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Kim JM, To TK, Matsui A, Tanoi K, Kobayashi NI, Matsuda F, Habu Y, Ogawa D, Sakamoto T, Matsunaga S, Bashir K, Rasheed S, Ando M, Takeda H, Kawaura K, Kusano M, Fukushima A, Takaho A E, Kuromori T, Ishida J, Morosawa T, Tanaka M, Torii C, Takebayashi Y, Sakakibara H, Ogihara Y, Saito K, Shinozaki K, Devoto A, Seki M. Erratum: Acetate-mediated novel survival strategy against drought in plants. Nat Plants 2017; 3:17119. [PMID: 28714955 DOI: 10.1038/nplants.2017.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This corrects the article DOI: 10.1038/nplants.2017.97.
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Kim JM, To TK, Matsui A, Tanoi K, Kobayashi NI, Matsuda F, Habu Y, Ogawa D, Sakamoto T, Matsunaga S, Bashir K, Rasheed S, Ando M, Takeda H, Kawaura K, Kusano M, Fukushima A, Endo TA, Kuromori T, Ishida J, Morosawa T, Tanaka M, Torii C, Takebayashi Y, Sakakibara H, Ogihara Y, Saito K, Shinozaki K, Devoto A, Seki M. Acetate-mediated novel survival strategy against drought in plants. Nat Plants 2017; 3:17097. [PMID: 28650429 DOI: 10.1038/nplants.2017.97] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/25/2017] [Indexed: 05/19/2023]
Abstract
Water deficit caused by global climate changes seriously endangers the survival of organisms and crop productivity, and increases environmental deterioration1,2. Plants' resistance to drought involves global reprogramming of transcription, cellular metabolism, hormone signalling and chromatin modification3-8. However, how these regulatory responses are coordinated via the various pathways, and the underlying mechanisms, are largely unknown. Herein, we report an essential drought-responsive network in which plants trigger a dynamic metabolic flux conversion from glycolysis into acetate synthesis to stimulate the jasmonate (JA) signalling pathway to confer drought tolerance. In Arabidopsis, the ON/OFF switching of this whole network is directly dependent on histone deacetylase HDA6. In addition, exogenous acetic acid promotes de novo JA synthesis and enrichment of histone H4 acetylation, which influences the priming of the JA signalling pathway for plant drought tolerance. This novel acetate function is evolutionarily conserved as a survival strategy against environmental changes in plants. Furthermore, the external application of acetic acid successfully enhanced the drought tolerance in Arabidopsis, rapeseed, maize, rice and wheat plants. Our findings highlight a radically new survival strategy that exploits an epigenetic switch of metabolic flux conversion and hormone signalling by which plants adapt to drought.
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Affiliation(s)
- Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Taiko Kim To
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Natsuko I Kobayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Fumio Matsuda
- Metabolic Engineering Laboratory, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5, Yamadaoka, Suita, Osaka 565-0871, Japan
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yoshiki Habu
- Plant Physiology Research Unit, Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Daisuke Ogawa
- Breeding Strategies Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Sultana Rasheed
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Marina Ando
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Hiroko Takeda
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Miyako Kusano
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Atsushi Fukushima
- Metabolome Informatics Research Team, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Centre for Integrative Medical Sciences, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Kuromori
- Gene Discovery Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Junko Ishida
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Taeko Morosawa
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Chieko Torii
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yumiko Takebayashi
- Plant Productivity System Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- Plant Productivity System Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Yasunari Ogihara
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN CSRS, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Alessandra Devoto
- School of Biological Sciences, Plant Molecular Sciences, Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama 244-0813, Japan
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Ninomiya M, Kondo Y, Kimura O, Funayama R, Nagashima T, Kogure T, Morosawa T, Tanaka Y, Nakayama K, Shimosegawa T. The expression of miR-125b-5p is increased in the serum of patients with chronic hepatitis B infection and inhibits the detection of hepatitis B virus surface antigen. J Viral Hepat 2016; 23:330-9. [PMID: 26924666 DOI: 10.1111/jvh.12522] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 01/14/2016] [Indexed: 01/20/2023]
Abstract
MicroRNAs were first discovered as small endogenous RNA molecules and some viruses have been reported to interact with host miRNAs. By investigating miRNA expression in serum derived from HBV-infected patients, we have clarified the relationship between miRNA expression and chronic HBV infection. Additionally, we demonstrate the use of miRNAs as both novel biomarkers and new therapies against HBV. We included the sera of 20 patients with chronic HBV infection, sera of 20 patients with HCV infection and sera of 10 healthy controls in this study. The miRNA libraries were sequenced using a 32-mer single end sequence. The validation study of circulating miRNA in serum was conducted by qRT-PCR. The HBV genomic regions of genotype B and genotype C that were speculated to be targeted by miRNA were constructed using complementary oligonucleotides in the vectors. Reporter assays were performed 48 h after transfection. The expression levels of 21 miRNAs were found to be differentially expressed in the three groups. 10 miRNAs (hsa-miR-100-5p, miR-125b-5p, miR-193b-3p, miR-194-3p, miR-30a-3p, miR-30c-2-3p, miR-3591-5p, miR-4709-3p, miR-574-3p and miR-99a-5p) were found to be upregulated in CH-B by deep sequence analysis. The computer analysis showed that two regions of HBsAg are potential targets of miR-125b-5p and miR-30c-2-3p and that these miRNAs may downregulate the expression of HBV-S. The HBV genotype C segment speculated to be targeted by hsa-miR-125b-5p significantly decreased the expression of the reporter. This study indicated that expression of miR-125b-5p was related to the etiology of chronic hepatitis B infection and regulated the expression of HBsAg.
