9 results on '"Natsuki Hayami"'
Search Results
2. Transcriptome Analysis and Identification of a Transcriptional Regulatory Network in the Response to H2O2
- Author
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Takashi Hirayama, Mika Nomoto, Yoshiharu Y. Yamamoto, Mieko Higuchi-Takeuchi, Ayaka Hieno, Hiroyuki Koyama, Minami Matsui, Yasuomi Tada, Takashi Yokogawa, Kosuke Hanada, Keiko Inaba-Hasegawa, Tomoko Yokogawa, Yuko Hojo, Yoko Ikeda, Kazutaka Kusunoki, Nobutaka Mitsuda, Natsuki Hayami, and Hushna Ara Naznin
- Subjects
0106 biological sciences ,Physiology ,Arabidopsis ,Regulator ,Plant Science ,01 natural sciences ,Transcriptome ,chemistry.chemical_compound ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Genetics ,Gene Regulatory Networks ,Promoter Regions, Genetic ,Gene ,Abscisic acid ,Transcription factor ,biology ,Arabidopsis Proteins ,Abiotic stress ,Gene Expression Profiling ,fungi ,food and beverages ,Hydrogen Peroxide ,Oxidants ,biology.organism_classification ,Cell biology ,Crosstalk (biology) ,chemistry ,Seedlings ,Salicylic Acid ,Research Article ,Abscisic Acid ,Signal Transduction ,Transcription Factors ,010606 plant biology & botany - Abstract
Hydrogen peroxide (H(2)O(2)) is a common signal molecule initiating transcriptional responses to all the known biotic and abiotic stresses of land plants. However, the degree of involvement of H(2)O(2) in these stress responses has not yet been well studied. Here we identify time-dependent transcriptome profiles stimulated by H(2)O(2) application in Arabidopsis (Arabidopsis thaliana) seedlings. Promoter prediction based on transcriptome data suggests strong crosstalk among high light, heat, and wounding stress responses in terms of environmental stresses and between the abscisic acid (ABA) and salicylic acid (SA) responses in terms of phytohormone signaling. Quantitative analysis revealed that ABA accumulation is induced by H(2)O(2) but SA is not, suggesting that the implied crosstalk with ABA is achieved through ABA accumulation while the crosstalk with SA is different. We identified potential direct regulatory pairs between regulator transcription factor (TF) proteins and their regulated TF genes based on the time-course transcriptome analysis for the H(2)O(2) response, in vivo regulation of the regulated TF by the regulator TF identified by expression analysis of mutants and overexpressors, and in vitro binding of the regulator TF protein to the target TF promoter. These analyses enabled the establishment of part of the transcriptional regulatory network for the H(2)O(2) response composed of 15 regulatory pairs of TFs, including five pairs previously reported. This regulatory network is suggested to be involved in a wide range of biotic and abiotic stress responses in Arabidopsis.
- Published
- 2019
3. Nobel Prizes for Research in Plant Science: Past, Present and Future
- Author
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Natsuki Hayami and Sachi Sri Kantha
- Subjects
General Agricultural and Biological Sciences - Published
- 2017
4. Prediction of bipartite transcriptional regulatory elements using transcriptome data of Arabidopsis
- Author
-
Hiroyuki Koyama, Mutsutomo Tokizawa, Ayaka Hieno, Mika Nomoto, Yoshiharu Y. Yamamoto, Hiroyuki Ichida, Yasuomi Tada, Natsuki Hayami, Kazutaka Kusunoki, and Daichi Obata
- Subjects
0106 biological sciences ,0301 basic medicine ,Transcriptional Regulatory Elements ,plant genome ,Arabidopsis ,Computational biology ,Bioinformatics ,01 natural sciences ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Genetics ,Binding site ,Promoter Regions, Genetic ,Molecular Biology ,Transcription factor ,biology ,Arabidopsis Proteins ,General Medicine ,Genomics ,Full Papers ,biology.organism_classification ,030104 developmental biology ,promoter prediction ,Bipartite graph ,True positive rate ,010606 plant biology & botany ,Transcription Factors - Abstract
In our previous study, a methodology was established to predict transcriptional regulatory elements in promoter sequences using transcriptome data based on a frequency comparison of octamers. Some transcription factors, including the NAC family, cannot be covered by this method because their binding sequences have non-specific spacers in the middle of the two binding sites. In order to remove this blind spot in promoter prediction, we have extended our analysis by including bipartite octamers that are composed of ‘4 bases—a spacer with a flexible length—4 bases’. 8,044 pre-selected bipartite octamers, which had an overrepresentation of specific spacer lengths in promoter sequences and sequences related to core elements removed, were subjected to frequency comparison analysis. Prediction of ER stress-responsive elements in the BiP/BiPL promoter and an ANAC017 target sequence resulted in precise detection of true positives, judged by functional analyses of a reported article and our own in vitro protein–DNA binding assays. These results demonstrate that incorporation of bipartite octamers with continuous ones improves promoter prediction significantly.
