Abstract
Plants respond and adapt to drought, cold, and high-salinity stresses. Stress-inducible gene products function in the stress response and tolerance in plants. Using cDNA microarrays and oligonucleotide microarrays, stress-inducible genes have been identified in various plant species so far. Recently, tiling array technology has become a powerful tool for the whole-genome transcriptome analysis. We applied the Arabidopsis Affymetrix tiling arrays to study the whole-genome transcriptome under drought, cold, and high-salinity stresses and identified a large number of drought, cold, and high-salinity stress-inducible genes and transcriptional units (TUs).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Seki, M., Narusaka, M., Ishida, J., Nanjo, T., Fujita, M., Oono, Y., et al. (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold, and high-salinity stresses using a full-length cDNA microarray. Plant J 31, 279–292.
Kreps, J.A., Wu, Y., Chang, H.S., Zhu, T., Wang, X., and Harper, J.F. (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130, 2129–2141.
Yamada, K., Lim, J., Dale, J. M., Chen, H., Shinn, P., Palm, C. J., et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842–846.
Stolc, V., Samanta, M.P., Tongprasit, W., Sethi, H., Liang, S., Nelson, D. C., et al. (2005) Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci USA 102, 4453–4458.
Li, X., Wang, X., He, K., Ma, Y., Su, N., He, H., et al. (2008) High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation and gene expression.Plant Cell 20, 259–276.
Hanada, K., Zhang, X., Borevitz, J. O., Li, W. H., and Shiu, S. H. (2007) A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res 17, 632–640.
Laubinger, S., Zeller, G., Henz, S. R., Sachsenberg, T., Widmer, C. K., Naouar, N., et al. (2008) At-TAX: a whole-genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol 9, R112.
Clark, T. A., Sugnet, C. W., and Ares, M., Jr. (2002) Genome wide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296, 907–910.
Katou, Y., Kanoh, Y., Bando, M., Noguchi, H., Tanaka, H., Ashikari, T., et al. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424, 1078–1083.
Thibaud-Nissen, F., Wu, H., Richmond, T., Redman, J. C., Johnson, C., Green, R., et al. (2006) Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants. Plant J 47, 152–162.
Turck, F., Roudier, F., Farrona, S., Martin-Magniette, M. L., Guillaume, E., Buisine, N., et al. (2007) Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3, 855–866.
Bignell, G. R., Huang, J., Greshock, J., Watt, S., Butler, A., West, S., et al. (2004) High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 14, 287–295.
Ishkanian, A. S., Malloff, C. A., Watson, S. K., DeLeeuw, R. J., Chi, B., Coe, B. P., et al. (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36, 299–303.
Martienssen, R. A., Doerge, R. W., and Colot, V. (2005) Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Res 13, 299–308.
Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S. W., Chen. H., et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201.
Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., and Henikoff, S. (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39, 61–69.
Zhang, X., Clarenz, O., Cokus, S., Bernatavichute, Y. V., Pellegrini, M., Goodrich, J., et al. (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5, 1026–1035.
Li, X., Wang, X., He, K., Ma, Y., Su, N., He. H., et al. (2008) High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation and gene expression. Plant Cell 20, 259–276.
Matsui, A., Ishida, J., Morosawa, T., Mochizuki, Y., Kaminuma, E., Endo, T. A., et al. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol 49, 1135–1149.
Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193.
Toyoda, T. and Shinozaki, K. (2005) Tiling-array-driven elucidation of transcriptional structures based on maximum likelihood and Markov models. Plant J 43, 611–621.
Mann, H. B. and Whitney, D.R. (1947) On a test of whether one of two random variables is stochastically larger than the other. Annals of Mathematical Statistics 18, 50–60.
Storey, J. D. and Tibshirani, R. (2003) Statistical significance for genome-wide studies. Proc Natl Acad Sci USA 100, 9440–9445.
Bieniawska, Z., Espinoza, C., Schlereth, A., Sulpice, R., Hincha, D.K., and Hannah, M.A. (2008) Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol 147, 263–279.
Acknowledgments
This work was supported by a Grant-in-Aid for Scientific Research on Priority Areas “Systems Genomics” from MECSST and the President Discretionary Fund from RIKEN to M.S. It was also supported in part by a grant for Genome Research from RIKEN to K.S.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Humana Press
About this protocol
Cite this protocol
Matsui, A. et al. (2010). Arabidopsis Tiling Array Analysis to Identify the Stress-Responsive Genes. In: Sunkar, R. (eds) Plant Stress Tolerance. Methods in Molecular Biology, vol 639. Humana Press. https://doi.org/10.1007/978-1-60761-702-0_8
Download citation
DOI: https://doi.org/10.1007/978-1-60761-702-0_8
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-701-3
Online ISBN: 978-1-60761-702-0
eBook Packages: Springer Protocols