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Affiliation(s)
- M Ninomiya
- Division of Gastroenterology, Tohoku University Hospital, Sendai, Japan
| | - Y Kondo
- Division of Gastroenterology, Tohoku University Hospital, Sendai, Japan.,Department of Hepatology, Sendai Kousei Hospital, Sendai, Japan
| | - O Kimura
- Division of Gastroenterology, Tohoku University Hospital, Sendai, Japan
| | - R Funayama
- Division of Cell Proliferation, Tohoku University of Medicine, Sendai, Japan
| | - T Nagashima
- Division of Cell Proliferation, Tohoku University of Medicine, Sendai, Japan
| | - T Kogure
- Division of Gastroenterology, Tohoku University Hospital, Sendai, Japan
| | - T Morosawa
- Division of Gastroenterology, Tohoku University Hospital, Sendai, Japan
| | - Y Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Science, Nagoya, Japan
| | - K Nakayama
- Division of Cell Proliferation, Tohoku University of Medicine, Sendai, Japan
| | - T Shimosegawa
- Division of Gastroenterology, Tohoku University Hospital, Sendai, Japan
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Okamoto M, Matsui A, Tanaka M, Morosawa T, Ishida J, Iida K, Mochizuki Y, Toyoda T, Seki M. Sm-Like Protein-Mediated RNA Metabolism Is Required for Heat Stress Tolerance in Arabidopsis. Front Plant Sci 2016; 7:1079. [PMID: 27493656 PMCID: PMC4954817 DOI: 10.3389/fpls.2016.01079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/08/2016] [Indexed: 05/04/2023]
Abstract
Sm-like proteins play multiple functions in RNA metabolism, which is essential for biological processes such as stress responses in eukaryotes. The Arabidopsis thaliana sad1 mutant has a mutation of sm-like protein 5 (LSM5) and shows impaired drought and salt stress tolerances. The lsm5/sad1 mutant also showed hypersensitivity to heat stress. GFP-fused LSM5/SAD1 was localized in the nucleus under optimal growth conditions. After heat stress treatment, GFP-fused LSM5/SAD1 fluorescence was also observed as small cytoplasmic dots, in addition to nuclear localization. Whole genome transcriptome analysis revealed that many genes in Arabidopsis were drastically changed in response to heat stress. More heat-responsive genes were highly expressed in lsm5/sad1 mutant at both 2 and 6 h after heat stress treatment. Additionally, intron-retained and capped transcripts accumulated in the lsm5/sad1 mutant after heat stress treatment. In this study, we also identified non-Arabidopsis Genome Initiative transcripts that were expressed from unannotated regions. Most of these transcripts were antisense transcripts, and many capped non-AGI transcripts accumulated in the lsm5/sad1 mutant during heat stress treatment. These results indicated that LSM5/SAD1 functions to degrade aberrant transcripts through appropriate mRNA splicing and decapping, and precise RNA metabolic machinery is required for heat stress tolerance.