- Published
- 2016
5. The Responses of Arabidopsis Early Light-Induced Protein2 to Ultraviolet B, High Light, and Cold Stress Are Regulated by a Transcriptional Regulatory Unit Composed of Two Elements
- Author
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Mutsutomo Tokizawa, Natsuki Hayami, Mitsuhiro Kimura, Yukio Kurihara, Satoshi Iuchi, Mika Nomoto, Minami Matsui, Yusaku Sakai, Yasuomi Tada, Yoshiharu Y. Yamamoto, and Tatsunori Saito
- Subjects
Zipper ,Transcription, Genetic ,Physiology ,Ultraviolet Rays ,Mutant ,Arabidopsis ,Plant Science ,Gene Expression Regulation, Plant ,Stress, Physiological ,Botany ,Genetics ,Arabidopsis thaliana ,Histone octamer ,Luciferases ,Promoter Regions, Genetic ,Transcription factor ,Oligonucleotide Array Sequence Analysis ,biology ,Models, Genetic ,Arabidopsis Proteins ,Gene Expression Profiling ,Nuclear Proteins ,Promoter ,Articles ,biology.organism_classification ,In vitro ,Cell biology ,Circadian Rhythm ,Cold Temperature ,Basic-Leucine Zipper Transcription Factors ,Organ Specificity ,Protein Binding - Abstract
The Arabidopsis (Arabidopsis thaliana) Early Light-Induced Protein (ELIP) is thought to act as a photoprotectant, reducing the damaging effects of high light (HL). Expression of ELIP2 is activated by multiple environmental stresses related to photoinhibition. We have identified putative regulatory elements in an ELIP2 promoter using an octamer-based frequency comparison method, analyzed the role of these elements using synthetic promoters, and revealed a key transcriptional regulatory unit for ultraviolet B (UV-B) radiation, HL, and cold stress responses. The unit is composed of two elements, designated as Elements A (TACACACC) and B (GGCCACGCCA), and shows functionality only when paired. Our genome-wide correlation analysis between possession of these elements in the promoter region and expression profiles in response to UV-B, HL, and cold suggests that Element B receives and integrates these multiple stress signals. In vitro protein-DNA binding assays revealed that LONG HYPOCOTYL5 (HY5), a basic domain-Leucine zipper transcription factor, directly binds to Element B. In addition, mutant analysis of HY5 showed partial involvement in the UV-B and HL responses but not in the cold stress response. These results suggest that signals for UV-B, HL, and cold stress join at Element B, which recognizes the signals of multiple transcription factors, including HY5.
- Published
- 2015
6. Transcriptome Analysis and Identification of a Transcriptional Regulatory Network in the Response to H2O2.
- Author
-
Ayaka Hieno, Hushna Ara Naznin, Keiko Inaba-Hasegawa, Tomoko Yokogawa, Natsuki Hayami, Mika Nomoto, Yasuomi Tada, Takashi Yokogawa, Mieko Higuchi-Takeuchi, Kosuke Hanada, Minami Matsui, Yoko Ikeda, Yuko Hojo, Takashi Hirayama, Kazutaka Kusunoki, Hiroyuki Koyama, Nobutaka Mitsuda, and Yamamoto, Yoshiharu Y.
- Published
- 2019
- Full Text
- View/download PDF
7. Prediction of bipartite transcriptional regulatory elements using transcriptome data of Arabidopsis.
- Author
-
Yamamoto, Yoshiharu Y., Hiroyuki Ichida, Ayaka Hieno, Daichi Obata, Mutsutomo Tokizawa, Mika Nomoto, Yasuomi Tada, Kazutaka Kusunoki, Hiroyuki Koyama, and Natsuki Hayami
- Abstract
In our previous study, a methodology was established to predict transcriptional regulatory elements in promoter sequences using transcriptome data based on a frequency comparison of octamers. Some transcription factors, including the NAC family, cannot be covered by this method because their binding sequences have non-specific spacers in the middle of the two binding sites. In order to remove this blind spot in promoter prediction, we have extended our analysis by including bipartite octamers that are composed of '4 bases--a spacer with a flexible length--4 bases'. 8,044 pre-selected bipartite octamers, which had an overrepresentation of specific spacer lengths in promoter sequences and sequences related to core elements removed, were subjected to frequency comparison analysis. Prediction of ER stress-responsive elements in the BiP/BiPL promoter and an ANAC017 target sequence resulted in precise detection of true positives, judged by functional analyses of a reported article and our own in vitro protein-DNA binding assays. These results demonstrate that incorporation of bipartite octamers with continuous ones improves promoter prediction significantly. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
8. The Responses of Arabidopsis Early Light-Induced Protein2 to Ultraviolet B, High Light, and Cold Stress Are Regulated by a Transcriptional Regulatory Unit Composed of Two Elements.
