Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays

被引：214

作者：

Zeller, Georg ^{[1
,2
]}

Henz, Stefan R. ^{[1
]}

Widmer, Christian K. ^{[2
]}

Sachsenberg, Timo ^{[1
]}

Raetsch, Gunnar ^{[2
]}

Weigel, Detlef ^{[1
]}

Laubinger, Sascha ^{[1
]}

机构：

[1] Max Planck Inst Dev Biol, Dept Mol Biol, D-72076 Tubingen, Germany

[2] Max Planck Gesell, Friedrich Miescher Lab, D-72076 Tubingen, Germany

来源：

PLANT JOURNAL | 2009年 / 58卷 / 06期

关键词：

tiling array; abiotic stress; Arabidopsis; ABA; At-TAX; GENE-EXPRESSION; REGULATED MICRORNAS; FREEZING TOLERANCE; ENDOGENOUS SIRNAS; COLD-ACCLIMATION; LOW-TEMPERATURE; DRAFT SEQUENCE; HIGH-SALINITY; CROSS-TALK; SMALL RNAS;

D O I：

10.1111/j.1365-313X.2009.03835.x

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

P>The responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.

引用

页码：1068 / 1082

页数：15

共 78 条

[1] Alteration of stimulus-specific guard cell calcium oscillations and stomatal closing in Arabidopsis det3 mutant [J].

Allen, GJ ;

Chu, SP ;

Schumacher, K ;

Shimazaki, CT ;

Vafeados, D ;

Kemper, A ;

Hawke, SD ;

Tallman, G ;

Tsien, RY ;

Harper, JF ;

Chory, J ;

Schroeder, JI .

SCIENCE, 2000, 289 (5488) :2338-2342

[2] Reactive oxygen species: Metabolism, oxidative stress, and signal transduction [J].

Apel, K ;

Hirt, H .

ANNUAL REVIEW OF PLANT BIOLOGY, 2004, 55 :373-399

[3] Both abscisic acid (ABA)-dependent and ABA-independent pathways govern the induction of NCED3, AAO3 and ABA1 in response to salt stress [J].

Barrero, Jose Maria ;

Rodriguez, Pedro L. ;

Quesada, Victor ;

Piqueras, Pedro ;

Ponce, Maria Rosa ;

Micol, Jose Luis .

PLANT CELL AND ENVIRONMENT, 2006, 29 (10) :2000-2008

[4] Sorghum genome sequencing by methylation filtration [J].

Bedell, JA ;

Budiman, MA ;

Nunberg, A ;

Citek, RW ;

Robbins, D ;

Jones, J ;

Flick, E ;

Rohlfing, T ;

Fries, J ;

Bradford, K ;

McMenamy, J ;

Smith, M ;

Holeman, H ;

Roe, BA ;

Wiley, G ;

Korf, IF ;

Rabinowicz, PD ;

Lakey, N ;

McCombie, WR ;

Jeddeloh, JA ;

Martienssen, RA .

PLOS BIOLOGY, 2005, 3 (01) :103-115

[5] A comparison of normalization methods for high density oligonucleotide array data based on variance and bias [J].

Bolstad, BM ;

Irizarry, RA ;

Åstrand, M ;

Speed, TP .

BIOINFORMATICS, 2003, 19 (02) :185-193

[6] Large-scale identification of single-feature polymorphisms in complex genomes [J].

Borevitz, JO ;

Liang, D ;

Plouffe, D ;

Chang, HS ;

Zhu, T ;

Weigel, D ;

Berry, CC ;

Winzeler, E ;

Chory, J .

GENOME RESEARCH, 2003, 13 (03) :513-523

[7]

Breitling Rainer, 2005, Journal of Bioinformatics and Computational Biology, V3, P1171, DOI 10.1142/S0219720005001442

[8] Fast and sensitive multiple alignment of large genomic sequences -: art. no. 66 [J].

Brudno, M ;

Chapman, M ;

Göttgens, B ;

Batzoglou, S ;

Morgenstern, B .

BMC BIOINFORMATICS, 2003, 4 (1)

[9] Profiling a plant:: expression analysis in Arabidopsis [J].

Busch, Wolfgang ;

Lohmann, Jan U. .

CURRENT OPINION IN PLANT BIOLOGY, 2007, 10 (02) :136-141

[10] ULTRAPETALA1 encodes a SAND domain putative transcriptional regulator that controls shoot and floral meristem activity in Arabidopsis [J].

Carles, CC ;

Choffnes-Inada, D ;

Reville, K ;

Lertpiriyapong, K ;

Fletcher, JC .

DEVELOPMENT, 2005, 132 (05) :897-911

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