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Affiliation(s)
- Masanori Okamoto
- Arid Land Research Center, Tottori UniversityHamasaka, Japan
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- PRESTO, Japan Science and Technology AgencyKawaguchi, Japan
| | - Akihiro Matsui
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Maho Tanaka
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Taeko Morosawa
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Junko Ishida
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Kei Iida
- Graduate School of Medicine, Kyoto UniversityKyoto, Japan
| | | | - Tetsuro Toyoda
- RIKEN Advanced Center for Computing and CommunicationWako, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
- CREST, Japan Science and Technology AgencyKawaguchi, Japan
- *Correspondence: Motoaki Seki,
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Komine H, Takeshita K, Abe S, Ishikawa T, Kimura M, Hashimoto T, Kitaura K, Morosawa T, Seki K, Kaji K. Relationships between capture-site characteristics and capture levels of the invasive mongoose on Amami-Oshima Island, Japan. Biol Invasions 2015. [DOI: 10.1007/s10530-015-1021-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nakaminami K, Matsui A, Nakagami H, Minami A, Nomura Y, Tanaka M, Morosawa T, Ishida J, Takahashi S, Uemura M, Shirasu K, Seki M. Analysis of differential expression patterns of mRNA and protein during cold-acclimation and de-acclimation in Arabidopsis. Mol Cell Proteomics 2014; 13:3602-11. [PMID: 25277243 DOI: 10.1074/mcp.m114.039081] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Overwintering plants are capable of exhibiting high levels of cold tolerance, which is acquired through the process of cold acclimation (CA). In contrast to CA, the acquired freezing tolerance is rapidly reduced during cold de-acclimation (DA) and plants resume growth after sensing warm temperatures. In order to better understand plant growth and development, and to aid in the breeding of cold-tolerant plants, it is important to decipher the functional mechanisms of the DA process. In this study, we performed comparative transcriptomic and proteomic analyses during CA and DA. As revealed by shotgun proteomics, we identified 3987 peptides originating from 1569 unique proteins and the corresponding mRNAs were analyzed. Among the 1569 genes, 658 genes were specifically induced at the transcriptional level during the process of cold acclimation. In order to investigate the relationship between mRNA and the corresponding protein expression pattern, a Pearson correlation was analyzed. Interestingly, 199 genes showed a positive correlation of mRNA and protein expression pattern, indicating that both their transcription and translation occurred during CA. However, 226 genes showed a negative correlation of mRNA and protein expression pattern, indicating that their mRNAs were transcribed during CA and were stored for the subsequent DA step. Under this scenario, those proteins were specifically increased during DA without additional transcription of mRNA. In order to confirm the negative correlation of mRNA and protein expression patterns, qRT-PCR and western blot analyses were performed. Mitochondrial malate dehydrogenase 1 (mMDH1) exhibited a negative correlation of mRNA and protein levels, which was characterized by CA-specific mRNA induction and protein accumulation specifically during DA. These data indicate that the expression of specific mRNAs and subsequent accumulation of corresponding proteins are not always in accordance under low temperature stress conditions in plants.
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Affiliation(s)
- Kentaro Nakaminami
- From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Akihiro Matsui
- From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Hirofumi Nakagami
- §Plant Proteomics Research Unit, RIKEN CSRS, Yokohama, Kanagawa, 230-0045, Japan
| | - Anzu Minami
- ¶Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Yuko Nomura
- §Plant Proteomics Research Unit, RIKEN CSRS, Yokohama, Kanagawa, 230-0045, Japan
| | - Maho Tanaka
- From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Taeko Morosawa
- From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Junko Ishida
- From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Satoshi Takahashi
- From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Matsuo Uemura
- ¶Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Ken Shirasu
- ‖Plant Immunity Research Group, RIKEN CSRS, Yokohama, Kanagawa, 230-0045, Japan
| | - Motoaki Seki
- From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan; ‡‡CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan **Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan;
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Utsumi Y, Tanaka M, Morosawa T, Kurotani A, Yoshida T, Mochida K, Matsui A, Umemura Y, Ishitani M, Shinozaki K, Sakurai T, Seki M. Transcriptome analysis using a high-density oligomicroarray under drought stress in various genotypes of cassava: an important tropical crop. DNA Res 2012; 19:335-45. [PMID: 22619309 PMCID: PMC3415295 DOI: 10.1093/dnares/dss016] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cassava is an important crop that provides food security and income generation in many tropical countries and is known for its adaptability to various environmental conditions. Despite its global importance, the development of cassava microarray tools has not been well established. Here, we describe the development of a 60-mer oligonucleotide Agilent microarray representing ∼20,000 cassava genes and how it can be applied to expression profiling under drought stress using three cassava genotypes (MTAI16, MECU72 and MPER417-003). Our results identified about 1300 drought stress up-regulated genes in cassava and indicated that cassava has similar mechanisms for drought stress response and tolerance as other plant species. These results demonstrate that our microarray is a useful tool for analysing the cassava transcriptome and that it is applicable for various cassava genotypes.
