signature=e64cb47a2472322d4560426084eb1b83,Genome-scale cold stress response regulatory networks in ...

1.

Hall BK, Hallgrímsson B, Strickberger MW: Strickberger’s evolution: the integration of genes, organisms and populations. 2008, Sudbury, Mass: Jones and Bartlett, 4

2.

Alonso-Blanco C, Aarts MGM, Bentsink L, Keurentjes JJB, Reymond M, Vreugdenhil D, Koornneef M: What has natural variation taught us about plant development, physiology, and adaptation?. Plant Cell. 2009, 21: 1877-1896. 10.1105/tpc.109.068114.

3.

Mitchell-Olds T, Schmitt J: Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature. 2006, 441: 947-952. 10.1038/nature04878.

4.

Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjalmsson BJ, et al: Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet. 2012, 44: 212-216. 10.1038/ng.1042.

5.

Alonso-Blanco C, Koornneef M: Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. Trends Plant Sci. 2000, 5: 22-29.

6.

Sanghera GS, Wani SH, Hussain W, Singh NB: Engineering cold stress tolerance in crop plants. Curr Genomics. 2011, 12: 30-43. 10.2174/138920211794520178.

7.

Thomashow MF: Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Physiol Plant Mol Biol. 1999, 50: 571-599. 10.1146/annurev.arplant.50.1.571.

8.

Penfield S: Temperature perception and signal transduction in plants. The New phytologist. 2008, 179: 615-628. 10.1111/j.1469-8137.2008.02478.x.

9.

Carvallo MA, Pino MT, Jeknic Z, Zou C, Doherty CJ, Shiu SH, Chen TH, Thomashow MF: A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana. J Exp Bot. 2011, 62: 3807-3819. 10.1093/jxb/err066.

10.

Yamaguchishinozaki K, Shinozaki K: A novel Cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell. 1994, 6: 251-264.

11.

Jaglo-Ottosen KR, Gilmour SJ, Zarka DG, Schabenberger O, Thomashow MF: Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science. 1998, 280: 104-106. 10.1126/science.280.5360.104.

12.

Fowler S, Thomashow MF: Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell. 2002, 14: 1675-1690. 10.1105/tpc.003483.

13.

Swindell WR, Huebner M, Weber AP: Plastic and adaptive gene expression patterns associated with temperature stress in Arabidopsis thaliana. Heredity. 2007, 99: 143-150. 10.1038/sj.hdy.6800975.

14.

Rohde P, Hincha DK, Heyer AG: Heterosis in the freezing tolerance of crosses between two Arabidopsis thaliana accessions (Columbia-0 and C24) that show differences in non-acclimated and acclimated freezing tolerance. Plant Journal. 2004, 38: 790-799. 10.1111/j.1365-313X.2004.02080.x.

15.

Alonso-Blanco C, Gomez-Mena C, Llorente F, Koornneef M, Salinas J, Martinez-Zapater JM: Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis. Plant Physiol. 2005, 139: 1304-1312. 10.1104/pp.105.068510.

16.

Zhen Y, Ungerer MC: Clinal variation in freezing tolerance among natural accessions of Arabidopsis thaliana. New Phytologist. 2008, 177: 419-427.

17.

McKhann HI, Gery C, Berard A, Leveque S, Zuther E, Hincha DK, De Mita S, Brunel D, Teoule E: Natural variation in CBF gene sequence, gene expression and freezing tolerance in the Versailles core collection of Arabidopsis thaliana. BMC Plant Biol. 2008, 8: 105-10.1186/1471-2229-8-105.

18.

Somerville C, Koornneef M: A fortunate choice: the history of Arabidopsis as a model plant. Nat Rev Genet. 2002, 3: 883-889.

19.

Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M: Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet. 2003, 19: 570-577. 10.1016/j.tig.2003.08.006.

20.

Rasmussen S, Barah P, Suarez-Rodriguez MC, Bressendorff S, Friis P, Costantino P, Bones AM, Nielsen HB, Mundy J: Transcriptome responses to combinations of stresses in Arabidopsis. Plant Physiol. 2013, 161: 1783-1794. 10.1104/pp.112.210773.

21.

Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, Bonetta D, Zhang J, Fung P, Gong Y, Wang PW, et al: Next-generation mapping of Arabidopsis genes. Plant J. 2011, 67: 715-725. 10.1111/j.1365-313X.2011.04619.x.

22.

Shimizu KK: Ecology meets molecular genetics in Arabidopsis. Popul Ecol. 2002, 44: 221-233. 10.1007/s101440200025.

23.

