Updated on 2025/07/16

写真a

 
IKEDA Yoko
 
Organization
Scheduled update Associate Professor
Position
Associate Professor
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Degree

  • Ph. D. ( Kyoto university )

Research Areas

  • Life Science / Genetics

  • Life Science / Plant molecular biology and physiology

Education

  • 京都大学大学院   理学研究科   生物科学専攻

    2002.4 - 2007.3

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  • Okayama University   農学部   総合農業科学科

    1998.4 - 2002.3

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Research History

  • 岡山大学 学術研究院先鋭研究領域 資源植物科学研究所   准教授

    2025.4

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  • Okayama univ. IPSR   Associate Professor

    2018.12 - 2025.3

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  • Okayama univ. IPSR

    2013.12 - 2018.11

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  • Université Clemont Auvergne

    2012.4 - 2013.11

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  • Université Clemont Auvergne

    2011.11 - 2012.3

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  • Nara Institute of Science and Technology

    2009.10 - 2011.10

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  • Nara Institute of Science and Technology

    2007.10 - 2009.9

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  • National Institute of Genetics

    2007.4 - 2007.9

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Committee Memberships

  • 日本学術会議   連携会員  

    2023.10   

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  • 日本植物学会   第六期代議員  

    2022.6 - 2024.5   

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  • 日本植物生理学会   広報委員  

    2022.3   

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  • 日本学術振興会   科学研究費助成事業 審査委員(若手研究)  

    2022   

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  • 日本植物学会   第五期代議員  

    2020.6   

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  • 日本植物学会   第五期代議員  

    2020.6 - 2022.5   

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  • 日本植物学会   ダイバーシティ推進委員  

    2020.4   

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  • 日本植物学会   ダイバーシティ推進委員  

    2020.4 - 2025.3   

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Papers

  • Rapid and dynamic evolution of a giant Y chromosome in Silene latifolia

    Takashi Akagi, Naoko Fujita, Kenta Shirasawa, Hiroyuki Tanaka, Kiyotaka Nagaki, Kanae Masuda, Ayano Horiuchi, Eriko Kuwada, Kanta Kawai, Riko Kunou, Koki Nakamura, Yoko Ikeda, Atsushi Toyoda, Takehiko Itoh, Koichiro Ushijima, Deborah Charlesworth

    Science   387 ( 6734 )   637 - 643   2025.2

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    Publishing type:Research paper (scientific journal)   Publisher:American Association for the Advancement of Science (AAAS)  

    Some plants have massive sex-linked regions. To test hypotheses about their evolution, we sequenced the genome of Silene latifolia , in which giant heteromorphic sex chromosomes were first discovered in 1923. It has long been known that the Y chromosome consists mainly of a male-specific region that does not recombine with the X chromosome and carries the sex-determining genes and genes with other male functions. However, only with a whole Y chromosome assembly can candidate genes be validated experimentally and their locations determined and related to the suppression of recombination. We describe the genomic changes as the ancestral chromosome evolved into the current XY pair, testing ideas about the evolution of large nonrecombining regions and the mechanisms that created the present recombination pattern.

    DOI: 10.1126/science.adk9074

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  • SHORT AND CROOKED AWN, encoding the epigenetic regulator EMF1, promotes barley awn development Reviewed

    Koki Nakamura, Yuichi Kikuchi, Mizuho Shiraga, Toshihisa Kotake, Kiwamu Hyodo, Shin Taketa, Yoko Ikeda

    Plant And Cell Physiology   66 ( 5 )   705 - 721   2024.12

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    The awn is a bristle-like extension from the tip of the lemma in grasses. In barley, the predominant cultivars possess long awns that contribute to grain yield and quality through photosynthesis. In addition, various awn morphological mutants are available in barley, rendering it a useful cereal crop to investigate the mechanims of awn development. Here, we identified the gene causative of the short and crooked awn (sca) mutant, which exhibits a short and curved awn phenotype. Intercrossing experiments revealed that the sca mutant induced in the Japanese cultivar (cv.) “Akashinriki” is allelic to the independently isolated moderately short-awn mutant breviaristatum-a (ari-a). Map-based cloning and sequencing revealed that SCA encodes the Polycomb group–associated protein EMBRYONIC FLOWER 1. We found that SCA affects awn development through the promotion of cell proliferation, elongation, and cell wall synthesis. RNA sequencing of cv. Bowman backcross-derived near-isogenic lines of sca and ari-a6 alleles showed that SCA is directly or indirectly involved in promoting the expression of genes related to awn development. Additionally, SCA represses various transcription factors essential for floral organ development and plant architecture, such as MADS-box and Knotted1-like homeobox genes. Notably, the repression of the C-class MADS-box gene HvMADS58 by SCA in awns is associated with the accumulation of the repressive histone modification H3K27me3. These findings highlight the potential role of SCA-mediated gene regulation, including histone modification, as a novel pathway in barley awn development.

    DOI: 10.1093/pcp/pcae150

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    Other Link: https://academic.oup.com/pcp/article-pdf/66/5/705/61243730/pcae150.pdf

  • The importin α proteins IMPA1, IMPA2, and IMPA4 play redundant roles in suppressing autoimmunity in Arabidopsis thaliana. Reviewed International journal

    Airi Mori, Shitomi Nakagawa, Toshiyuki Suzuki, Takamasa Suzuki, Valérie Gaudin, Takakazu Matsuura, Yoko Ikeda, Kentaro Tamura

