AN INTEGRATED BIOINFORMATICS APPROACH TO THE DISCOVERY OF CIS -REGULATORY ELEMENTS INVOLVED IN PLANT GRAVITROPIC SIGNAL TRANSDUCTION

X. Liang, K. Shen, J. Lichtenberg, S.E. Wyatt, and L.R. Welch

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References

  1. [1] F.D. Sack, Plant gravity sensing International Review ofCytology-a Survey of Cell Biology, 127, 1991, 193–252.
  2. [2] J.Z. Kiss, Mechanisms of the early phases of plant gravitropism,CRC Critical Review Plant Science, 19(6), 2000, 551–573.
  3. [3] T. Caspar & B.G. Pickard, Gravitropism in a starchless mutantof Arabidopsis – Implications for the Starch-Statolith Theoryof Gravity Sensing, Planta, 177(2), 1989, 185–197.
  4. [4] F.D. Sack & J.Z. Kiss, Rootcap structure in wild-type andin a starchless Mutant of Arabidopsis, American Journal ofBotany, 76(2), 1989, 454–464.
  5. [5] B.R. Harrison & P.H. Masson, ARL2, ARG1 and PIN3 definea gravity signal transduction pathway in root statocytes, PlantJournal, 53(2), 2008, 380–392.
  6. [6] A.C. Scott & N.S. Allen, Changes in cytosolic pH withinArabidopsis root columella cells play a key role in the earlysignaling pathway for root gravitropism, Plant Physiol, 121(4),1999, 1291–1298.
  7. [7] E.B. Blancaflor & P.H. Masson, Plant gravitropism: Unravelingthe ups and downs of a complex process, Plant Physiology,133(4), 2003, 1677–1690.
  8. [8] I.Y. Perera, I. Heilmann, & W.F. Boss, Transient and sustainedincreases in inositol 1,4,5-trisphosphate precede the differentialgrowth response in gravistimulated maize pulvini. ProceedingsNational Academy Sciences United States of America, 96(10),1999, 5838–5843.
  9. [9] W.F. Boss, I.Y. Perera, J. Love, & I. Heilmann, Alteringphosphoinositide metabolism by expressing human type I inos-52itol polyphosphate 5’ phosphatise in tobacco cells. MolecularBiology of the Cell, 12: 2001, 820.
  10. [10] J.H. Joo, Y.S. Bae, & J.S. Lee, Role of auxin-induced reactiveoxygen species in root gravitropism, Plant Physiology, 126(3),2001, 1055–1060.
  11. [11] A.M. Clore, S.M. Doore, & S.M.N. Tinnirello, Increased levelsof reactive oxygen species and expression of a cytoplasmicaconitase/iron regulatory protein 1 homolog during the earlyresponse of maize pulvini to gravistimulation, Plant Cell andEnvironment, 31(1), 2008, 144–158.
  12. [12] P.B. Kaufman, L.-L. Wu, T.G. Brock, & D. Kim, Hormonesand the orientation of growth, in P.J. Davies (Ed.), Plant Hor-mones, Second Edition, Dordrecht, The Netherlands: KluwerAcademic Publishers, 547–571.
  13. [13] J.M. Kimbrough, R. Salinas-Mondragon, W.F. Boss, C.S.Brown, & H.W. Sederoff, The fast and transient transcrip-tional network of gravity and mechanical stimulation in theArabidopsis root apex, Plant Physiology, 136(1), 2004, 2790–2805.
  14. [14] J. Lichtenberg, E. Jacox, J.D. Welch, K. Kurz, X. Liang, M.Q.Yang, F. Drews, K. Ecker, S.S. Lee, L. Elnitski, & L.R. Welch,Word-based characterization of promoters involved in humanDNA repair pathways, BMC Genomics, 10(Suppl 1), 2009,S18.
  15. [15] J. Lichtenberg, A. Yilmaz, J.D. Welch, K. Kurz, X. Liang,F. Drews, K. Ecker, S.S. Lee, M. Geisler, E. Grotewold, &R.W. Lonnie, The word landscape of the non-coding segmentsof the Arabidopsis thaliana genome, BMC Genomics, 10, 2009,463.
  16. [16] S.K. Palaniswamy, S. James, H. Sun, R.S. Lamb, R.V. Davuluri,& E. Grotewold, AGRIS and AtRegNet: A platform to link cis-regulatory elements and transcription factors into regulatorynetworks, Plant Physiology, 140(3), 2006, 818–829.
  17. [17] R.V. Davuluri, H. Sun, S.K. Palaniswamy, N. Matthews,C. Molina, M. Kurtz, & E. Grotewold, AGRIS: ArabidopsisGene Regulatory Information Server, an information resource ofArabidopsis cis-regulatory elements and transcription factors,BMC Bioinformatics, 4(1), 2003, 25.
