Kazuo Shinozaki

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. ncbi request reprint Gene networks involved in drought stress response and tolerance
    Kazuo Shinozaki
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 203 0045 Japan
    J Exp Bot 58:221-7. 2007
  2. doi request reprint Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis
    Yukio Kurihara
    Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama shi, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 376:553-7. 2008
  3. pmc Plasma membrane protein OsMCA1 is involved in regulation of hypo-osmotic shock-induced Ca2+ influx and modulates generation of reactive oxygen species in cultured rice cells
    Takamitsu Kurusu
    Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
    BMC Plant Biol 12:11. 2012
  4. pmc A flexible representation of omic knowledge for thorough analysis of microarray data
    Yoshikazu Hasegawa
    Phenome Informatics Team, Functional Genomics Research Group, Genomic Sciences Center, RIKEN, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan
    Plant Methods 2:5. 2006
  5. pmc Effects of abiotic stress on plants: a systems biology perspective
    Grant R Cramer
    Department of Biochemistry and Molecular Biology, Mail Stop 330, University of Nevada, Reno, Nevada 89557, USA
    BMC Plant Biol 11:163. 2011
  6. pmc A simple and high-sensitivity method for analysis of ubiquitination and polyubiquitination based on wheat cell-free protein synthesis
    Hirotaka Takahashi
    Cell Free Science and Technology Research Center, Ehime University, Matsuyama 790 8577, Japan
    BMC Plant Biol 9:39. 2009
  7. pmc Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila
    Teruaki Taji
    Faculty of Applied Bioscience, Tokyo University of Agriculture, 1 1 1 Sakuragaoka, Setagaya Ku, Tokyo 156 8502, Japan
    BMC Plant Biol 8:115. 2008
  8. pmc TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae
    Keiichi Mochida
    Plant Science Center, RIKEN, Yokohama 230 0045, Japan
    BMC Plant Biol 8:72. 2008
  9. pmc Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, Thellungiella halophila
    Teruaki Taji
    Faculty of Applied Bioscience, Tokyo University of Agriculture, 1 1 1 Sakuragaoka, Setagaya Ku, Tokyo 156 8502, Japan
    BMC Plant Biol 10:261. 2010
  10. pmc Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili
    Norihiro Futamura
    Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305 8687, Japan
    BMC Genomics 9:383. 2008

Detail Information

Publications126 found, 100 shown here

  1. ncbi request reprint Gene networks involved in drought stress response and tolerance
    Kazuo Shinozaki
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 203 0045 Japan
    J Exp Bot 58:221-7. 2007
    ..A description is also provided of how various genes involved in stress tolerance were applied in genetic engineering of dehydration stress tolerance in transgenic Arabidopsis plants...
  2. doi request reprint Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis
    Yukio Kurihara
    Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama shi, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 376:553-7. 2008
    ..Our study provided important information for understanding the relationship between RdDM and the identified candidate genes...
  3. pmc Plasma membrane protein OsMCA1 is involved in regulation of hypo-osmotic shock-induced Ca2+ influx and modulates generation of reactive oxygen species in cultured rice cells
    Takamitsu Kurusu
    Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
    BMC Plant Biol 12:11. 2012
    ..However, molecular bases and regulatory mechanisms for early osmotic signaling events remain poorly elucidated...
  4. pmc A flexible representation of omic knowledge for thorough analysis of microarray data
    Yoshikazu Hasegawa
    Phenome Informatics Team, Functional Genomics Research Group, Genomic Sciences Center, RIKEN, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan
    Plant Methods 2:5. 2006
    ..GSCope3 and BiKLi are available for academic users at our web site http://omicspace.riken.jp...
  5. pmc Effects of abiotic stress on plants: a systems biology perspective
    Grant R Cramer
    Department of Biochemistry and Molecular Biology, Mail Stop 330, University of Nevada, Reno, Nevada 89557, USA
    BMC Plant Biol 11:163. 2011
    ..New insights obtained from the integration of omics datasets are highlighted. Gaps in our knowledge are identified, providing additional focus areas for crop improvement research in the future...