    The Plant journal : for cell and molecular biology   2024.12

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    Proteins in the importin α (IMPA) family play pivotal roles in intracellular nucleocytoplasmic transport. Arabidopsis thaliana possesses nine IMPA members, with diverse tissue-specific expression patterns. Among these nine IMPAs, IMPA1, IMPA2, and IMPA4 cluster together phylogenetically, suggesting potential functional redundancy. To explore this redundancy, we analyzed single and multiple T-DNA mutants for these genes and discovered severe growth defects in the impa1 impa2 impa4 triple knockout mutant but not in the single or double mutants. Complementation with IMPA1, IMPA2, or IMPA4 fused to green fluorescent protein (GFP) rescued the growth defects observed in the impa1 impa2 impa4 mutant, indicating the functional redundancy of these three IMPAs. The IMPA-GFP fusion proteins were localized in the nucleus and nuclear envelope, suggesting their involvement in nucleocytoplasmic transport processes. Comparative transcriptomics revealed that salicylic acid (SA)-responsive genes were significantly upregulated in the impa1 impa2 impa4 triple mutant. Consistent with this observation, impa1 impa2 impa4 mutant plants accumulated SA and reactive oxygen species to high levels compared with wild-type plants. We also found enhanced resistance to the anthracnose pathogen Colletotrichum higginsianum in the impa1 impa2 impa4 mutants, suggesting that defense responses were constitutively activated in the impa1 impa2 impa4 mutant. Our findings shed light on the redundant roles of IMPA1, IMPA2, and IMPA4 in suppressing the autoimmune responses and suggest avenues of research to clarify their potentially unique roles.

    DOI: 10.1111/tpj.17203

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  • Dormancy regulator Prunus mume DAM6 promotes ethylene-mediated leaf senescence and abscission Reviewed

    Tzu-Fan Hsiang, Yue-Yu Chen, Ryohei Nakano, Akira Oikawa, Takakazu Matsuura, Yoko Ikeda, Hisayo Yamane

    Plant Molecular Biology   114 ( 5 )   2024.9

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1007/s11103-024-01497-y

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    Other Link: https://link.springer.com/article/10.1007/s11103-024-01497-y/fulltext.html

  • The sixth Japanese meeting on biological function and evolution through interactions between hosts and transposable elements. International journal

    Kenji Ichiyanagi, Yoko Ikeda, Kuniaki Saito

    Mobile DNA   14 ( 1 )   22 - 22   2023.12

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (conference, symposium, etc.)  

    The sixth Japanese meeting on host-transposon interactions, titled "Biological Function and Evolution through Interactions between Hosts and Transposable Elements," was held on August 24th and 25th, 2023, at the National Institute of Genetics as well as online. This meeting was supported by the National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs in genome function and evolution, as well as host defense systems against TE mobility, TE bursts during evolution, and intron mobility in mammals, insects, land plants, yeast, protozoa, and bacteria. Here, we have presented the highlights of the discussion.Organizers: Kenji Ichiyanagi, Yoko Ikeda, and Kuniaki Saito.

    DOI: 10.1186/s13100-023-00310-9

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  • Ab-GALFA, A bioassay for insect gall formation using the model plant Arabidopsis thaliana Reviewed

    Tomoko Hirano, Ayaka Okamoto, Yoshihisa Oda, Tomoaki Sakamoto, Seiji Takeda, Takakazu Matsuura, Yoko Ikeda, Takumi Higaki, Seisuke Kimura, Masa H. Sato

    Scientific Reports   13   2554   2023.1

  • Reinvention of hermaphroditism via activation of a RADIALIS-like gene in hexaploid persimmon. International journal

    Kanae Masuda, Yoko Ikeda, Takakazu Matsuura, Taiji Kawakatsu, Ryutaro Tao, Yasutaka Kubo, Koichiro Ushijima, Isabelle M Henry, Takashi Akagi

    Nature plants   8 ( 3 )   217 - 224   2022.3

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    In flowering plants, different lineages have independently transitioned from the ancestral hermaphroditic state into and out of various sexual systems1. Polyploidizations are often associated with this plasticity in sexual systems2,3. Persimmons (the genus Diospyros) have evolved dioecy via lineage-specific palaeoploidizations. More recently, hexaploid D. kaki has established monoecy and also exhibits reversions from male to hermaphrodite flowers in response to natural environmental signals (natural hermaphroditism, NH), or to artificial cytokinin treatment (artificial hermaphroditism, AH). We sought to identify the molecular pathways underlying these polyploid-specific reversions to hermaphroditism. Co-expression network analyses identified regulatory pathways specific to NH or AH transitions. Surprisingly, the two pathways appeared to be antagonistic, with abscisic acid and cytokinin signalling for NH and AH, respectively. Among the genes common to both pathways leading to hermaphroditic flowers, we identified a small-Myb RADIALIS-like gene, named DkRAD, which is specifically activated in hexaploid D. kaki. Consistently, ectopic overexpression of DkRAD in two model plants resulted in hypergrowth of the gynoecium. These results suggest that production of hermaphrodite flowers via polyploidization depends on DkRAD activation, which is not associated with a loss-of-function within the existing sex determination pathway, but rather represents a new path to (or reinvention of) hermaphroditism.

    DOI: 10.1038/s41477-022-01107-z

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  • Epigenetic regulation of ecotype-specific expression of the heat-activated transposon ONSEN. International journal

    Kosuke Nozawa, Seiji Masuda, Hidetoshi Saze, Yoko Ikeda, Takamasa Suzuki, Hiroki Takagi, Keisuke Tanaka, Naohiko Ohama, Xiaoying Niu, Atsushi Kato, Hidetaka Ito

    Frontiers in plant science   13   899105 - 899105   2022

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    Transposable elements are present in a wide variety of organisms; however, our understanding of the diversity of mechanisms involved in their activation is incomplete. In this study, we analyzed the transcriptional activation of the ONSEN retrotransposon, which is activated by high-temperature stress in Arabidopsis thaliana. We found that its transcription is significantly higher in the Japanese ecotype Kyoto. Considering that transposons are epigenetically regulated, DNA methylation levels were analyzed, revealing that CHH methylation was reduced in Kyoto compared to the standard ecotype, Col-0. A mutation was also detected in the Kyoto CMT2 gene, encoding a CHH methyltransferase, suggesting that it may be responsible for increased expression of ONSEN. CHH methylation is controlled by histone modifications through a self-reinforcing loop between DNA methyltransferase and histone methyltransferase. Analysis of these modifications revealed that the level of H3K9me2, a repressive histone marker for gene expression, was lower in Kyoto than in Col-0. The level of another repressive histone marker, H3K27me1, was decreased in Kyoto; however, it was not impacted in a Col-0 cmt2 mutant. Therefore, in addition to the CMT2 mutation, other factors may reduce repressive histone modifications in Kyoto.

