Genome-wide discovery of cis-elements in promoter sequences using gene expression

OMICS A Journal of Integrative Biology

Volumn 13, Issue 2, 2009, Pages 139-151

  Troukhan, Maxim ^a   Tatarinova, Tatiana ^b   Bouck, John ^a   Flavell, Richard B ^a   Alexandrov, Nickolai N ^a  

^a Ceres Inc   (United States)

^b LOYOLA MARYMOUNT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT;

AMINO ACID SEQUENCE; ARTICLE; CORRELATION ANALYSIS; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENOME; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; STATISTICAL SIGNIFICANCE; TATA BOX; TRANSCRIPTION INITIATION SITE;

ALGORITHMS; ANIMALS; ARABIDOPSIS; GENE EXPRESSION; GENOME-WIDE ASSOCIATION STUDY; MICE; PROMOTER REGIONS, GENETIC;

ARABIDOPSIS THALIANA; MUS MUSCULUS;

EID: 64549127763     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2008.0034     Document Type: Article

References (54)

1. Abeel, T., Saeys, Y., Bonnet, E., Rouze, P., and Van de Peer, Y. (2008). Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res 18, 310-323.
2. Alexandrov, N.N., Troukhan, M.E., Brover, V.V., Tatarinova, T., Flavell, R.B., and Feldmann, K.A. (2006). Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 60, 69-85.
3. Argüello-Astorga, G., and Herrera-Estrella, L. (1998). Evolution of light-regulated plant promoters. Annu Rev Plant Physiol Plant Mol Biol 49, 525-555.
4. Bailey, T.L., and Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36. (AAAI Press, Menlo Park, CA).
5. Basehoar, A.D., Janton, S.J., and Pugh, B.F. (2004). Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709.
6. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D.L. (2007). GenBank. Nucleic Acids Res. 2007 35(Database issue):D21-D25.
7. Berendzen, K., Stuber, K., Harter, K., and Wanke, D. (2006). cis- Motifs upstream of the transcription and translation initiation sites and effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. BMC Bioinformatics 7, 522.
8. Bobb, A.J., Chern, M. S., and Bustos, M.M. (1997). Conserved RY-repeats mediate transactivation of seed-specific promoters by the developmental regulator PvALF. Nucleic Acids Res 25, 641-647.
9. Bolstad, B.M., Irizarry, R. A., Astrand, M., and Speed, T.P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193.
10. Bussemaker, H. J., Foat, B.C., and Ward, L.D. (2007). Predictive modeling of genome-wide mRNA expression: from modules to molecules. Ann Rev Biophys Biomol Struct 36, 329-347.
11. Down, T.A, and Hubbard, J.P. (2002). Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 12, 458-461.
12. Fickett, J.W., and Hatzigeorgiou, A.G. (1997) Eukaryotic promoter recognition. Genome Res 7, 861-878.
13. Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. (1998). A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 8, 967-974.
14. Foat, B.C., Houshmandi, S.S, Olivas, W.M., and Bussemaker, H.J. (2005). Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci USA 102, 17675-17680.
15. Foat, B.C., Morozov, A.V., and Bussemaker, H.J. (2006). Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics 22, e141- e149.
16. Fujimori, S., Washio, T., and Tomita, M. (2005). GC-compositional strand bias around transcription start sites in plants and fungi. 1: BMC Genomics. 28, 26.
17. Galas, D.J., Eggert, M., and Waterman, M.S. (1985). Rigorous pattern recognition methods for DNA sequences: analysis of promoter sequences from E. coli. J Mol Biol 186, 117-128.
18. Garcia-Hernandez, M., Berardini, T. Z., Chen, G., Crist, D., Doyle, A., Huala, E. et al. (2002). TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics 2, 239-253.
19. Ghosh, S., and Echols, H. (1972). Purification and properties of D protein: a transcription factor of Escherichia coli. Proc Natl Acad Sci USA 69, 3660-3664.
20. Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K., Jr., Hannick, L.I., et al. (2003). Improving the Arabidopsisgenome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31, 5654-5666.
21. Hertz, G.Z., and Stormo, G.D. (1999). Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15, 563.
22. 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.
23. Initiative, T.A.G. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
24. Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., et al. (2003). Summaries of affymetrix GeneChip probe level data. Nucleic Acids Res 31, e15.
25. Janaki, C., and Joshi, R.R. (2004). Motif detection in Arabidopsis: Correlation with gene expression data. In Silico Biol 4, 0014. Kawaji, H., Frith, M.C., Katayama, S., Sandelin, A., Kai, C., Kawai, J., et al. (2006). Dynamic usage of transcription start sites within core promoters. Genome Biol 7, R118.
26. Kent, W.J. (2002). BLAT-The BLAST-like alignment tool. Genome Res 4, 656-664.
27. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., et al. (2007). The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50, 347-363.
28. Koike, S., Schaeffer, L., and Changeux, J.P (1995). Identification of a DNA element determining synaptic expression of the mouse acetylcholine receptor delta-subunit gene. Proc Natl Acad Sci USA 92, 10624-10628.
29. Mencia, M., Moqtaderi, Z., Geisberg, J.V., Kuras, L., and Struhl, K. (2002). Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol Cell 22, 8122-8134.
30. Meyersa, B.C., Kozika, A., Griegoa, A., Kuanga, H., and Michelmore, R.W (2003). Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15, 809-834.
31. Molina, C., and Grotewold, E. (2005). Genome wide analysis of Arabidopsis core promoters. BMC Genomics 6, 25.
32. NCBI Press Releases. (2005). Public Collections of DNA and RNA Sequence Reach 100 Gigabases. http://www.nlm.nih. gov/news/press-releases/dna-rna-100- gig.html
33. Ohler, U., (2006) Identification of core promoter modules in Drosophila and their application to accurate TSS prediction. Nucleic Acid Res 34, 5943-5950.
34. Ohler, U., Liao, G., Niemann, H., and Rubin, G.M. (2002). Computational analysis of core promoters in the Drosophila genome. Genome Biol 3, 12.
35. Pritsker, M., Liu, Y.-C., Beer, M.A., and Tavazoie, S. (2004). Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome Res 14, 99-108.
36. Rapp, P.W., Carlson, J.M., Michael, T.P., McClung, C.R., and Gross, R.H. (2001). Examination of Arabidopsis thaliana upstream regions for possible promoter motifs. 5th Annual Conference on Computational Genomics, TIGR Computational Genomics Presentation, Baltimore, MD; 2001.
37. Roth, F.R., Hughes, J.D., Estep, P.E., and Church, G.M. (1998). Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole-genome mRNA quantization. Nat Biotechnol 16, 939-945.
38. Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., et al. (2005). A gene expression map of Arabidopsis thaliana development. Nat Genet 37, 501-506.
39. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Shinozaki, K., Carninci, P., et al. (2001). Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13, 61-72.
40. Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., et al. (2002). Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 99, 4465-4470.
41. Sugahara, Y., Carninci, P., Itoh, M., Shibata, K., Konno, H., Endo, T., et al. (2001). Comparative evaluation of 5-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries. Gene 263, 93-102.
42. Suzuki, M., Koide, Y., Hattori, T., Nakamura, K., and Asahi, T. (1995). Different Sets of cis-elements contribute to the expression of a catalase gene from castor bean during seed formation and postembryonic development in transgenic tobacco. Plant Cell Physiol 36, 1067-1074.
43. Suzuki, Y., Yoshitomo-Nakagawa, K., Maruyama, K., Suyama, A., and Sugano, S. (1997). Construction and characterization of a full length-enriched and a 5-end-enriched cDNA library. Gene 200, 149-156.
44. TAIR, The Arabidopsis Information Resource. Available at ftp. arabidopsis.org/home/tair/Genes/TAIR7-genome-release Tatarinova, T., Brover, V., Troukhan, M., and Alexandrov, N. (2003). Skew in CG content near the TSS in Arabidopsis thaliana. Bioinformatics 19(Suppl. 1):i313-i314.
45. Tharakaraman, K., Bodenreider, O., Landsman, D., Spouge, J., and Marino-Ramirez, L. (2008). The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. Nucleic Acids Res 36, 2777-2786.
46. Tirosh, I., and Weinberger, A. (2006). A genetic signature of interspecies variation in gene expression. Nat Genet 38.
47. Tompa, M., Li, N., Bailey, T.L., Church, G.M., De Moor, B., Eskin, E., et al. (2005). Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23, 137-144.
48. Von Koskull-Döring, P., Scharf, K.D., and Nover, L. (2007). The diversity of plant heat stress transcription factors.. Trends Plant Sci. 12, 452-457.
49. Wang, R., Okamoto, M., Xing, X., and Crawford, N.M., (2003). Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol 132, 556-567.
50. Welchen, E., and Gonzalez, D.H. (2006). Overrepresentation of elements recognized by TCP-domain transcription factors in the upstream regions of nuclear genes encoding components of the mitochondrial oxidative phosphorylation Machinery. Plant Physiol 141, 540-545.
51. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., et al. (2001). The TRANSFAC system on gene expression regulation. Nucleic Acids Res 29, 281-283.
52. Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J. et al. (2003). Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842-846.
53. Yamamoto, Y.Y., Ichida, H., Matsui, M., Obokata, J., Sakurai, T., Satou, M. et al. (2007). Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics 8, 67.
54. Yamamoto, Y.Y., and Obokata, J. (2008). Ppdb: a plant promoter database. Nucleic Acids Res 36, D977-D981.