  6. pmc A simple and high-sensitivity method for analysis of ubiquitination and polyubiquitination based on wheat cell-free protein synthesis
    Hirotaka Takahashi
    Cell Free Science and Technology Research Center, Ehime University, Matsuyama 790 8577, Japan
    BMC Plant Biol 9:39. 2009
    ..Here we demonstrate a novel, simple and high-sensitive method for in vitro analysis of ubiquitination and polyubiquitination based on wheat cell-free protein synthesis and luminescent detection...
  7. pmc Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila
    Teruaki Taji
    Faculty of Applied Bioscience, Tokyo University of Agriculture, 1 1 1 Sakuragaoka, Setagaya Ku, Tokyo 156 8502, Japan
    BMC Plant Biol 8:115. 2008
    ..Furthermore, Thellungiella not only shows tolerance to extreme salinity stress, but also to chilling, freezing, and ozone stress, supporting the use of Thellungiella as a good genomic resource in studies of abiotic stress tolerance...
  8. pmc TriMEDB: a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae
    Keiichi Mochida
    Plant Science Center, RIKEN, Yokohama 230 0045, Japan
    BMC Plant Biol 8:72. 2008
    ....
  9. pmc Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, Thellungiella halophila
    Teruaki Taji
    Faculty of Applied Bioscience, Tokyo University of Agriculture, 1 1 1 Sakuragaoka, Setagaya Ku, Tokyo 156 8502, Japan
    BMC Plant Biol 10:261. 2010
    ..halophila from various tissues and from whole plants treated with salinity, chilling, freezing stress, or ABA. We determined the DNA sequences of 20 000 cDNAs at both the 5'- and 3' ends, and identified 9569 distinct genes...
  10. pmc Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili
    Norihiro Futamura
    Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305 8687, Japan
    BMC Genomics 9:383. 2008
    ..japonica should help us to clarify the overall expression of genes during the process of pollen development, we constructed a full-length enriched cDNA library that was derived from male strobili at various developmental stages...
  11. pmc Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones
    Tokihiko Nanjo
    Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute FFPRI, 1 Matsunosato, Tsukuba, Ibaraki 305 8687 JAPAN
    BMC Genomics 8:448. 2007
    ..ESTs from full-length cDNA clones are especially powerful for accurate molecular annotation. We promoted collection and annotation of the ESTs from Populus full-length enriched cDNA clones as part of functional genomics of tree species...
  12. ncbi request reprint [Molecular mechanisms of abiotic stress responses: light and nutrient environment--overview]
    Kazuo Shinozaki
    Tanpakushitsu Kakusan Koso 52:585-6. 2007
  13. doi request reprint Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays
    Masanori Okamoto
    RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Plant J 62:39-51. 2010
    ..Our results suggest that transcription in Arabidopsis seeds is more complex and dynamic than previously thought...
  14. doi request reprint Arabidopsis tiling array analysis to identify the stress-responsive genes
    Akihiro Matsui
    Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Japan
    Methods Mol Biol 639:141-55. 2010
    ....
  15. pmc RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome
    Tetsuya Sakurai
    Bioinformatics Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Nucleic Acids Res 33:D647-50. 2005
    ..The RARGE web interface can be accessed at http://rarge.gsc.riken.jp/. Additionally, we report 90 000 new RAFL cDNA clones here...
  16. doi request reprint Transcriptome analyses revealed diverse expression changes in ago1 and hyl1 Arabidopsis mutants
    Yukio Kurihara
    Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    Plant Cell Physiol 50:1715-20. 2009
    ..The data in this paper are valuable for understanding the relationship between the miRNA pathway and its effect on transcriptomes...
  17. pmc Identification and expression analysis of cytokinin metabolic genes in soybean under normal and drought conditions in relation to cytokinin levels
    Dung Tien Le
    Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    PLoS ONE 7:e42411. 2012
    ....
  18. doi request reprint The Chloroplast Function Database: a large-scale collection of Arabidopsis Ds/Spm- or T-DNA-tagged homozygous lines for nuclear-encoded chloroplast proteins, and their systematic phenotype analysis
    Fumiyoshi Myouga
    RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Plant J 61:529-42. 2010
    ..psc.riken.jp/chloroplast/. The homozygous lines generated in this project are also available from the various Arabidopsis stock centers. We have donated the insertion homozygotes to their originating seed stock centers...