    DOI: 10.3389/fpls.2022.899105

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  • Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. International journal

    Qingxin Song, Atsumi Ando, Ning Jiang, Yoko Ikeda, Z Jeffrey Chen

    Genome biology   21 ( 1 )   178 - 178   2020.7

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    BACKGROUND: Polyploidy provides new genetic material that facilitates evolutionary novelty, species adaptation, and crop domestication. Polyploidy often leads to an increase in cell or organism size, which may affect transcript abundance or transcriptome size, but the relationship between polyploidy and transcriptome changes remains poorly understood. Plant cells often undergo endoreduplication, confounding the polyploid effect. RESULTS: To mitigate these effects, we select female gametic cells that are developmentally stable and void of endoreduplication. Using single-cell RNA sequencing (scRNA-seq) in Arabidopsis thaliana tetraploid lines and isogenic diploids, we show that transcriptome abundance doubles in the egg cell and increases approximately 1.6-fold in the central cell, consistent with cell size changes. In the central cell of tetraploid plants, DEMETER (DME) is upregulated, which can activate PRC2 family members FIS2 and MEA, and may suppress the expression of other genes. Upregulation of cell size regulators in tetraploids, including TOR and OSR2, may increase the size of reproductive cells. In diploids, the order of transcriptome abundance is central cell, synergid cell, and egg cell, consistent with their cell size variation. Remarkably, we uncover new sets of female gametophytic cell-specific transcripts with predicted biological roles; the most abundant transcripts encode families of cysteine-rich peptides, implying roles in cell-cell recognition during double fertilization. CONCLUSIONS: Transcriptome in single cells doubles in tetraploid plants compared to diploid, while the degree of change and relationship to the cell size depends on cell types. These scRNA-seq resources are free of cross-contamination and are uniquely valuable for advancing plant hybridization, reproductive biology, and polyploid genomics.

    DOI: 10.1186/s13059-020-02094-0

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  • Reprogramming of the Developmental Program of Rhus javanica During Initial Stage of Gall Induction by Schlechtendalia chinensis. Reviewed International journal

    Tomoko Hirano, Seisuke Kimura, Tomoaki Sakamoto, Ayaka Okamoto, Takumi Nakayama, Takakazu Matsuura, Yoko Ikeda, Seiji Takeda, Yoshihito Suzuki, Issei Ohshima, Masa H Sato

    Frontiers in plant science   11   471 - 471   2020.5

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    Insect galls are unique organs that provide shelter and nutrients to the gall-inducing insects. Although insect galls are fascinating structures for their unique shapes and functions, the process by which gall-inducing insects induce such complex structures is not well understood. Here, we performed RNA-sequencing-based comparative transcriptomic analysis of the early developmental stage of horned gall to elucidate the early gall-inducing process carried out by the aphid, Schlechtendalia chinensis, in the Chinese sumac, Rhus javanica. There was no clear similarity in the global gene expression profiles between the gall tissue and other tissues, and the expression profiles of various biological categories such as phytohormone metabolism and signaling, stress-response pathways, secondary metabolic pathways, photosynthetic reaction, and floral organ development were dramatically altered. Particularly, master transcription factors that regulate meristem, flower, and fruit development, and biotic and abiotic stress-responsive genes were highly upregulated, whereas the expression of genes related to photosynthesis strongly decreased in the early stage of the gall development. In addition, we found that the expression of class-1 KNOX genes, whose ectopic overexpression is known to lead to the formation of de novo meristematic structures in leaf, was increased in the early development stage of gall tissue. These results strengthen the hypothesis that gall-inducing insects convert source tissues into fruit-like sink tissues by regulating the gene expression of host plants and demonstrate that such manipulation begins from the initial process of gall induction.

    DOI: 10.3389/fpls.2020.00471

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  • Life-course monitoring of endogenous phytohormone levels under field conditions reveals diversity of physiological states among barley accessions. Reviewed

    Takashi Hirayama, Daisuke Saisho, Takakazu Matsuura, Satoshi Okada, Kotaro Takahagi, Asaka Kanatani, Jun Ito, Hiroyuki Tsuji, Yoko Ikeda, Keiichi Mochida

    Plant & cell physiology   61 ( 8 )   1438 - 1448   2020.4

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    Agronomically important traits often develop during the later stages of crop growth as consequences of various plant-environment interactions. Therefore, the temporal physiological states that change and accumulate during the crop's life course can significantly affect the eventual phenotypic differences in agronomic traits among crop varieties. Thus, to improve productivity, it is important to elucidate the associations between temporal physiological responses during the growth of different crop varieties and their agronomic traits. However, data representing the dynamics and diversity of physiological states in plants grown under field conditions is sparse. In this study, we quantified the endogenous levels of five phytohormones-auxin, cytokinins, abscisic acid, jasmonate, and salicylic acid-in the leaves of eight diverse barley (Hordeum vulgare) accessions grown under field conditions sampled weekly over their life course to assess the ongoing fluctuations in hormone levels in the different accessions under field growth conditions. Notably, we observed enormous changes over time in the development-related plant hormones, such as auxin and cytokinins. Using 3' RNA-seq-based transcriptome data from the same samples, we investigated the expression of barley genes orthologous to known hormone-related genes of Arabidopsis throughout the life course. These data illustrated the dynamics and diversity of the physiological states of these field-grown barley accessions. Together our findings provide new insights into plant-environment interaction, highlighting that there is cultivar diversity in physiological responses during growth under field conditions.