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Affiliation(s)
- Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Plant Science Center, Tsurumi-ku, Yokohama, Kanagawa, Japan
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To TK, Kim JM, Matsui A, Kurihara Y, Morosawa T, Ishida J, Tanaka M, Endo T, Kakutani T, Toyoda T, Kimura H, Yokoyama S, Shinozaki K, Seki M. Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1. PLoS Genet 2011; 7:e1002055. [PMID: 21552333 PMCID: PMC3084210 DOI: 10.1371/journal.pgen.1002055] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 03/12/2011] [Indexed: 02/01/2023] Open
Abstract
Heterochromatin silencing is pivotal for genome stability in eukaryotes. In
Arabidopsis, a plant-specific mechanism called
RNA–directed DNA methylation (RdDM) is involved in heterochromatin
silencing. Histone deacetylase HDA6 has been identified as a component of such
machineries; however, its endogenous targets and the silencing mechanisms have
not been analyzed globally. In this study, we investigated the silencing
mechanism mediated by HDA6. Genome-wide transcript profiling revealed that the
loci silenced by HDA6 carried sequences corresponding to the RDR2-dependent
24-nt siRNAs, however their transcript levels were mostly unaffected in the
rdr2 mutant. Strikingly, we observed significant overlap of
genes silenced by HDA6 to those by the CG DNA methyltransferase MET1.
Furthermore, regardless of dependence on RdDM pathway, HDA6 deficiency resulted
in loss of heterochromatic epigenetic marks and aberrant enrichment for
euchromatic marks at HDA6 direct targets, along with ectopic expression of these
loci. Acetylation levels increased significantly in the hda6
mutant at all of the lysine residues in the H3 and H4 N-tails, except H4K16.
Interestingly, we observed two different CG methylation statuses in the
hda6 mutant. CG methylation was sustained in the
hda6 mutant at some HDA6 target loci that were surrounded
by flanking DNA–methylated regions. In contrast, complete loss of CG
methylation occurred in the hda6 mutant at the HDA6 target loci
that were isolated from flanking DNA methylation. Regardless of CG methylation
status, CHG and CHH methylation were lost and transcriptional derepression
occurred in the hda6 mutant. Furthermore, we show that HDA6
binds only to its target loci, not the flanking methylated DNA, indicating the
profound target specificity of HDA6. 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. Eukaryotes are defended from potentially harmful DNA elements, such as
transposons, by forming inactive genomic structure. Chromatin, which consists of
DNA and histone proteins, is densely packed in the silent structure, and
chromatin chemical modifications such as DNA methylation and histone
modifications are known to be essential for this packing. In plants, small RNA
molecules have been thought to trigger DNA methylation and resulting silent
chromatin formation. We revealed that elimination of specific histone
modifications concomitant with DNA methylation is pivotal for the silent
chromatin. Furthermore, the histone deacetylase was shown to have more profound
target specificity than the DNA methyltransferase and is required for
locus-directed DNA methylation, implying the involvement of the histone
deacetylase for targeting the DNA methyltransferase to specific places on the
genome. These proteins and their functions for gene silencing are evolutionarily
conserved in higher eukaryotes, and several proteins involved in small RNA
production are plant-specific. Thus, we present a hypothesis that the plant
genome may build the protecting foundation by the conserved genome surveillance
in eukaryotes, and the reinforcing machinery involving small RNAs could be
evolutionarily added to the plant heterochromatin silencing system.