  18. [18] E. Wingender, X. Chen, R. Hehl, H. Karas, & I. Liebich,TRANSFAC: An integrated system for gene expression regu-lation, Nucleic Acids Research, 28, 2000, 316–319.
  19. [19] J.C. Bryne, E. Valen, M.H. Tang, T. Marstrand, & O. Winther,JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update,Nucleic Acids Research, 36, 2008, D102–106.
  20. [20] H.M. Hsu, S.J. Ong, M.C. Lee, & J.H. Tai, Transcriptionalregulation of an iron-inducible gene by differential and alternatepromoter entries of multiple myb proteins in the protozoanparasite Trichomonas vaginalis, Eukaryotic Cell, 8(3), 2009,362–372.
  21. [21] J.H. Yoo, C.Y. Park, J.C. Kim, W.D. Heo, M.S. Cheong, H.C.Park, M.C. Kim, B.C. Moon, M.S. Choi, Y.H. Kang, J.H. Lee,H.S. Kim, S.M. Lee, H.W. Yoon, C.O. Lim, D.J. Yun, S.Y. Lee,W.S. Chung, & M.J. Cho, Direct interaction of a divergentCaM isoform and the transcription factor, MYB2, enhances salttolerance in arabidopsis. The Journal of Biological Chemistry,280(5), 2005, 3697–3707.
  22. [22] R.C. Gentleman, V.J. Carey, D.M. Bates, B. Bolstad, M.Dettling, S. Dudoit, B. Ellis, L. Gautier, Y.C. Ge, J. Gentry,K. Hornik, T. Hothorn, W. Huber, S. Lacus, R. Irizarry, F.Leisch, C. Li, M. Maechler, A.J. Rossini, G. Sawitzki, C.Smith, G. Smyth, L. Tierney, J.Y.H. Yang, & J.H. Zhang,Bioconductor: open software development for computationalbiology and bioinformatics, Genome Biology, 5(10), 2004, R80.
  23. [23] Z. Wu, R.A. Irizarry, R. Gentleman, F. Martinez-Murillo,& F. Spencer, A model-based background adjustment foroligonucleotide expression arrays, Journal of the AmericanStatistical Association, 99(468), 2004, 909–917.
  24. [24] R. Breitling, P. Armengaud, A. Amtmann, & P. Herzyk,Rank products: A simple, yet powerful, new method todetect differentially regulated genes in replicated microarrayexperiments, FEBS Letter, 573(1–3), 2004, 83–92.
  25. [25] L. Kaufman & P.J. Rousseeuw, Finding groups in data (JohnWiley & Sons, Inc. 1990), 190, 191, 212, 217.
  26. [26] T. Beissbarth & T.P. Speed, GOstat: Find statistically over-represented gene ontologies within a group of genes, Bioinfor-matics, 20(9), 2004, 1464–1465.
  27. [27] B. Lenhard & W.W. Wasserman, TFBS: Computational frame-work for transcription factor binding site analysis, Bioinfor-matics, 18, 2002, 1135–1136.
  28. [28] E. Jacox & L. Elnitski, Finding occurrences of relevant func-tional elements in genomic signatures, International Journalof Computational Science, 2(5), 2008, 599–606.
  29. [29] C. Martin & J. Paz-Ares, MYB transcription factors in plants,Trends in Genet, 13, 1997, 67–73.
  30. [30] G.R. Teakle, I.W. Manfield, J.F. Graham, & P.M. Gilmartin,Arabidopsis Thaliana GATA factors: Organisation, expressionand DNA-binding characteristics, Plant Molecular Biology,50(1), 2002, 43–57.
  31. [31] U. Hartmann, W.J. Valentine, J.M. Christie, J. Hays, G.I.Jenkins, & B. Weisshaar, Identification of UV/blue light-response elements in the Arabidopsis thaliana chalcone synthasepromoter using a homologous protoplast transient expressionsystem, Plant Molecular Biology, 36, 1998 741–754.
  32. [32] R. Solano, A. Stepanova, Q. Chao, & J.R. Ecker, Nuclear eventsin Ethylene signaling: A transcriptional cascade mediated byethylene-insensitive3 and ethylene-response-factor1, Genes ofDevelopment, 12, 1998, 3703–3714.
  33. [33] J.J. Tilly, D.W. Allen, & T. Jack, The CArG boxes inthe promoter of the Arabidopsis floral organ identity geneAPETALA3 mediate diverse regulatory effects, Development,125(9), 1998, 1647–1657.
  34. [34] C. Despres, C. Delong, S. Glaze, E. Liu, & P.R. Fovert, TheArabidopsis NPR1/NIM1 protein enhances the DNA bindingactivity of a subgroup of the TGA family of bZIP transcriptionfactors, Plant Cell, 12, 2000, 279–290.

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