    DOI: 10.1093/pcp/pcaa046

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  • Regulation of the Poly(A) Status of Mitochondrial mRNA by Poly(A)-Specific Ribonuclease Is Conserved among Land Plants. Reviewed

    Mai Kanazawa, Yoko Ikeda, Ryuichi Nishihama, Shohei Yamaoka, Nam-Hee Lee, Katsuyuki T Yamato, Takayuki Kohchi, Takashi Hirayama

    Plant & cell physiology   61 ( 3 )   470 - 480   2020.3

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    Regulation of the stability and the quality of mitochondrial RNA is essential for the maintenance of mitochondrial and cellular functions in eukaryotes. We have previously reported that the eukaryotic poly(A)-specific ribonuclease (PARN) and the prokaryotic poly(A) polymerase encoded by AHG2 and AGS1, respectively, coordinately regulate the poly(A) status and the stability of mitochondrial mRNA in Arabidopsis. Mitochondrial function of PARN has not been reported in any other eukaryotes. To know how much this PARN-based mitochondrial mRNA regulation is conserved among plants, we studied the AHG2 and AGS1 counterparts of the liverwort, Marchantia polymorpha, a member of basal land plant lineage. We found that M. polymorpha has one ortholog each for AHG2 and AGS1, named MpAHG2 and MpAGS1, respectively. Their Citrine-fused proteins were detected in mitochondria of the liverwort. Molecular genetic analysis showed that MpAHG2 is essential and functionally interacts with MpAGS1 as observed in Arabidopsis. A recombinant MpAHG2 protein had a deadenylase activity in vitro. Overexpression of MpAGS1 and the reduced expression of MpAHG2 caused an accumulation of polyadenylated Mpcox1 mRNA. Furthermore, MpAHG2 suppressed Arabidopsis ahg2-1 mutant phenotype. These results suggest that the PARN-based mitochondrial mRNA regulatory system is conserved in land plants.

    DOI: 10.1093/pcp/pcz212

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  • Transcriptome Analysis and Identification of a Transcriptional Regulatory Network in the Response to H2O2 Reviewed

    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, Yoshiharu Y. Yamamoto

    Plant Physiology   2019.7

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    Publishing type:Research paper (scientific journal)   Publisher:American Society of Plant Biologists ({ASPB})  

    DOI: 10.1104/pp.18.01426

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  • Overexpression of Prunus DAM6 inhibits growth, represses bud break competency of dormant buds and delays bud outgrowth in apple plants Reviewed

    Yamane, Hisayo, Wada, Masato, Honda, Chikako, Matsuura, Takakazu, Ikeda, Yoko, Hirayama, Takashi, Osako, Yutaro, Gao-Takai, Mei, Kojima, Mikiko, Sakakibara, Hitoshi, Tao, Ryutaro

    PLOS ONE   14 ( 4 )   e0214788   2019.4

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    DOI: 10.1371/journal.pone.0214788

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  • Global transcriptome analyses reveal that infection with chrysanthemum stunt viroid (CSVd) affects gene expression profile of chrysanthemum plants, but the genes involved in plant hormone metabolism and signaling may not be silencing target of CSVd-siRNAs Reviewed

    Takino H, Kitajima S, Hirano S, Oka M, Matsuura T, Ikeda Y, Kojima M, Takebayashi Y, Sakakibara H, Mino M

    Plant Gene   18 ( Article100181 )   100181 - 100181   2019

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.plgene.2019.100181

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  • Loss of CG methylation in Marchantia polymorpha causes disorganization of cell division and reveals unique DNA methylation regulatory mechanisms of non-CG methylation. Reviewed

    Ikeda Y, Nishihama R, Yamaoka S, Arteaga-Vazquez MA, Aguilar-Cruz A, Grimanelli D, Pogorelcnik R, Martienssen RA, Yamato KT, Kohchi T, Hirayama T, Mathieu O

    Plant and Cell Physiology   59 ( 12 )   2421 - 2431   2018.12

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    DOI: 10.1093/pcp/pcy161

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  • FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis Reviewed

    Jennifer M. Frost, M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, Jaemyung Choi, Yoko Ikeda, Tetsu Kinoshita, Yeonhee Choi, Daniel Zilberman, Robert L. Fischer

    Proceedings of the National Academy of Sciences of the United States of America   115 ( 20 )   E4720 - E4729   2018.5

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:National Academy of Sciences  

    DOI: 10.1073/pnas.1713333115

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  • Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Reviewed International journal