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Affiliation(s)
- Taiko Kim To
- Plant Genomic Network Research Team, RIKEN
Plant Science Center, Yokohama, Kanagawa, Japan
- Graduate School of Science, The University of
Tokyo, Tokyo, Japan
| | - Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN
Plant Science Center, Yokohama, Kanagawa, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN
Plant Science Center, Yokohama, Kanagawa, Japan
| | - Yukio Kurihara
- Plant Genomic Network Research Team, RIKEN
Plant Science Center, Yokohama, Kanagawa, Japan
| | - Taeko Morosawa
- Plant Genomic Network Research Team, RIKEN
Plant Science Center, Yokohama, Kanagawa, Japan
| | - Junko Ishida
- Plant Genomic Network Research Team, RIKEN
Plant Science Center, Yokohama, Kanagawa, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN
Plant Science Center, Yokohama, Kanagawa, Japan
| | - Takaho Endo
- Bioinformatics and Systems Engineering
Division, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Tetsuji Kakutani
- Department of Integrated Genetics, National
Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tetsuro Toyoda
- Bioinformatics and Systems Engineering
Division, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka
University, Suita, Osaka, Japan
| | | | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Plant
Science Center, Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN
Plant Science Center, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research,
Yokohama City University, Yokohama, Kanagawa, Japan
- * E-mail:
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To TK, Nakaminami K, Kim JM, Morosawa T, Ishida J, Tanaka M, Yokoyama S, Shinozaki K, Seki M. Arabidopsis HDA6 is required for freezing tolerance. Biochem Biophys Res Commun 2011; 406:414-9. [DOI: 10.1016/j.bbrc.2011.02.058] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 02/11/2011] [Indexed: 01/22/2023]
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Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, Tanaka M, Morosawa T, Seki M, Toyoda T. ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. Plant Cell Physiol 2011; 52:254-64. [PMID: 21227933 PMCID: PMC3037080 DOI: 10.1093/pcp/pcq202] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 12/20/2010] [Indexed: 05/19/2023]
Abstract
Recent advances in technologies for observing high-resolution genomic activities, such as whole-genome tiling arrays and high-throughput sequencers, provide detailed information for understanding genome functions. However, the functions of 50% of known Arabidopsis thaliana genes remain unknown or are annotated only on the basis of static analyses such as protein motifs or similarities. In this paper, we describe dynamic structure-based dynamic expression (DSDE) analysis, which sequentially predicts both structural and functional features of transcripts. We show that DSDE analysis inferred gene functions 12% more precisely than static structure-based dynamic expression (SSDE) analysis or conventional co-expression analysis based on previously determined gene structures of A. thaliana. This result suggests that more precise structural information than the fixed conventional annotated structures is crucial for co-expression analysis in systems biology of transcriptional regulation and dynamics. Our DSDE method, ARabidopsis Tiling-Array-based Detection of Exons version 2 and over-representation analysis (ARTADE2-ORA), precisely predicts each gene structure by combining two statistical analyses: a probe-wise co-expression analysis of multiple transcriptome measurements and a Markov model analysis of genome sequences. ARTADE2-ORA successfully identified the true functions of about 90% of functionally annotated genes, inferred the functions of 98% of functionally unknown genes and predicted 1,489 new gene structures and functions. We developed a database ARTADE2DB that integrates not only the information predicted by ARTADE2-ORA but also annotations and other functional information, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana. URL: http://artade.org.
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Affiliation(s)
- Kei Iida
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
- These authors contributed equally to this work
| | - Shuji Kawaguchi
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
- These authors contributed equally to this work
| | - Norio Kobayashi
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
| | - Yuko Yoshida
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
| | - Manabu Ishii
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
| | - Erimi Harada
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
| | - Kousuke Hanada
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Akihiro Matsui
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Masanori Okamoto
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
- Present address: Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Junko Ishida
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Maho Tanaka
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Taeko Morosawa
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Motoaki Seki
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Tetsuro Toyoda
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
- *Corresponding author: E-mail, ; Fax, +81-45-503-9553
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Okamoto M, Tatematsu K, Matsui A, Morosawa T, Ishida J, Tanaka M, Endo TA, Mochizuki Y, Toyoda T, Kamiya Y, Shinozaki K, Nambara E, Seki M. Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant J 2010; 62:39-51. [PMID: 20088898 DOI: 10.1111/j.1365-313x.2010.04135.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The phytohormone abscisic acid (ABA) plays important roles in the induction and maintenance of seed dormancy. Although application of exogenous ABA inhibits germination, the effects of exogenous ABA on ABA-mediated gene transcription differ from those of endogenous ABA. To understand how endogenous ABA regulates the transcriptomes in seeds, we performed comprehensive expression analyses using whole-genome Affymetrix tiling arrays in two ABA metabolism mutants - an ABA-deficient mutant (aba2) and an ABA over-accumulation mutant (cyp707a1a2a3 triple mutant). Hierarchical clustering and principal components analyses showed that differences in endogenous ABA levels do not influence global expression of stored mRNA in dry seeds. However, the transcriptome after seed imbibition was related to endogenous ABA levels in both types of mutant. Endogenous ABA-regulated genes expressed in imbibed seeds included those encoding key ABA signaling factors and gibberellin-related components. In addition, cohorts of ABA-upregulated genes partially resembled those of dormant genes, whereas ABA-downregulated genes were partially overlapped with after-ripening-regulated genes. Bioinformatic analyses revealed that 6105 novel genes [non-Arabidopsis Genome Initiative (AGI) transcriptional units (TUs)] were expressed from unannotated regions. Interestingly, approximately 97% of non-AGI TUs possibly encoded hypothetical non-protein-coding RNAs, including a large number of antisense RNAs. In dry and imbibed seeds, global expression profiles of non-AGI TUs were similar to those of AGI genes. For both non-AGI TUs and AGI code genes, we identified those that were regulated differently in embryo and endosperm tissues. Our results suggest that transcription in Arabidopsis seeds is more complex and dynamic than previously thought.