- Author
-
Natsuki Hayami, Yusaku Sakai, Mitsuhiro Kimura, Tatsunori Saito, Mutsutomo Tokizawa, Satoshi Iuchi, Yukio Kurihara, Minami Matsui, Mika Nomoto, Yasuomi Tada, and Yamamoto, Yoshiharu Y.
- Subjects
- *
ARABIDOPSIS thaliana , *PLANT proteins , *PROMOTERS (Genetics) , *GENETIC transcription in plants , *EFFECT of ultraviolet radiation on plants , *EFFECT of light on plants , *EFFECT of cold on plants , *LEUCINE zippers , *PHYSIOLOGY - Abstract
The Arabidopsis (Arabidopsis thaliana) Early Light-Induced Protein (ELIP) is thought to act as a photoprotectant, reducing the damaging effects of high light (HL). Expression of ELIP2 is activated by multiple environmental stresses related to photoinhibition. We have identified putative regulatory elements in an ELIP2 promoter using an octamer-based frequency comparison method, analyzed the role of these elements using synthetic promoters, and revealed a key transcriptional regulatory unit for ultraviolet B (UV-B) radiation, HL, and cold stress responses. The unit is composed of two elements, designated as Elements A (TACACACC) and B (GGCCACGCCA), and shows functionality only when paired. Our genome-wide correlation analysis between possession of these elements in the promoter region and expression profiles in response to UV-B, HL, and cold suggests that Element B receives and integrates these multiple stress signals. In vitro protein-DNA binding assays revealed that LONG HYPOCOTYL5 (HY5), a basic domain-Leucine zipper transcription factor, directly binds to Element B. In addition, mutant analysis of HY5 showed partial involvement in the UV-B and HL responses but not in the cold stress response. These results suggest that signals for UV-B, HL, and cold stress join at Element B, which recognizes the signals of multiple transcription factors, including HY5. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
9. Transcriptome Analysis and Identification of a Transcriptional Regulatory Network in the Response to H2O2.
- Author
-
Ayaka Hieno, Hushna Ara Naznin, Keiko Inaba-Hasegawa, Tomoko Yokogawa, Natsuki Hayami, Mika Nomoto, Yasuomi Tada, Takashi Yokogawa, Mieko Higuchi-Takeuchi, Kosuke Hanada, Minami Matsui, Yoko Ikeda, Yuko Hojo, Takashi Hirayama, Kazutaka Kusunoki, Hiroyuki Koyama, Nobutaka Mitsuda, and Yamamoto, Yoshiharu Y.
- Abstract
Hydrogen peroxide (H2O2) is a common signal molecule initiating transcriptional responses to all the known biotic and abiotic stresses of land plants. However, the degree of involvement of H2O2 in these stress responses has not yet been well studied. Here we identify time-dependent transcriptome profiles stimulated by H2O2 application in Arabidopsis (Arabidopsis thaliana) seedlings. Promoter prediction based on transcriptome data suggests strong crosstalk among high light, heat, and wounding stress responses in terms of environmental stresses and between the abscisic acid (ABA) and salicylic acid (SA) responses in terms of phytohormone signaling. Quantitative analysis revealed that ABA accumulation is induced by H2O2 but SA is not, suggesting that the implied crosstalk with ABA is achieved through ABA accumulation while the crosstalk with SA is different. We identified potential direct regulatory pairs between regulator transcription factor (TF) proteins and their regulated TF genes based on the time-course transcriptome analysis for the H2O2 response, in vivo regulation of the regulated TF by the regulator TF identified by expression analysis of mutants and overexpressors, and in vitro binding of the regulator TF protein to the target TF promoter. These analyses enabled the establishment of part of the transcriptional regulatory network for the H2O2 response composed of 15 regulatory pairs of TFs, including five pairs previously reported. This regulatory network is suggested to be involved in a wide range of biotic and abiotic stress responses in Arabidopsis. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
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