  19. pmc Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis
    Yukio Kurihara
    Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Proc Natl Acad Sci U S A 106:2453-8. 2009
    ..This finding demonstrates that one of the most important roles of NMD is the genome-wide suppression of the aberrant mlncRNAs including nat-RNAs...
  20. pmc Differential gene expression in soybean leaf tissues at late developmental stages under drought stress revealed by genome-wide transcriptome analysis
    Dung Tien Le
    Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    PLoS ONE 7:e49522. 2012
    ..This study has identified excellent drought-responsive candidate genes for in-depth characterization and future development of improved drought-tolerant transgenic soybeans...
  21. pmc Transcriptome analyses of a salt-tolerant cytokinin-deficient mutant reveal differential regulation of salt stress response by cytokinin deficiency
    Rie Nishiyama
    Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    PLoS ONE 7:e32124. 2012
    ..This study highlights the impact of CK regulation on the well-known stress-responsive signaling pathways, which regulate plant adaptation to high salinity as well as other environmental stresses...
  22. pmc Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1
    Taiko Kim To
    Plant Genomic Network Research Team, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    PLoS Genet 7:e1002055. 2011
    ..We propose that HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1, possibly recruiting MET1 to specific loci, thus forming the foundation of silent chromatin structure for subsequent non-CG methylation...
  23. ncbi request reprint Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays
    Youko Oono
    Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Funct Integr Genomics 6:212-34. 2006
    ..We compared genes that are regulated during deacclimation with those regulated during rehydration after dehydration to discuss the similarity and difference of each recovery process...
  24. doi request reprint Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana
    Jong Myong Kim
    Plant Functional Genomics Research Group, RIKEN Plant Science Center, Tsurumi ku, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 49:1580-8. 2008
    ....
  25. pmc A heterocomplex of iron superoxide dismutases defends chloroplast nucleoids against oxidative stress and is essential for chloroplast development in Arabidopsis
    Fumiyoshi Myouga
    Gene Discovery Research Group, RIKEN Plant Science Center, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Plant Cell 20:3148-62. 2008
    ..We propose that heteromeric FSD2 and FSD3 act as ROS scavengers in the maintenance of early chloroplast development by protecting the chloroplast nucleoids from ROS...
  26. pmc Phenome analysis in plant species using loss-of-function and gain-of-function mutants
    Takashi Kuromori
    Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    Plant Cell Physiol 50:1215-31. 2009
    ..In this review, the present status of mutant resources for large-scale studies of gene function in plant research and the current perspective on using loss-of-function and gain-of-function mutants in phenome research will be discussed...
  27. ncbi request reprint RARTF: database and tools for complete sets of Arabidopsis transcription factors
    Kei Iida
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Japan
    DNA Res 12:247-56. 2005
    ..We will report expression profiles of all transcription factor genes in various plant tissues under various stress and hormone conditions in the near future...
  28. doi request reprint Arabidopsis HDA6 is required for freezing tolerance
    Taiko Kim To
    Plant Genomic Network Research Team, RIKEN Plant Science Center, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 406:414-9. 2011
    ..We conclude that HDA6 plays a critical role in regulating cold acclimation process that confers freezing resistance on Arabidopsis...
  29. pmc Genome-wide analysis of two-component systems and prediction of stress-responsive two-component system members in soybean
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 17:303-24. 2010
    ..In addition, we provide a new resource for studying the conservation and divergence among the TCSs within plant species and/or between plants and other organisms...
  30. doi request reprint Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array
    Akihiro Matsui
    Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 49:1135-49. 2008
    ....
  31. ncbi request reprint CYP707A3, a major ABA 8'-hydroxylase involved in dehydration and rehydration response in Arabidopsis thaliana
    Taishi Umezawa
    Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Plant J 46:171-82. 2006
    ..Taken together, our results indicate that CYP707A3 plays an important role in determining threshold levels of ABA during dehydration and after rehydration...
  32. pmc Arabidopsis AHP2, AHP3, and AHP5 histidine phosphotransfer proteins function as redundant negative regulators of drought stress response
    Rie Nishiyama
    Signaling Pathway Research Unit, RIKEN Plant Science Center, Yokohama, 230 0045, Japan
    Proc Natl Acad Sci U S A 110:4840-5. 2013
    ..The knowledge gained from this study also has broad potential for biotechnological applications to increase abiotic stress tolerance in plants...