    John L Bowman, Takayuki Kohchi, Katsuyuki T Yamato, Jerry Jenkins, Shengqiang Shu, Kimitsune Ishizaki, Shohei Yamaoka, Ryuichi Nishihama, Yasukazu Nakamura, Frédéric Berger, Catherine Adam, Shiori Sugamata Aki, Felix Althoff, Takashi Araki, Mario A Arteaga-Vazquez, Sureshkumar Balasubrmanian, Kerrie Barry, Diane Bauer, Christian R Boehm, Liam Briginshaw, Juan Caballero-Perez, Bruno Catarino, Feng Chen, Shota Chiyoda, Mansi Chovatia, Kevin M Davies, Mihails Delmans, Taku Demura, Tom Dierschke, Liam Dolan, Ana E Dorantes-Acosta, D Magnus Eklund, Stevie N Florent, Eduardo Flores-Sandoval, Asao Fujiyama, Hideya Fukuzawa, Bence Galik, Daniel Grimanelli, Jane Grimwood, Ueli Grossniklaus, Takahiro Hamada, Jim Haseloff, Alexander J Hetherington, Asuka Higo, Yuki Hirakawa, Hope N Hundley, Yoko Ikeda, Keisuke Inoue, Shin-Ichiro Inoue, Sakiko Ishida, Qidong Jia, Mitsuru Kakita, Takehiko Kanazawa, Yosuke Kawai, Tomokazu Kawashima, Megan Kennedy, Keita Kinose, Toshinori Kinoshita, Yuji Kohara, Eri Koide, Kenji Komatsu, Sarah Kopischke, Minoru Kubo, Junko Kyozuka, Ulf Lagercrantz, Shih-Shun Lin, Erika Lindquist, Anna M Lipzen, Chia-Wei Lu, Efraín De Luna, Robert A Martienssen, Naoki Minamino, Masaharu Mizutani, Miya Mizutani, Nobuyoshi Mochizuki, Isabel Monte, Rebecca Mosher, Hideki Nagasaki, Hirofumi Nakagami, Satoshi Naramoto, Kazuhiko Nishitani, Misato Ohtani, Takashi Okamoto, Masaki Okumura, Jeremy Phillips, Bernardo Pollak, Anke Reinders, Moritz Rövekamp, Ryosuke Sano, Shinichiro Sawa, Marc W Schmid, Makoto Shirakawa, Roberto Solano, Alexander Spunde, Noriyuki Suetsugu, Sumio Sugano, Akifumi Sugiyama, Rui Sun, Yutaka Suzuki, Mizuki Takenaka, Daisuke Takezawa, Hirokazu Tomogane, Masayuki Tsuzuki, Takashi Ueda, Masaaki Umeda, John M Ward, Yuichiro Watanabe, Kazufumi Yazaki, Ryusuke Yokoyama, Yoshihiro Yoshitake, Izumi Yotsui, Sabine Zachgo, Jeremy Schmutz

    Cell   171 ( 2 )   287 - 304   2017.10

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    The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

    DOI: 10.1016/j.cell.2017.09.030

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  • The SAL-PAP Chloroplast Retrograde Pathway Contributes to Plant Immunity by Regulating Glucosinolate Pathway and Phytohormone Signaling

    Yasuhiro Ishiga, Mutsumi Watanabe, Takako Ishiga, Takayuki Tohge, Takakazu Matsuura, Yoko Ikeda, Rainer Hoefgen, Alisdair R. Fernie, Kirankumar S. Mysore

    Molecular Plant-Microbe Interactions®   30 ( 10 )   829 - 841   2017.10

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    DOI: 10.1094/mpmi-03-17-0055-r

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  • Global profiling of phytohormone dynamics during combined drought and pathogen stress in Arabidopsis thaliana reveals ABA and JA as major regulators Reviewed

    Aarti Gupta, Hiroshi Hisano, Yuko Hojo, Takakazu Matsuura, Yoko Ikeda, Izumi C. Mori, Muthappa Senthil-Kumar

    SCIENTIFIC REPORTS   7 ( 1 )   4017   2017.6

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    DOI: 10.1038/s41598-017-03907-2

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  • Arabidopsis proteins with a transposon-related domain act in gene silencing Reviewed

    Yoko Ikeda, Thierry Pelissier, Pierre Bourguet, Claude Becker, Marie-Noelle Pouch-Pelissier, Romain Pogorelcnik, Magdalena Weingartner, Detlef Weigel, Jean-Marc Deragon, Olivier Mathieu

    NATURE COMMUNICATIONS   8   15122   2017.5

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    DOI: 10.1038/ncomms15122

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  • Ectopic accumulation of linalool confers resistance to Xanthomonas citri subsp citri in transgenic sweet orange plants Reviewed

    Takehiko Shimada, Tomoko Endo, Ana Rodriguez, Hiroshi Fujii, Shingo Goto, Takakazu Matsuura, Yuko Hojo, Yoko Ikeda, Izumi C. Mori, Takashi Fujikawa, Leandro Pena, Mitsuo Omura

    TREE PHYSIOLOGY   37 ( 5 )   654 - 664   2017.5

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    DOI: 10.1093/treephys/tpw134

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  • Phytohormones in red seaweeds: a technical review of methods for analysis and a consideration of genomic data Reviewed

    Izumi C. Mori, Yoko Ikeda, Takakazu Matsuura, Takashi Hirayama, Koji Mikami

    BOTANICA MARINA   60 ( 2 )   153 - 170   2017.4

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    DOI: 10.1515/bot-2016-0056

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  • Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids Reviewed

    Melanie Rigal, Claude Becker, Thierry Pelissier, Romain Pogorelcnik, Jane Devos, Yoko Ikeda, Detlef Weigel, Olivier Mathieu

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   113 ( 14 )   E2083 - E2092   2016.4

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    DOI: 10.1073/pnas.1600672113

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  • NADPH-dependent thioredoxin reductase C plays a role in nonhost disease resistance against Pseudomonas syringae pathogens by regulating chloroplast-generated reactive oxygen species Reviewed

    Yasuhiro Ishiga, Takako Ishiga, Yoko Ikeda, Takakazu Matsuura, Kirankumar S. Mysore

    PEERJ   4   e1938   2016.4

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    DOI: 10.7717/peerj.1938

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  • Light Inhibition of Shoot Regeneration Is Regulated by Endogenous Abscisic Acid Level in Calli Derived from Immature Barley Embryos Reviewed

    Kazuhide Rikiishi, Takakazu Matsuura, Yoko Ikeda, Masahiko Maekawa

    PLOS ONE   10 ( 12 )   e0145242   2015.12

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    DOI: 10.1371/journal.pone.0145242

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  • Comprehensive quantification and genome survey reveal the presence of novel phytohormone action modes in red seaweeds. Reviewed

    Mikami, K, Mori, I.C, Matsuura, T, Ikeda, Y, Kojima, M, Sakakibara, H, Hirayama, T