Keurentjes JJB, Fu JY, Terpstra IR, Garcia JM, van den Ackerveken G, Snoek LB, Peeters AJM, Vreugdenhil D, Koornneef M, Jansen RC: Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci U S A. 2007, 104: 1708-1713. 10.1073/pnas.0610429104.

24.

Ideker T, Krogan NJ: Differential network biology. Mol Syst Biol. 2012, 8: 565-

25.

Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J: DATF: a database of Arabidopsis transcription factors. Bioinformatics. 2005, 21: 2568-2569. 10.1093/bioinformatics/bti334.

26.

Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E: AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic acids research. 2011, 39: D1118-1122. 10.1093/nar/gkq1120.

27.

Tirosh I, Barkai N: Inferring regulatory mechanisms from patterns of evolutionary divergence. Mol Syst Biol. 2011, 7: 530-

28.

Segal E, Shapira M, Regev A, Pe’er D, Botstein D, Koller D, Friedman N: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet. 2003, 34: 166-176. 10.1038/ng1165.

29.

Alter O, Brown PO, Botstein D: Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA. 2000, 97: 10101-10106. 10.1073/pnas.97.18.10101.

30.

Herrgard MJ, Covert MW, Palsson BO: Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol. 2004, 15: 70-77. 10.1016/j.copbio.2003.11.002.

31.

Liao JC, Boscolo R, Yang YL, Tran LM, Sabatti C, Roychowdhury VP: Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci USA. 2003, 100: 15522-15527. 10.1073/pnas.2136632100.

32.

Kao KC, Yang YL, Boscolo R, Sabatti C, Roychowdhury V, Liao JC: Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc Natl Acad Sci USA. 2004, 101: 641-646. 10.1073/pnas.0305287101.

33.

Wang J, Qiu X, Li Y, Deng Y, Shi T: A transcriptional dynamic network during Arabidopsis thaliana pollen development. Bmc Syst Biol. 2011, 5 (Suppl 3): S8-10.1186/1752-0509-5-S3-S8.

34.

Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31: e15-10.1093/nar/gng015.

35.

Carvalho BS, Irizarry RA: A framework for oligonucleotide microarray preprocessing. Bioinformatics. 2010, 26: 2363-2367. 10.1093/bioinformatics/btq431.

36.

R Core Team: R: A language and environment for statistical computing. Book R: A language and environment for statistical computing. Edited by: City. 2012, Vienna, Austria: R Foundation for Statistical Computing, http://www.R-project.org/ ISBN 3-900051-07-0

37.

Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, et al: The Arabidopsis information resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012, 40: D1202-1210. 10.1093/nar/gkr1090.

38.

Guberman JM, Ai J, Arnaiz O, Baran J, Blake A, Baldock R, Chelala C, Croft D, Cros A, Cutts RJ: BioMart central portal: an open database network for the biological community. Database (Oxford). 2011, 2011: bar041-10.1093/database/bar041.

39.

Cui X, Churchill GA: Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 2003, 4: 210-10.1186/gb-2003-4-4-210.

40.

Kerr MK, Martin M, Churchill GA: Analysis of variance for gene expression microarray data. J Comput Biol. 2000, 7: 819-837. 10.1089/10665270050514954.

41.

Saeed AI, Hagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li JW, Thiagarajan M, White JA, Quackenbush J: TM4 microarray software suite. Method Enzymol. 2006, 411: 134-193.

42.

Maere S, Heymans K, Kuiper M: BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005, 21: 3448-3449. 10.1093/bioinformatics/bti551.

43.

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25: 25-29. 10.1038/75556.

44.

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD: Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003, 31: 3497-3500. 10.1093/nar/gkg500.

45.

Tajima F: Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989, 123: 585-595.

46.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011, 28: 2731-2739. 10.1093/molbev/msr121.

47.

Galbraith SJ, Tran LM, Liao JC: Transcriptome network component analysis with limited microarray data. Bioinformatics. 2006, 22: 1886-1894. 10.1093/bioinformatics/btl279.

48.

Hannah MA, Wiese D, Freund S, Fiehn O, Heyer AG, Hincha DK: Natural genetic variation of freezing tolerance in Arabidopsis. Plant Physiol. 2006, 142: 98-112. 10.1104/pp.106.081141.

49.

Ziolkowski PA, Koczyk G, Galganski L, Sadowski J: Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes. Nucleic Acids Res. 2009, 37: 3189-3201. 10.1093/nar/gkp183.

50.

Lee BH, Henderson DA, Zhu JK: The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell. 2005, 17: 3155-3175. 10.1105/tpc.105.035568.

51.

Kashkush K, Feldman M, Levy AA: Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics. 2002, 160: 1651-1659.

52.

Wang X, Weigel D, Smith LM: Transposon variants and their effects on gene expression in Arabidopsis. Plos Genetics. 2013, 9 (2): 1-13.