  33. ncbi request reprint Expression and interaction analysis of Arabidopsis Skp1-related genes
    Naoki Takahashi
    Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suyehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 45:83-91. 2004
    ..Both histochemical and RT-PCR analysis of eight ASK genes expression revealed unique expression patterns for the respective genes...
  34. doi request reprint Origin and evolution of genes related to ABA metabolism and its signaling pathways
    Kousuke Hanada
    Gene Discovery Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    J Plant Res 124:455-65. 2011
    ..Taken together, these results suggest that expansion of the gene families related to ABA signaling pathways may have contributed to the sophisticated stress tolerance mechanisms of higher land plants...
  35. pmc PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation
    Tetsuya Sakurai
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Japan
    Plant Cell Physiol 54:e5. 2013
    ..PRIMeLink offers a bi-directional searchable function, from the gene and the metabolite perspective, to search for targets seamlessly and effectively...
  36. doi request reprint The Chloroplast Function Database II: a comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins
    Fumiyoshi Myouga
    RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    Plant Cell Physiol 54:e2. 2013
    ..It can be freely accessed at http://rarge.psc.riken.jp/chloroplast/...
  37. pmc Transcriptome analysis using a high-density oligomicroarray under drought stress in various genotypes of cassava: an important tropical crop
    Yoshinori Utsumi
    Plant Genomic Network Research Team, RIKEN Plant Science Center, Tsurumi ku, Yokohama, Kanagawa, Japan
    DNA Res 19:335-45. 2012
    ..These results demonstrate that our microarray is a useful tool for analysing the cassava transcriptome and that it is applicable for various cassava genotypes...
  38. pmc Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana
    Keiko Yonekura-Sakakibara
    RIKEN Plant Science Center, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Plant J 69:154-67. 2012
    ..These data suggest major routes from cyanidin 3-O-glucoside to the most highly modified cyanidin in the potential intricate anthocyanin modification pathways in Arabidopsis...
  39. pmc Analysis of cytokinin mutants and regulation of cytokinin metabolic genes reveals important regulatory roles of cytokinins in drought, salt and abscisic acid responses, and abscisic acid biosynthesis
    Rie Nishiyama
    RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Plant Cell 23:2169-83. 2011
    ....
  40. pmc In silico analysis of transcription factor repertoires and prediction of stress-responsive transcription factors from six major gramineae plants
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 18:321-32. 2011
    ....
  41. doi request reprint Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources
    Masami Yokota Hirai
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    J Plant Res 123:291-8. 2010
    ..In this paper, we release approximately 3,000 metabolic profiles obtained by targeted analysis for 36 metabolites and discuss the possible regulation of amino acid accumulation...
  42. ncbi request reprint PRIMe: a Web site that assembles tools for metabolomics and transcriptomics
    Kenji Akiyama
    RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    In Silico Biol 8:339-45. 2008
    ....
  43. pmc Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences
    Kei Iida
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Nucleic Acids Res 32:5096-103. 2004
    ..In particular, cold-stress conditions affected alternative splicing profiles. The change in alternative splicing profiles under cold stress may be mediated by alternative splicing and transcriptional regulation of splicing factors...
  44. doi request reprint Potential utilization of NAC transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach
    Lam Son Phan Tran
    RIKEN Plant Science Center, Signaling Pathway Research Unit, Suehiro cho, Tsurumi, Yokohama, Kanagawa, Japan
    GM Crops 1:32-9. 2010
    ..In this review the NAC TF family will be described and the potential use of NAC TFs in development of improved stress tolerant transgenic crops will be discussed...
  45. pmc Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads
    Shuji Kawaguchi
    Bioinformatics and Systems Engineering Division, RIKEN Yokohama Institute, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    Bioinformatics 28:929-37. 2012
    ..However, problems of high-level noises and biases still remain and interrupt the reconstruction. A method is required that is robust against noise and bias and correctly reconstructs transcripts regardless of equipment used...
  46. pmc In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 16:353-69. 2009
    ..This study provides a basic framework and an important user-friendly public information resource which enables analyses of transcriptional regulation in soybean...
  47. pmc Increased expression and protein divergence in duplicate genes is associated with morphological diversification
    Kousuke Hanada
    Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    PLoS Genet 5:e1000781. 2009
    ..thaliana had not experienced expression or protein divergence that resulted in morphological diversification. These results indicate that most duplicate genes have experienced minor functionalization...