    J. Applied Phycology.   28   2539 - 2548   2015

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  • Plant Imprinted Genes Identified by Genome-wide Approaches and Their Regulatory Mechanisms Reviewed

    Yoko Ikeda

    PLANT AND CELL PHYSIOLOGY   53 ( 5 )   809 - 816   2012.5

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  • HMG Domain containing SSRP1 is required for DNA demethylation and genomic imprinting in arabidopsis Reviewed

    Yoko Ikeda, Yuki Kinoshita, Daichi Susaki, Yuriko Ikeda, Megumi Iwano, Seiji Takayama, Tetsuya Higashiyama, Tetsuji Kakutani, Tetsu Kinoshita

    Developmental Cell   21 ( 3 )   589 - 596   2011.9

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    DOI: 10.1016/j.devcel.2011.08.013

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  • DNA demethylation: A lesson from the garden Reviewed

    Yoko Ikeda, Tetsu Kinoshita

    Chromosoma   118 ( 1 )   37 - 41   2009

  • Genomic imprinting: A balance between antagonistic roles of parental chromosomes Reviewed

    Tetsu Kinoshita, Yoko Ikeda, Ryo Ishikawa

    Seminars in Cell and Developmental Biology   19 ( 6 )   574 - 579   2008.12

  • Molecular basis of late-flowering phenotype caused by dominant epi-alleles of the FWA locus in Arabidopsis Reviewed

    Yoko Ikeda, Yasushi Kobayashi, Ayako Yamaguchi, Mitsutomo Abe, Takashi Araki

    PLANT AND CELL PHYSIOLOGY   48 ( 2 )   205 - 220   2007.2

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    DOI: 10.1093/pcp/pcl061

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  • FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex Reviewed

    M Abe, Y Kobayashi, S Yamamoto, Y Daimon, A Yamaguchi, Y Ikeda, H Ichinoki, M Notaguchi, K Goto, T Araki

    SCIENCE   309 ( 5737 )   1052 - 1056   2005.8

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    DOI: 10.1126/science.1115983

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  • Flagella are required for complete virulence of Pseudomonas syringae pv. tabaci: genetic analysis with flagella-defective mutants, ΔfliC andΔfliD, in host tobacco plants. Reviewed

    Ichinose, Y, Shimizu, R, Ikeda, Y, Taguchi, F, Marutani, M, Mukaihara, T, Inagaki, Y, Toyoda, K, Shiraishi, T

    Journal of General Plant Pathology   69 ( 4 )   244 - 249   2003

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Books

MISC

  • ゼニゴケにおける生殖を介したDNAメチル化の伝達機構

    池田陽子, 池田陽子, 中村光希, 十川太輔, 西浜竜一, 山岡尚平, 荒木崇, 河内孝之, MATHIEU Olivier, 大和勝幸

    日本植物学会大会研究発表記録(CD-ROM)   87th   2023

  • Developmental state transition in the shoot apical meristem of barley

    井藤純, 野村有子, 高萩航太郎, 岡田聡史, 久下修平, 佐藤奈緒, 新井駿一, 松本大輝, 杉村みどり, 関緑, 服部公央亮, 梅崎太造, 池田陽子, 最相大輔, 持田恵一, 平山隆志, 辻寛之

    日本植物生理学会年会(Web)   63rd   2022

  • Data driven crop design technology

    平山隆志, 最相大輔, 井藤純, 服部公央亮, 岡田聡史, 池田陽子, 梅崎太造, 辻寛之, 持田恵一

    日本植物生理学会年会(Web)   63rd   2022

  • ゼニゴケMpROS1a,MpROS1xによるDNA脱メチル化制御

    池田陽子, 中村光希, 十川太輔, 西浜竜一, 山岡尚平, 荒木崇, 河内孝之, 大和勝幸

    日本植物学会大会研究発表記録(CD-ROM)   86th   2022

  • Data driven crop design technology

    平山隆志, 岡田聡史, 最相大輔, 井藤純, 服部公央亮, 池田陽子, 梅崎太造, 辻寛之, 持田恵一

    日本分子生物学会年会プログラム・要旨集(Web)   44th   2021

  • Genomic research across the barley life cycle toward ’preemptive breeding’

    最相大輔, 岡田聡史, 金谷麻加, 金谷麻加, 池田陽子, 井藤純, 辻寛之, 持田恵一, 持田恵一, 持田恵一, 平山隆志

    育種学研究   23   2021

  • Developmental trajectory analysis of barley life cycle using field transcriptome data

    岡田聡史, 最相大輔, 金谷麻加, 金谷麻加, 池田陽子, 井藤純, 辻寛之, 井上小槙, 上原由紀子, 清水みなみ, 持田恵一, 持田恵一, 持田恵一, 平山隆志

    育種学研究   23   2021

  • Pseudo-time transition of barley life cycle in the field

    最相大輔, 岡田聡史, 金谷麻加, 金谷麻加, 池田陽子, 井藤純, 辻寛之, 持田恵一, 持田恵一, 持田恵一, 平山隆志

    育種学研究   23   2021

  • Reinvention of hermaphroditism triggered by activation of a RADIALIS-like gene in hexaploid persimmon

    増田佳苗, 池田陽子, 松浦恭和, 川勝泰二, 田尾龍太郎, 久保康隆, 牛島幸一郎, HENRY Isabelle M., 赤木剛士, 赤木剛士

    園芸学研究 別冊   20 ( 2 )   2021

  • ゼニゴケの新規DNAメチル化制御機構:植物と動物の狭間で

    池田陽子, 十川太輔, 西浜竜一, 山岡尚平, 荒木崇, 河内孝之, 平山隆志, 大和勝幸

    日本植物学会大会研究発表記録(CD-ROM)   84th   2020

  • 圃場オオムギを用いた時系列クロマチン修飾解析

    池田陽子, 金谷麻加, 井上小槙, 最相大輔, 井藤純, 辻寛之, 持田恵一, 持田恵一, 持田恵一, 平山隆志

    日本植物生理学会年会(Web)   60th   2019

  • PARN and PAP regulate the poly(A) status of mitochondrial mRNA in liverwort.