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Kurihara Y, Kaminuma E, Matsui A, Kawashima M, Tanaka M, Morosawa T, Ishida J, Mochizuki Y, Shinozaki K, Toyoda T, Seki M. Transcriptome analyses revealed diverse expression changes in ago1 and hyl1 Arabidopsis mutants. Plant Cell Physiol 2009; 50:1715-1720. [PMID: 19633021 DOI: 10.1093/pcp/pcp109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide endogenous regulatory molecules conserved in higher eukaryotes. In Arabidopsis, miRNAs are produced through step-wise cleavages of primary miRNA precursors (pri-miRNAs) by DICER-LIKE1 (DCL1). This cleavage step is also supported by a double-stranded RNA-binding protein, HYPONASTIC LEAVES1 (HYL1). In many cases, mature miRNA is predominantly incorporated into an endonuclease, ARGONAUTE1 (AGO1), which degrades miRNA-targeted mRNAs. Here, we examined and revealed whole genome transcriptomes in ago1-25 and hyl1-2 mutants using tiling arrays. The data in this paper are valuable for understanding the relationship between the miRNA pathway and its effect on transcriptomes.
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Affiliation(s)
- Yukio Kurihara
- Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
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Kurihara Y, Matsui A, Kawashima M, Kaminuma E, Ishida J, Morosawa T, Mochizuki Y, Kobayashi N, Toyoda T, Shinozaki K, Seki M. Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis. Biochem Biophys Res Commun 2008; 376:553-7. [DOI: 10.1016/j.bbrc.2008.09.046] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 09/06/2008] [Indexed: 01/26/2023]
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Kim JM, To TK, Ishida J, Morosawa T, Kawashima M, Matsui A, Toyoda T, Kimura H, Shinozaki K, Seki M. Alterations of Lysine Modifications on the Histone H3 N-Tail under Drought Stress Conditions in Arabidopsis thaliana. ACTA ACUST UNITED AC 2008; 49:1580-8. [DOI: 10.1093/pcp/pcn133] [Citation(s) in RCA: 248] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, Endo TA, Okamoto M, Nambara E, Nakajima M, Kawashima M, Satou M, Kim JM, Kobayashi N, Toyoda T, Shinozaki K, Seki M. Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol 2008; 49:1135-49. [PMID: 18625610 DOI: 10.1093/pcp/pcn101] [Citation(s) in RCA: 330] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants respond and adapt to drought, cold and high-salinity stresses in order to survive. In this study, we applied Arabidopsis Affymetrix tiling arrays to study the whole genome transcriptome under drought, cold, high-salinity and ABA treatment conditions. The bioinformatic analysis using the tiling array data showed that 7,719 non-AGI transcriptional units (TUs) exist in the unannotated "intergenic" regions of Arabidopsis genome. These include 1,275 and 181 TUs that are induced and downregulated, respectively, by the stress or ABA treatments. Most of the non-AGI TUs are hypothetical non-protein-coding RNAs. About 80% of the non-AGI TUs belong to pairs of the fully overlapping sense-antisense transcripts (fSATs). Significant linear correlation between the expression ratios (treated/untreated) of the sense TUs and the ratios of the antisense TUs was observed in the SATs of AGI code/non-AGI TU. We studied the biogenesis mechanisms of the stress- or ABA-inducible antisense RNAs and found that the expression of sense TUs is necessary for the stress- or ABA-inducible expression of the antisense TUs in the fSATs (AGI code/non-AGI TU).
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Affiliation(s)
- 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
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