependent element in the SW14, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription. Genes Dev. 11: 1277-1288.
24. Mewes, H.W., Frishman, D., Gruber, C., Geier, B., Haase, D., Kaps, A., Lemcke, K., Mannhaupt, G., Pfeiffer, F., Schuller, C., et al. 2000. MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 28: 37-40.
25. Pilpel, Y., Sudarsanam, P., and Church, G.M. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29: 153-159.
26. Quandt, K., Grote, K., and Werner, T. 1996. Genome Inspector: Basic software tools for analysis of spatial correlations between genomic structures within megabase sequences. Genomics 33: 301-304.
27. Roberts, C.J., Nelson, B., Marton, M.J., Stoughton, R., Meyer, M.R., Bennett, H.A., He, Y.D., Dai, H., Walker, W.L., Hughes, T.R., et al. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873-880.
28. Sherlock, G. 2000. Analysis of large-scale gene expression data. Curr. Opin. Immunol. 12: 201-205.
29. Shore, P. and Sharrocks, A.D. 1995. The MADS-box family of transcription factors. Eur. J. Biochem. 229: 1-13.
30. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., and Futcher, B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9: 3273-3297.
31. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., and Church, G.M. 1999. Systematic determination of genetic network architecture. Nat. Genet. 22: 281-285.
32. Wagner, A. 1997. A computational genomics approach to the identification of gene networks. Nucleic Acids Res. 25: 3594-3604.
33. Wagner, A. 1999. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 15: 776-784.
34. Wasserman, W.W. and Fickett, J.W. 1998. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278: 167-181.