    KANAZAWA Mai, IKEDA Yoko, NISHIHAMA Ryuichi, YAMAOKA Shohei, KOCHI Takayuki, HIRAYAMA Takashi

    日本RNA学会年会要旨集   18th   2016

  • Control of genomic imprinting by ALARM CLOCK1 gene in Arabidopsis

    Yoko Ikeda, Yuki Kinoshita, Tetsuji Kakutani, Tetsu Kinoshita

    GENES & GENETIC SYSTEMS   83 ( 6 )   534 - 534   2008.12

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  • Molecular basis of late-flowering phenotype caused by dominant epi-alleles of the FWA locus in Arabidopsis (vol 48, pg 205, 2007)

    Yoko Ikeda, Yasushi Kobayashi, Ayako Yamaguchi, Mitsutomo Abe, Takashi Araki

    PLANT AND CELL PHYSIOLOGY   48 ( 3 )   562 - 562   2007.3

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  • GL2-class HD-ZIP protein FWA delays flowering through specific interaction with FT protein

    Yoko Ikeda, Ayako Yamaguchi, Mitsutomo Abe, Takashi Araki

    PLANT AND CELL PHYSIOLOGY   48   S113 - S113   2007

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  • Dissection of flowering pathways using GL2-class HD-ZIP protein FWA

    Y Ikeda, M Abe, T Araki

    PLANT AND CELL PHYSIOLOGY   47   S65 - S65   2006

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  • Long-distance signals to promote floral transition in Arabidopsis

    M Abe, Y Daimon, S Yamamoto, A Yamaguchi, Y Ikeda, M Notaguchi, T Araki

    PLANT AND CELL PHYSIOLOGY   47   S2 - S2   2006

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  • Functional analysis of Arabidopsis FD protein by the C-terminal modification

    S Yamamoto, Y Ikeda, M Abe, T Araki

    PLANT AND CELL PHYSIOLOGY   46   S95 - S95   2005

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  • Moleculer basis of late-flowering phenotype in dominant fwa mutants

    Y Ikeda, M Abe, T Araki

    PLANT AND CELL PHYSIOLOGY   46   S96 - S96   2005

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  • Reevaluation of the florigen hypothesis: A molecular genetic approach with Arabidopsis

    T Araki, Y Daimon, S Yamamoto, A Yamaguchi, Y Ikeda, M Notaguchi, M Kobayashi, K Goto, M Abe

    PLANT AND CELL PHYSIOLOGY   46   S10 - S10   2005

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  • Dissection of flowering pathways using a GL2-type HD-ZIP gene FWA

    Y Ikeda, Y Kobayashi, M Abe, T Araki

    PLANT AND CELL PHYSIOLOGY   45   S71 - S71   2004

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  • Integration of regulatory pathways by flowering-genes FT and FD

    M Abe, S Yamamoto, Y Daimon, A Yamaguchi, Y Ikeda, H Ichinoki, M Notaguchi, T Araki

    PLANT AND CELL PHYSIOLOGY   45   S20 - S20   2004

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  • Dissection of flowering pathways using a GL2-type HD-ZIP gene FWA

    Y Ikeda, Y Kobayashi, M Abe, T Araki

    PLANT AND CELL PHYSIOLOGY   44   S133 - S133   2003

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  • The importance of post-translational modification of bacterial HR-elicitor, flagellin on HR-inducing ability and pathogenicity

    F Taguchi, Y Ikeda, R Shimizu, K Takeuchi, Y Inagaki, T Shiraishi, Y Ichinose

    PLANT AND CELL PHYSIOLOGY   43   S201 - S201   2002

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Awards

  • 奨励賞受賞

    2019.5   日本エピジェネティクス研究会  

    池田 陽子

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  • 年会長賞

    2009.5   日本エピジェネティクス研究会  

    池田 陽子

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Research Projects

  • Regulatory mechanism of DNA methylation and transposon in early land plant evolution

    Grant number:23H04747  2023.04 - 2025.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Transformative Research Areas (A)

    池田 陽子

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    Grant amount:\10400000 ( Direct expense: \8000000 、 Indirect expense:\2400000 )

    植物の性決定機構の変化を介した繁殖戦略の構築メカニズムや、雌雄のゲノムの制御には、エピゲノム制御が重要な役割を果たしていることが知られている。エピゲノム修飾の中でも、シトシンのメチル化は遺伝子やトランスポゾンの発現に影響を与える。性決定関連因子やインプリント遺伝子なども、トランスポゾンの挿入がトリガーとなって構築されたと考えられており、繁殖戦略の進化と、エピゲノム制御及びトランスポゾン転移は密接な関係がある。
    申請者らは、DNAメチル化などの植物のエピゲノム制御機構がどのように進化してきたかを明らかにするため、進化上、陸上植物の基部に位置するゼニゴケを用い解析を進めた。これまでに、ゼニゴケは被子植物で明らかになったDNAメチル化の制御機構との共通点だけでなく、動物と似たDNAメチル化制御システムの特徴を複数有することが明らかになってきた。また、最近の報告から、ゼニゴケでは、これまで被子植物で知られている報告とは異なり、DNAメチル化だけでなく、ヒストンH3K27me3の修飾がトランスポゾン領域に局在しており、発現の抑制に関わることが示唆されている。これらを踏まえ、ゼニゴケにおけるDNAメチル化とH3K27me3などのヒストンによるトランスポゾン制御の多層的な制御の全体像を明らかにすることを目的として、DNAメチル化に関与する変異体を用いてDNAメチル化とトランズポゾンの制御について解析するとともに、DNAメチル化とヒストン修飾の相互作用についても解析を行った。