  48. ncbi request reprint A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis
    Takashi Kuromori
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Plant J 37:897-905. 2004
    ..gsc.riken.go.jp/) and are depositing these lines in the RIKEN BioResource Center as available resources (http://www.brc.riken.go.jp/Eng/)...
  49. ncbi request reprint An Arabidopsis chloroplast-targeted Hsp101 homologue, APG6, has an essential role in chloroplast development as well as heat-stress response
    Fumiyoshi Myouga
    Plant Functional Genomics Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Plant J 48:249-60. 2006
    ..The APG6 protein is not only involved in heat-stress response in chloroplasts, but is also essential for chloroplast development...
  50. doi request reprint sORF finder: a program package to identify small open reading frames with high coding potential
    Kousuke Hanada
    Plant Science Center, RIKEN, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Bioinformatics 26:399-400. 2010
    ....
  51. pmc Genome-wide expression profiling of soybean two-component system genes in soybean root and shoot tissues under dehydration stress
    Dung Tien Le
    Signaling Pathway Research Unit, Plant Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi, Yokohama, Japan
    DNA Res 18:17-29. 2011
    ....
  52. pmc RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function
    Tetsuya Sakurai
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045 Japan
    Plant Cell Physiol 52:265-73. 2011
    ..The RiceFOX database is available at http://ricefox.psc.riken.jp/...
  53. pmc Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response
    Tetsuya Sakurai
    Metabolomics Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    BMC Plant Biol 7:66. 2007
    ..A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs)...
  54. ncbi request reprint Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future
    Taishi Umezawa
    Gene Discovery Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Yokohama, Kanagawa 203 0045, Japan
    Curr Opin Biotechnol 17:113-22. 2006
    ..Recent studies have increased our understanding of the regulatory networks controlling the drought stress response and have led to practical approaches for engineering drought tolerance in plants...
  55. pmc Genome-wide discovery and information resource development of DNA polymorphisms in cassava
    Tetsuya Sakurai
    RIKEN Center for Sustainable Resource Science, Tsurumi ku, Yokohama, Kanagawa, Japan
    PLoS ONE 8:e74056. 2013
    ..All data on the discovered DNA polymorphisms were organized into the Cassava Online Archive database, which is available at http://cassava.psc.riken.jp/. ..
  56. pmc Genomics and bioinformatics resources for crop improvement
    Keiichi Mochida
    RIKEN Plant Science Center, Yokohama, 230 0045 Japan
    Plant Cell Physiol 51:497-523. 2010
    ..We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology...
  57. ncbi request reprint RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    J Exp Bot 55:213-23. 2004
    ..In this review, recent progress on transcriptome analysis using the RAFL cDNA microarray is highlighted...
  58. doi request reprint The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access
    Hideki Goda
    RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    Plant J 55:526-42. 2008
    ..The data set presented here will be a versatile resource for future hormone studies, and constitutes a reference for genome-wide gene expression in Arabidopsis...
  59. pmc TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    DNA Res 20:151-62. 2013
    ....
  60. doi request reprint Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum
    Eisuke Chikayama
    Metabolome Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Anal Chem 82:1653-8. 2010
    ..It enables simultaneous annotation of more than 200 candidate metabolites from the single (13)C-HSQC (heteronuclear single quantum coherence) NMR spectrum of a single sample of cell extract...
  61. doi request reprint Homologous chromosome pairing is completed in crossover defective atzip4 mutant
    Takashi Kuromori
    Gene Discovery Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 370:98-103. 2008
    ..The relationship of AtZIP4 and other related proteins in meiotic events is discussed and compared with that in yeast...
  62. pmc Advances in omics and bioinformatics tools for systems analyses of plant functions
    Keiichi Mochida
    RIKEN Biomass Engineering Program, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 52:2017-38. 2011
    ..From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances...
  63. pmc Evolutionary persistence of functional compensation by duplicate genes in Arabidopsis
    Kousuke Hanada
    Gene Discovery Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Biol Evol 2009:409-14. 2009
    ..Taken together, we conclude that duplicate genes contribute to genetic robustness mainly by preserving compensation for severe phenotypic effects in A. thaliana...
