Evolutionary forces act on promoter length: Identification of enriched cis-regulatory elements

Molecular Biology and Evolution

Volumn 26, Issue 6, 2009, Pages 1299-1307

  Kristiansson, Erik ^a,b,c   Thorsen, Michael ^d   Tamás, Markus J ^a   Nerman, Olle ^a,c  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

^c CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Cis regulatory element; Gene regulation; Promoter; Transcription factor

Indexed keywords

CIS ACTING ELEMENT; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CONTROLLED STUDY; FUNGUS; GENE EXPRESSION; GENE FUNCTION; MOLECULAR EVOLUTION; NONHUMAN; PLANT; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; SEQUENCE DATABASE; TRANSCRIPTION REGULATION; YEAST;

ARSENIC; BINDING SITES; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; EVOLUTION, MOLECULAR; FUNGI; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENES, PLANT; LOGISTIC MODELS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANTS; PROMOTER REGIONS, GENETIC; SACCHAROMYCES CEREVISIAE; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS;

FUNGI; SACCHAROMYCES CEREVISIAE;

EID: 66249129718     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp040     Document Type: Article

References (49)

1. Ashburner M, Ball CA, Blake JA, et al. (20 co-authors). 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29.
2. Birney E, Stamatoyannopoulos JA, Dutta A, et al. (414 coauthors). 2007. Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project. Nature. 447:799-816.
3. Boer VM, de Winde JH, Pronk JT, Piper MD. 2003. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem. 278:3265-3274.
4. Bussemaker HJ, Li H, Siggia ED. 2001. Regulatory element detection using correlation with expression. Nat Genet. 27: 167-171.
5. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell. 12:323-337.
6. Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bahler J. 2003. Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell. 14:214-229.
7. Cherry JM, Ball C, Weng S, et al. (11 co-authors). 1997. Genetic and physical maps of Saccharomyces cerevisiae. Nature. 387:67-73.
8. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science. 301:71-76.
9. Copley RR. 2005. The EH1 motif in metazoan transcription factors. BMC Genomics. 6:169.
10. Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH, Pronk JT. 2004. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem. 279:9125-9138.
11. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM. 2006. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA. 103:5320-5325.
12. Dietrich FS, Voegeli S, Brachat S, et al. (14 co-authors). 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 304:304-307.
13. Eden E, Lipson D, Yogev S, Yakhini Z. 2007. Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol. 3:e39.
14. Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. 2005. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol. 6:R104.
15. Garcia R, Bermejo C, Grau C, Perez R, Rodriguez-Pena JM, Francois J, Nombela C, Arroyo J. 2004. The global transcriptional response to transient cell wall damage in Saccharomyces cerevisiae and its regulation by the cell integrity signaling pathway. J Biol Chem. 279:15183-15195.
16. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 11:4241-4257.
17. Gattiker A, Rischatsch R, Demougin P, Voegeli S, Dietrich FS, Philippsen P, Primig M. 2007. Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists. BMC Genomics. 8:9.
18. Hastie TJ, Tibshirani RJ. 1987. Generalized additive models: some applications. J Am Stat Assoc. 82:371-386.
19. Hastie TJ, Tibshirani RJ. 1990. Generalized additive models. London: Chapman and Hall.
20. Haverty PM, Hansen U, Weng Z. 2004. Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res. 32:179-188.
21. Hedges SB. 2002. The origin and evolution of model organisms. Nat Rev Genet. 3:838-849.
22. Heintzman ND, Stuart RK, Hon G, et al. (15 co-authors). 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 39:311-318.
23. Hertz-Fowler C, Peacock CS, Wood V, et al. (14 co-authors). 2004. GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res. 32:D339-D343.
24. Holm S. 1979. A simple sequentially rejective multiple test procedure. Scand J Stat. 6:65-70.
25. Hughes JD, Estep PW, Tavazoie S, Church GM. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 296:1205-1214.
26. Keles S, van der Laan MJ, Vulpe C. 2004. Regulatory motif finding by logic regression. Bioinformatics. 20:2799-2811.
27. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 423:241-254.
28. Kheradpour P, Stark A, Roy S, Kellis M. 2007. Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res. 17:1919-1931.
29. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K. 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.
30. Kornberg RD. 1996. RNA polymerase II transcription control. Trends Biochem Sci. 21:325-326.
31. Linder T, Rasmussen NN, Samuelsen CO, Chatzidaki E, Baraznenok V, Beve J, Henriksen P, Gustafsson CM, Holmberg S. 2008. Two conserved modules of Schizosaccharomyces pombe Mediator regulate distinct cellular pathways. Nucleic Acids Res. 36:2489-2504.
32. Liu Y, Ringner M. 2007. Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis. Genome Biol. 8:R77.
33. Nelander S, Larsson E, Kristiansson E, Mansson R, Nerman O, Sigvardsson M, Mostad P, Lindahl P. 2005. Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. BMC Genomics. 6:68.
34. Patil CK, Li H, Walter P. 2004. Gcn4p and novel upstream activating sequences regulate targets of the unfolded protein response. PLoS Biol. 2:E246.
35. R Development Core Team. 2008. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
36. Rhee SY, Beavis W, Berardini TZ, et al. (21 co-authors). 2003. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 31:224-228.
37. Sekinger EA, Moqtaderi Z, Struhl K. 2005. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell. 18:735-748.
38. Sharan R, Ovcharenko I, Ben-Hur A, Karp RM. 2003. CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics. 19(Suppl 1): i283-i291.
39. Simon I, Barnett J, Hannett N, et al. (11 co-authors). 2001. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell. 106:697-708.
40. Smith AD, Sumazin P, Zhang MQ. 2007. Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol. 3:73.
41. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 9:3273-3297.
42. Stark A, Lin MF, Kheradpour P, et al. (46 co-authors). 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450:219-232.
43. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. 1999. Systematic determination of genetic network architecture. Nat Genet. 22:281-285.
44. Thorsen M, Lagniel G, Kristiansson E, Junot C, Nerman O, Labarre J, Tamas MJ. 2007. Quantitative transcriptome, proteome and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiol Genomics.
45. Tsai HK, Lu HH, Li WH. 2005. Statistical methods for identifying yeast cell cycle transcription factors. Proc Natl Acad Sci USA. 102:13532-13537.
46. Vinogradov AE. 2004. Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet. 20:248-253.
47. Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K. 2008. DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res. 36:D97-D101.
48. Wood SN. 2006. Generalized additive models. Boca Raton (FL): Chapman & Hall.
49. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science. 309:626-630.