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  • 植物進化過程における転写サイレンシング機能獲得機構

    Grant number:22K06266  2022.04 - 2025.03

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    池田 陽子

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    Grant amount:\4160000 ( Direct expense: \3200000 、 Indirect expense:\960000 )

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  • DNAメチル化ダイナミクス解析による生殖過程のDNAメチル化消去・維持機構の解明

    Grant number:22H04693  2022.04 - 2024.03

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    池田 陽子

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    Grant amount:\8580000 ( Direct expense: \6600000 、 Indirect expense:\1980000 )

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  • Understanding for mechanism of DNA methylation erasure and maintenance in meiosis

    Grant number:20H05391  2020.04 - 2022.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    池田 陽子

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    Grant amount:\8320000 ( Direct expense: \6400000 、 Indirect expense:\1920000 )

    DNAメチル化は'非ゲノム情報'のうち唯一世代を超えて安定的に伝わることが証明されている修飾であり、クロマチンとの相互作用を介して遺伝子の発現制御に関わることが知られている。DNAメチル化の次世代への伝達機構については、動物と植物の間で違いがみられ、動物では生殖系列でDNAメチル化がリプログラミングされ、雌雄のゲノムの差が生じる一方、被子植物では減数分裂後、胚乳系列でのみDNAメチル化が解除され、卵及び精細胞ではDNAメチル化が維持される。そのため植物ではDNAメチル化の変化が次の世代に伝わりうるとされている。
    そこで、植物特有のDNAメチル化維持機構がどのように進化してきたかを明らかにするため、本研究では、進化上、陸上植物の基部に位置するゼニゴケを用い解析を進めた。これまでに、我々の解析により、ゼニゴケにおけるDNAメチル化制御機構は被子植物と共通した特徴だけでなく、異なる制御の特徴を持つことを示唆する結果が得られている。本研究では特に、ゼニゴケの減数分裂前後におけるDNAメチル化の制御機構に焦点を当て、解析を行った。
    今年度は、ゼニゴケのDNAメチル化の詳細な解析を進めるための育成環境や生殖器の誘導条件など、実験に必要な材料の準備を行った。環境が整い、サンプリングの技術等の条件が整い、次世代シーケンサを用いたゲノムワイドバイサルファイト解析を行う状況が整った。また、ゼニゴケにおいてDNAメチル化に関与する因子の変異体を作成し、詳細な機能解析を進めている。

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  • 植物における新規転写型遺伝子サイレンシング機構の解析

    2018.04 - 2022.03

    文部科学省  科学研究費助成事業 基盤研究(C) 

    池田 陽子

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  • レトロトランスポゾン転写制御機構の解析

    2015.04 - 2018.03

    文部科学省  科学研究費助成事業 若手研究(B) 

    池田 陽子

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  • 組織特異的なヘテロクロマチンサイレンシングに関わる新規因子の解析

    2014.04 - 2015.03

    文部科学省  科学研究費助成事業 研究活動スタート支援 

    池田 陽子

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Class subject in charge

  • Seminar in Signaling Mechanisms (2024academic year) Prophase  - その他

  • Seminar in Signaling Mechanisms (2024academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2024academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2024academic year) Prophase  - その他

  • Seminar in Signaling Mechanisms (2024academic year) Year-round  - その他

  • Plant Epigenome Regulation Mechanisms (2024academic year) Prophase  - その他

  • Plant physiology 1 (2024academic year) Third semester  - 金1,金2

  • Plant physiology 2 (2024academic year) Fourth semester  - 金1,金2

  • Advanced Study (2024academic year) Other  - その他

  • Environmental Stress Response Systems (2024academic year) Late  - 火5~8

  • Seminar in Signaling Mechanisms (2023academic year) Prophase  - その他

  • Seminar in Signaling Mechanisms (2023academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2023academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2023academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2023academic year) Prophase  - その他

  • Seminar in Signaling Mechanisms (2023academic year) Prophase  - その他

  • Seminar in Signaling Mechanisms (2023academic year) Year-round  - その他

  • Plant Epigenome Regulation Mechanisms (2023academic year) Prophase  - その他

  • Plant Epigenome Regulation Mechanisms (2023academic year) Prophase  - その他

  • Plant physiology 1 (2023academic year) Third semester  - 金1,金2

  • Plant physiology 2 (2023academic year) Fourth semester  - 金1,金2

  • Advanced Study (2023academic year) Other  - その他

  • Environmental Stress Response Systems (2023academic year) Late  - 火5~8

  • Environmental Stress Response Systems (2023academic year) Late  - 火5~8

  • Specific Research of Bioresources Science (2023academic year) Year-round  - その他

  • Seminar in Signaling Mechanisms (2022academic year) Prophase  - その他

  • Seminar in Signaling Mechanisms (2022academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2022academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2022academic year) Prophase  - その他

  • Plant Epigenome Regulation Mechanisms (2022academic year) Prophase  - その他

  • Plant physiology 1 (2022academic year) Third semester  - 金1,金2

  • Environmental Stress Response Systems (2022academic year) Late  - 火5~8

  • Specific Research of Bioresources Science (2022academic year) Year-round  - その他

  • Seminar in Signaling Mechanisms (2021academic year) Prophase  - その他

  • Seminar in Signaling Mechanisms (2021academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2021academic year) Late  - その他

  • Seminar in Signaling Mechanisms (2021academic year) Prophase  - その他

  • Plant Epigenome Regulation Mechanisms (2021academic year) Prophase  - その他

  • Plant physiology 1 (2021academic year) Third semester  - 金1,金2

  • Environmental Stress Response Systems (2021academic year) Late  - 火5~8

  • Specific Research of Bioresources Science (2021academic year) Year-round  - その他

  • Seminar in Signaling Mechanisms (2020academic year) Prophase  - その他

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