53.

Chen WJ, Chang SH, Hudson ME, Kwan WK, Li J, Estes B, Knoll D, Shi L, Zhu T: Contribution of transcriptional regulation to natural variations in Arabidopsis. Genome Biol. 2005, 6: R32-10.1186/gb-2005-6-4-r32.

54.

Catala R, Medina J, Salinas J: Integration of low temperature and light signaling during cold acclimation response in Arabidopsis. Proc Natl Acad Sci USA. 2011, 108: 16475-16480. 10.1073/pnas.1107161108.

55.

Franklin KA, Whitelam GC: Light-quality regulation of freezing tolerance in Arabidopsis thaliana. Nat Genet. 2007, 39: 1410-1413. 10.1038/ng.2007.3.

56.

Havaux M, Kloppstech K: The protective functions of carotenoid and flavonoid pigments against excess visible radiation at chilling temperature investigated in Arabidopsis npq and tt mutants. Planta. 2001, 213: 953-966. 10.1007/s004250100572.

57.

Heddad M, Noren H, Reiser V, Dunaeva M, Andersson B, Adamska I: Differential expression and localization of early light-induced proteins in Arabidopsis. Plant Physiol. 2006, 142: 75-87. 10.1104/pp.106.081489.

58.

Rapacz M, Wolanin B, Hura K, Tyrka M: The effects of cold acclimation on photosynthetic apparatus and the expression of COR14b in four genotypes of barley (Hordeum vulgare) contrasting in their tolerance to freezing and high-light treatment in cold conditions. Ann Bot-London. 2008, 101: 689-699. 10.1093/aob/mcn008.

59.

Zuther E, Schulz E, Childs LH, Hincha DK: Clinal variation in the non-acclimated and cold-acclimated freezing tolerance of Arabidopsis thaliana accessions. Plant Cell Environ. 2012, 35 (10): 1860-78. 10.1111/j.1365-3040.2012.02522.x.

60.

Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JCW, Lynn JR, Straume M, Smith JQ, Millar AJ: Flowering Locus C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell. 2006, 18: 639-650. 10.1105/tpc.105.038315.

61.

Harmer SL, Hogenesch LB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA: Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 2000, 290: 2110-2113. 10.1126/science.290.5499.2110.

62.

Salter MG, Franklin KA, Whitelam GC: Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature. 2003, 426: 680-683. 10.1038/nature02174.

63.

Fowler SG, Cook D, Thomashow ME: Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol. 2005, 137: 961-968. 10.1104/pp.104.058354.

64.

Mikkelsen MD, Thomashow MF: A role for circadian evening elements in cold-regulated gene expression in Arabidopsis. Plant Journal. 2009, 60: 328-339. 10.1111/j.1365-313X.2009.03957.x.

65.

Zust T, Heichinger C, Grossniklaus U, Harrington R, Kliebenstein DJ, Turnbull LA: Natural enemies drive geographic variation in plant defenses. Science. 2012, 338: 116-119. 10.1126/science.1226397.

66.

Plazek A, Zur I: Cold-induced plant resistance to necrotrophic pathogens and antioxidant enzyme activities and cell membrane permeability. Plant Sci. 2003, 164: 1019-1028. 10.1016/S0168-9452(03)00089-X.

67.

Zhu Y, Qian WQ, Hua J: Temperature modulates plant defense responses through NB-LRR proteins. Plos Pathog. 2010, 6 (4): 1-13.

68.

Kuwabara C, Imai R: Molecular basis of disease resistance acquired through cold acclimation in overwintering plants. J Plant Biol. 2009, 52: 19-26. 10.1007/s12374-008-9006-6.

69.

Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shinozaki K: Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol. 2006, 9: 436-442. 10.1016/j.pbi.2006.05.014.

70.

Atkinson NJ, Urwin PE: The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot. 2012, 63: 3523-3543. 10.1093/jxb/ers100.

71.

Mittler R: Abiotic stress, the field environment and stress combination. Trends Plant Sci. 2006, 11: 15-19. 10.1016/j.tplants.2005.11.002.

72.

Hoshino T, Xiao N, Tkachenko OB: Cold adaptation in the phytopathogenic fungi causing snow molds. Mycoscience. 2009, 50: 26-38. 10.1007/S10267-008-0452-2.

73.

Medina J, Catala R, Salinas J: The CBFs: Three arabidopsis transcription factors to cold acclimate. Plant Sci. 2011, 180: 3-11. 10.1016/j.plantsci.2010.06.019.

74.

Haake V, Cook D, Riechmann JL, Pineda O, Thomashow MF, Zhang JZ: Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis. Plant Physiol. 2002, 130: 639-648. 10.1104/pp.006478.