  64. ncbi request reprint Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks
    Miki Fujita
    Gene Discovery Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Yokohama, Kanagawa 203 0045, Japan
    Curr Opin Plant Biol 9:436-42. 2006
    ....
  65. doi request reprint Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs
    Motoaki Seki
    Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, RIKEN Yokohama Institute, Yokohama 230 0045, Japan
    J Plant Res 122:355-66. 2009
    ..The RAFL cDNA collection was also used for determination of the domain structure of proteins by NMR. In this review, we summarize the present state and perspectives of functional genomics using RAFL cDNAs...
  66. doi request reprint LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors
    Keiichi Mochida
    Plant Science Center, Gene Discovery Research Group, RIKEN, Yokohama 230 0045 Japan
    Bioinformatics 26:290-1. 2010
    ..AVAILABILITY: http://legumetfdb.psc.riken.jp/. SUPPLEMENTARY INFORMATION: Supplementary data available at Bioinformatics online...
  67. pmc Correlation exploration of metabolic and genomic diversity in rice
    Keiichi Mochida
    RIKEN Plant Science Center, 1 7 22, Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    BMC Genomics 10:568. 2009
    ..To assess the correlative relationship between the metabolic and genomic diversity found in rice accessions, we compared the distance matrices for these two "omics" patterns in the rice accessions...
  68. pmc Zinc finger protein STOP1 is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance
    Satoshi Iuchi
    BioResources Center, RIKEN, 3 1 1 Koyadai, Tsukuba, Ibaraki 305 0074, Japan
    Proc Natl Acad Sci U S A 104:9900-5. 2007
    ..There was no induction of AtALMT1 by Al(3+) treatment in the stop1 mutant. These results indicate that STOP1 plays a critical role in Arabidopsis tolerance to major stress factors in acid soils...
  69. pmc Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops
    Keiichi Mochida
    RIKEN Biomass Engineering Program, Yokohama 230 0045, Japan
    Plant Cell Physiol 52:785-803. 2011
    ..Furthermore, the insights obtained should be transferable to investigations of Triticeae plants. The associated data set generated in this analysis is publicly accessible at http://coexpression.psc.riken.jp/barley/...
  70. ncbi request reprint A novel ethanol-hypersensitive mutant of Arabidopsis
    Takashi Hirayama
    Graduate School of Integrated Science, Yokohama City University, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 45:703-11. 2004
    ....
  71. pmc Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana
    Kousuke Hanada
    Plant Science Center, RIKEN, Yokohama, Kanagawa, Japan
    Mol Biol Evol 28:377-82. 2011
    ..In conclusion, recently duplicated genes play an important role in the compensation of metabolic products only when the number of alternative pathways is small...
  72. ncbi request reprint Armadillo repeat-containing kinesins and a NIMA-related kinase are required for epidermal-cell morphogenesis in Arabidopsis
    Tatsuya Sakai
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Plant J 53:157-71. 2008
    ..We discuss the function of NIMA-related protein kinases and armadillo repeat-containing kinesins in the cell morphogenesis of eukaryotes...
  73. pmc Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: coarse grained views of metabolic pathways
    Eisuke Chikayama
    RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
    PLoS ONE 3:e3805. 2008
    ..Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems...
  74. pmc MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites
    Fumio Matsuda
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Plant J 57:555-77. 2009
    ..Thus, non-targeted metabolic profiling analysis using MS2T annotation methods could prove to be useful for investigating novel functions of secondary metabolites in plants...
  75. ncbi request reprint Classification and expression analysis of Arabidopsis F-box-containing protein genes
    Hirofumi Kuroda
    Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suyehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045 Japan
    Plant Cell Physiol 43:1073-85. 2002
    ..Macro array analysis showed that several F-box protein genes are expressed in a tissue-specific manner...
  76. pmc Role of cytokinin responsive two-component system in ABA and osmotic stress signalings
    Lam Son Phan Tran
    RIKEN Plant Science Center, Signaling Pathway Research Unit, Tsurumi, Yokohama, Japan
    Plant Signal Behav 5:148-50. 2010
    ....
