Bernard et al. BMC Genomics 2010, 11:166 http://www.biomedcentral.com/1471-2164/11/166 Acknowledgements We thank Marie-Laure Martin-Magniette for her statistical advices. We thank Jérémy Just and Franck Samson for their advices for orthologous gene analysis. We thank Sébastien Aubourg for his helpful comments on the manuscript. We thank Jean-Philippe Tamby, Fabrice Touzain, Joan Sobota and Emily Witty for their careful reading of the manuscript. Author details 1Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165 -CNRS 8114 -UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France. 2Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP), UMR CNRS 8618 -UPS, Bâtiment 630, 91405 Orsay Cedex, France. Authors’ contributions VBe performed the analyses and wrote the manuscript. VBr coordinated the analyses and helped to write the manuscript. AL managed the study and helped to write the manuscript. All authors read and approved the final manuscript. Received: 27 July 2009 Accepted: 12 March 2010 Published: 12 March 2010 References 1. Muller F, Demeny MA, Tora L: New problems in RNA polymerase II transcription initiation: matching the diversity of core promoters with a variety of promoter recognition factors. J Biol Chem 2007, 282(20):14685-14689. 2. Gross P, Oelgeschlager T: Core promoter-selective RNA polymerase II transcription. Biochem Soc Symp 2006, 73: 225-236. 3. Shi W, Zhou W: Frequency distribution of TATA Box and extension sequences on human promoters. BMC Bioinformatics 2006, 7(Suppl 4):S2. 4. Basehoar AD, Zanton SJ, Pugh BF: Identification and distinct regulation of yeast TATA box-containing genes. Cell 2004, 116(5):699-709. 5. Tsai FT, Sigler PB: Structural basis of preinitiation complex assembly on human pol II promoters. Embo J 2000, 19(1):25-36. 6. Moshonov S, Elfakess R, Golan-Mashiach M, Sinvani H, Dikstein R: Links between core promoter and basic gene features influence gene expression. BMC Genomics 2008, 9(1):92. 7. Nakamura M, Tsunoda T, Obokata J: Photosynthesis nuclear genes generally lack TATA-boxes: a tobacco photosystem I gene responds to light through an initiator. Plant J 2002, 29(1):1-10. 8. Patikoglou GA, Kim JL, Sun L, Yang SH, Kodadek T, Burley SK: TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev 1999, 13(24):3217-3230. 9. Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E: Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 2007, 389(1):52-65. 10. Javahery R, Khachi A, Lo K, Zenzie-Gregory B, Smale ST: DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol Cell Biol 1994, 14(1):116-127. 11. Burke TW, Kadonaga JT: The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 1997, 11(22):3020-3031. 12. Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH: New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev 1998, 12(1):34-44. 13. Gershenzon NI, Trifonov EN, Ioshikhes IP: The features of Drosophila core promoters revealed by statistical analysis. BMC Genomics 2006, 7:161. 14. Thompson W, Rouchka EC, Lawrence CE: Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 2003, 31(13):3580-3585. 15. van Helden J: Regulatory sequence analysis tools. Nucleic Acids Res 2003, 31(13):3593-3596. 16. Bellora N, Farre D, Alba MM: Positional bias of general and tissue- specific regulatory motifs in mouse gene promoters. BMC Genomics 2007, 8:459. 17. Berendzen KW, Stuber K, Harter K, Wanke D: Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. BMC Bioinformatics 2006, 7:522. Page 14 of 15 18. Kielbasa SM, Korbel JO, Beule D, Schuchhardt J, Herzel H: Combining frequency and positional information to predict transcription factor binding sites. Bioinformatics 2001, 17(11):1019-1026. 19. Molina C, Grotewold E: Genome wide analysis of Arabidopsis core promoters. BMC Genomics 2005, 6(1):25. 20. Narang V, Sung WK, Mittal A: Computational modeling of oligonucleotide positional densities for human promoter prediction. Artif Intell Med 2005, 35(1-2):107-119. 21. Yamamoto YY, Ichida H, Matsui M, Obokata J, Sakurai T, Satou M, Seki M, Shinozaki K, Abe T: Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics 2007, 8:67. 22. Defrance M, Touzet H: Predicting transcription factor binding sites using local over-representation and comparative genomics. BMC Bioinformatics 2006, 7:396. 23. Cowan MJ, Yao XL, Pawliczak R, Huang X, Logun C, Madara P, Alsaaty S, Wu T, Shelhamer JH: The role of TFIID, the initiator element and a novel 5’ TFIID binding site in the transcriptional control of the TATA-less human cytosolic phospholipase A2-alpha promoter. Biochim Biophys Acta 2004, 1680(3):145-157. 24. Bogomolski-Yahalom V, Klein A, Greenblat I, Haviv Y, Tur-Kaspa R: The TATA-less promoter of hepatitis B virus S gene contains a TBP binding site and an active initiator. Virus Res 1997, 49(1):1-7. 25. Abeel T, Saeys Y, Bonnet E, Rouze P, Peer Van de Y: Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res 2008, 18(2):310-323. 26. Civan P, Svec M: Genome-wide analysis of rice (Oryza sativa L. subsp. japonica) TATA box and Y Patch promoter elements. Genome 2009, 52(3):294-297. 27. FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C: Clustering of DNA sequences in human promoters. Genome Res 2004, 14(8):1562-1574. 28. Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH: Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 1989, 86(16):6201-6205. 29. Chaw SM, Chang CC, Chen HL, Li WH: Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol 2004, 58(4):424-441. 30. Smale ST, Kadonaga JT: The RNA polymerase II core promoter. Annu Rev Biochem 2003, 72:449-479. 31. Joshi CP: An inspection of the domain between putative TATA box and translation start site in 79 plant genes. Nucleic Acids Res 1987, 15(16):6643-6653. 32. Singer VL, Wobbe CR, Struhl K: A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev 1990, 4(4):636-645. 33. Loganantharaj R: Discriminating TATA box from putative TATA boxes in plant genome. Int J Bioinform Res Appl 2006, 2(1):36-51. 34. Kiran K, Ansari SA, Srivastava R, Lodhi N, Chaturvedi CP, Sawant SV, Tuli R: The TATA-box sequence in the basal promoter contributes to determining light-dependent gene expression in plants. Plant Physiol 2006, 142(1):364-376. 35. Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, et al: A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 2003, 554(1-2):17-22. 36. Morgante M, Hanafey M, Powell W: Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 2002, 30(2):194-200. 37. Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E: AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 2003, 4:25. 38. Higo K, Ugawa Y, Iwamoto M, Korenaga T: Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 1999, 27(1):297-300. 39. Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K: DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res 2008, , 36 Database: D97-101. 40. Drawid A, Gupta N, Nagaraj VH, Gelinas C, Sengupta AM: OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. BMC Bioinformatics 2009, 10(1):208.