75.

Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, et al: Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011, 43: 956-963. 10.1038/ng.911.

76.

Zhen Y, Ungerer MC: Relaxed selection on the CBF/DREB1 regulatory genes and reduced freezing tolerance in the southern range of Arabidopsis thaliana. Mol Biol Evol. 2008, 25: 2547-2555. 10.1093/molbev/msn196.

77.

Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, et al: The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 2005, 3: e196-10.1371/journal.pbio.0030196.

78.

Sterken R, Kiekens R, Coppens E, Vercauteren I, Zabeau M, Inze D, Flowers J, Vuylsteke M: A population genomics study of the Arabidopsis core cell cycle genes shows the signature of natural selection. Plant Cell. 2009, 21: 2987-2998. 10.1105/tpc.109.067017.

79.

Bakker EG, Toomajian C, Kreitman M, Bergelson J: A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell. 2006, 18: 1803-1818. 10.1105/tpc.106.042614.

80.

Fowler DB, Limin AE: Interactions among factors regulating phenological development and acclimation rate determine low-temperature tolerance in wheat. Ann Bot-London. 2004, 94: 717-724. 10.1093/aob/mch196.

81.

Delker C, Poschl Y, Raschke A, Ullrich K, Ettingshausen S, Hauptmann V, Grosse I, Quint M: Natural variation of transcriptional auxin response networks in Arabidopsis thaliana. Plant Cell. 2010, 22: 2184-2200. 10.1105/tpc.110.073957.

82.

Clauset A, Shalizi CR, Newman MEJ: Power-Law distributions in empirical data. Siam Rev. 2009, 51: 661-703. 10.1137/070710111.

83.

Barabasi AL, Oltvai ZN: Network biology: understanding the cell’s functional organization. Nat Rev Genet. 2004, 5: 101-113. 10.1038/nrg1272.

84.

Barabasi AL: Scale-free networks: a decade and beyond. Science. 2009, 325: 412-413. 10.1126/science.1173299.

85.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003, 13: 2498-2504. 10.1101/gr.1239303.

86.

Qian J, Lin J, Luscombe NM, Yu H, Gerstein M: Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics. 2003, 19: 1917-1926. 10.1093/bioinformatics/btg347.

87.

Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV: Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci USA. 2000, 97: 8409-8414. 10.1073/pnas.150242097.

88.

Carrera J, Rodrigo G, Jaramillo A, Elena SF: Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome biology. 2009, 10: R96-10.1186/gb-2009-10-9-r96.

89.

Espinosa-Soto C, Padilla-Longoria P, Alvarez-Buylla ER: A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. The Plant cell. 2004, 16: 2923-2939. 10.1105/tpc.104.021725.

90.

Middleton AM, Farcot E, Owen MR, Vernoux T: Modeling regulatory networks to understand plant development: small is beautiful. The Plant cell. 2012, 24: 3876-3891. 10.1105/tpc.112.101840.

91.

Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, et al: A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol. 2011, 7: 459-

92.

Riano-Pachon DM, Ruzicic S, Dreyer I, Mueller-Roeber B: PlnTFDB: an integrative plant transcription factor database. BMC bioinformatics. 2007, 8: 42-10.1186/1471-2105-8-42.

93.

AbuQamar S, Chen X, Dhawan R, Bluhm B, Salmeron J, Lam S, Dietrich RA, Mengiste T: Expression profiling and mutant analysis reveals complex regulatory networks involved in Arabidopsis response to Botrytis infection. Plant J. 2006, 48: 28-44. 10.1111/j.1365-313X.2006.02849.x.

94.

Scacchi E, Salinas P, Gujas B, Santuari L, Krogan N, Ragni L, Berleth T, Hardtke CS: Spatio-temporal sequence of cross-regulatory events in root meristem growth. Proc Natl Acad Sci USA. 2010, 107: 22734-22739. 10.1073/pnas.1014716108.

95.

Li G, Siddiqui H, Teng Y, Lin R, Wan XY, Li J, Lau OS, Ouyang X, Dai M, Wan J, et al: Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol. 2011, 13: 616-622. 10.1038/ncb2219.

96.

Wang W, Barnaby JY, Tada Y, Li H, Tor M, Caldelari D, Lee DU, Fu XD, Dong X: Timing of plant immune responses by a central circadian regulator. Nature. 2011, 470: 110-114. 10.1038/nature09766.

97.

Feng S, Martinez C, Gusmaroli G, Wang Y, Zhou J, Wang F, Chen L, Yu L, Iglesias-Pedraz JM, Kircher S, et al: Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature. 2008, 451: 475-479. 10.1038/nature06448.