  77. doi request reprint Arabidopsis mutants of AtABCG22, an ABC transporter gene, increase water transpiration and drought susceptibility
    Takashi Kuromori
    Gene Discovery Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro, Tsurumi ku, Yokohama 230 0045, Japan
    Plant J 67:885-94. 2011
    ..Also, the atabcg22 mutation enhanced the phenotype of nced3 mutants, which were defective in ABA biosynthesis. Accordingly, the additive roles of AtABCG22 functions in ABA signalling and ABA biosynthesis are discussed...
  78. ncbi request reprint A combination of the Arabidopsis DREB1A gene and stress-inducible rd29A promoter improved drought- and low-temperature stress tolerance in tobacco by gene transfer
    Mie Kasuga
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, 1 1 Ohwashi, Tsukuba, Ibaraki, 305 8686 Japan
    Plant Cell Physiol 45:346-50. 2004
    ..These results indicate that a combination of the rd29A promoter and DREB1A is useful for improvement of various kinds of transgenic plants that are tolerant to environmental stress...
  79. ncbi request reprint A novel Arabidopsis gene TONSOKU is required for proper cell arrangement in root and shoot apical meristems
    Takamasa Suzuki
    Laboratory of Biochemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Furo cho, Chikusa, Nagoya 464 8601, Japan
    Plant J 38:673-84. 2004
    ....
  80. pmc Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter
    Lam Son Phan Tran
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305 8686, Japan
    Plant Cell 16:2481-98. 2004
    ..However, erd1 was not upregulated in the transgenic plants. Other interacting factors may be necessary for the induction of erd1 in Arabidopsis under stress conditions...
  81. pmc In planta functions of the Arabidopsis cytokinin receptor family
    Masayuki Higuchi
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Proc Natl Acad Sci U S A 101:8821-6. 2004
    ..These results confirm that cytokinins are a pivotal class of plant growth regulators but provide no evidence that cytokinins are required for the processes of gametogenesis and embryogenesis...
  82. ncbi request reprint Quantitative trait loci analysis of nitrate storage in Arabidopsis leading to an investigation of the contribution of the anion channel gene, AtCLC-c, to variation in nitrate levels
    Hisatomi Harada
    National Institute of Livestock and Grassland Science, 768, Senbonmatsu, NASU, Tochigi, 329 2793, Japan
    J Exp Bot 55:2005-14. 2004
    ..These and published results suggest that multiple genes affect nitrate concentrations in plants and that AtCLC-c and other members of the AtCLC gene family play some role in this...
  83. ncbi request reprint A novel Arabidopsis gene required for ethanol tolerance is conserved among plants and archaea
    Naoko Fujishige
    Graduate School of Integrated Science, Yokohama City University, Yokohama, 230 0045 Japan
    Plant Cell Physiol 45:659-66. 2004
    ..These results might suggest that plants, and presumably archaea, have a novel mechanism for protection from acetaldehyde toxicity...
  84. pmc Comparative genomics in salt tolerance between Arabidopsis and aRabidopsis-related halophyte salt cress using Arabidopsis microarray
    Teruaki Taji
    Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, Tsukuba, Ibaraki 305 0074, Japan
    Plant Physiol 135:1697-709. 2004
    ..Stress tolerance of salt cress may be due to constitutive overexpression of many genes that function in stress tolerance and that are stress inducible in Arabidopsis...
  85. ncbi request reprint DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression
    Yoh Sakuma
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki, 305 8686, Japan
    Biochem Biophys Res Commun 290:998-1009. 2002
    ..The DREB subfamily included three novel DREB1A- and six DREB2A-related proteins. We analyzed expression of novel genes for these proteins and discuss their roles in stress-responsive gene expression...
  86. ncbi request reprint Overexpression of LSH1, a member of an uncharacterised gene family, causes enhanced light regulation of seedling development
    Li Zhao
    Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN Yokohama Institute 1 7 22 Suyehirocho, Tsurumiku, Yokohama 230 0045, Kanagawa, Japan
    Plant J 37:694-706. 2004
    ..These results indicate that LSH1 is functionally dependent on phytochrome to mediate light regulation of seedling development...
  87. ncbi request reprint Functional annotation of a full-length Arabidopsis cDNA collection
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center GSC, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Science 296:141-5. 2002
    ..Furthermore, the full-length cDNAs are useful resources for analyses of the expression profiles, functions, and structures of plant proteins...
  88. ncbi request reprint [Morphological changes responding to abiotic environmental stress]
    Tokihiko Nanjo
    Tanpakushitsu Kakusan Koso 47:1684-9. 2002
  89. pmc Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling
    Hiroshi Abe
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant Cell 15:63-78. 2003
    ..These results indicate that both AtMYC2 and AtMYB2 proteins function as transcriptional activators in ABA-inducible gene expression under drought stress in plants...
  90. ncbi request reprint OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression
    Joseph G Dubouzet
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant J 33:751-63. 2003
    ..OsDREB1A is potentially useful for producing transgenic monocots that are tolerant to drought, high-salt, and/or cold stresses...
  91. ncbi request reprint Identification of photorespiratory glutamate:glyoxylate aminotransferase (GGAT) gene in Arabidopsis
    Daisuke Igarashi
    Institute of Life Sciences, Ajinomoto Co, Inc, 1 1 Suzuki cho, Kawasaki 210 8681, Japan
    Plant J 33:975-87. 2003
    ..Based on these results, it was concluded that AOAT1 is targeted to peroxisomes, functions as a photorespiratory GGAT, plays a markedly important role for plant growth and the metabolism of amino acids...
  92. ncbi request reprint Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses
    Yoshihiro Narusaka
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant J 34:137-48. 2003
    ..These results indicate that DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A gene in response to ABA in Arabidopsis...
  93. ncbi request reprint The cDNA microarray analysis using an Arabidopsis pad3 mutant reveals the expression profiles and classification of genes induced by Alternaria brassicicola attack
    Yoshihiro Narusaka
    Kobe University Graduate School of Science and Technology, 1 1 Rokkodai cho, Nada Ku, Kobe, 657 8501 Japan
    Plant Cell Physiol 44:377-87. 2003
    ..brassicicola. Furthermore, the plants integrate two or more signals that act together for promoting the induction of multiple defense pathways...
  94. ncbi request reprint Identification of Arabidopsis genes regulated by high light-stress using cDNA microarray
    Mitsuhiro Kimura
    Plant Function Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomics Sciences Center, Yokohama, Kanagawa, Japan
    Photochem Photobiol 77:226-33. 2003
    ..These genes include RD29A, ERD7, ERD10, KIN1, LEA14 and COR15a, most of which are thought to be involved in the protection of cellular components...
  95. ncbi request reprint Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca 7000 full-length cDNA microarray
    Youko Oono
    Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Plant J 34:868-87. 2003
    ..Functional analysis of rehydration-inducible and rehydration-repressed genes revealed their functions not only in the release from a stressed status but also in the recovery of growth in plants...
  96. ncbi request reprint Empirical analysis of transcriptional activity in the Arabidopsis genome
    Kayoko Yamada
    Plant Gene Expression Center, Albany, CA 94710, USA
    Science 302:842-6. 2003
    ..This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome...
  97. ncbi request reprint [Arabidopsis functional genomics using full-length cDNAs]
    Motoaki Seki
    Tanpakushitsu Kakusan Koso 48:1890-8. 2003
  98. pmc Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses
    M Ashiq Rabbani
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, 1 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant Physiol 133:1755-67. 2003
    ..Transcriptome analysis revealed novel stress-inducible genes, suggesting some differences between Arabidopsis and rice in their response to stress...
  99. ncbi request reprint Important roles of drought- and cold-inducible genes for galactinol synthase in stress tolerance in Arabidopsis thaliana
    Teruaki Taji
    Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3 1 1 Koyadai, Tsukuba, Ibaraki 305 0074, Japan
    Plant J 29:417-26. 2002
    ....
  100. ncbi request reprint Cloning and functional analysis of a novel DREB1/CBF transcription factor involved in cold-responsive gene expression in Zea mays L
    Feng Qin
    Department of Biological Sciences and Biotechnology, Tsinghua University, 100084 Beijing, China
    Plant Cell Physiol 45:1042-52. 2004
    ..ZmDREB1A is suggested to be potentially useful for producing transgenic plants that is tolerant to drought, high-salinity and/or cold stresses...
  101. ncbi request reprint Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice
    Kazuo Nakashima
    Biological Resources Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305 8686, Japan
    Plant J 51:617-30. 2007
    ..We conclude that OsNAC6 may serve as a useful biotechnological tool for the improvement of stress tolerance in various kinds of plants...