Soichi Inagaki

Publications of Soichi Inagaki

• Programmed induction of endoreduplication by DNA double-strand breaks in Arabidopsis.

  Authors: Sumiko Adachi, Kazunori Minamisawa, Yoko Okushima, Soichi Inagaki, Kaoru Yoshiyama, Youichi Kondou, Eli Kaminuma, Mika Kawashima, Tetsuro Toyoda, Minami Matsui, Daisuke Kurihara, Sachihiro Matsunaga, Masaaki Umeda

  Proceedings of the National Academy of Sciences of the United States of America. 06/2011; 108(24):10004-9.

  Genome integrity is continuously threatened by external stresses and endogenous hazards such as DNA replication errors and reactive oxygen species. The DNA damage checkpoint in metazoans ensuresGenome integrity is continuously threatened by external stresses and endogenous hazards such as DNA replication errors and reactive oxygen species. The DNA damage checkpoint in metazoans ensures genome integrity by delaying cell-cycle progression to repair damaged DNA or by inducing apoptosis. ATM and ATR (ataxia-telangiectasia-mutated and -Rad3-related) are sensor kinases that relay the damage signal to transducer kinases Chk1 and Chk2 and to downstream cell-cycle regulators. Plants also possess ATM and ATR orthologs but lack obvious counterparts of downstream regulators. Instead, the plant-specific transcription factor SOG1 (suppressor of gamma response 1) plays a central role in the transmission of signals from both ATM and ATR kinases. Here we show that in Arabidopsis, endoreduplication is induced by DNA double-strand breaks (DSBs), but not directly by DNA replication stress. When root or sepal cells, or undifferentiated suspension cells, were treated with DSB inducers, they displayed increased cell size and DNA ploidy. We found that the ATM-SOG1 and ATR-SOG1 pathways both transmit DSB-derived signals and that either one suffices for endocycle induction. These signaling pathways govern the expression of distinct sets of cell-cycle regulators, such as cyclin-dependent kinases and their suppressors. Our results demonstrate that Arabidopsis undergoes a programmed endoreduplicative response to DSBs, suggesting that plants have evolved a distinct strategy to sustain growth under genotoxic stress.

• Cell-cycle control and plant development.

  Authors: Soichi Inagaki, Masaaki Umeda

  International review of cell and molecular biology. 01/2011; 291:227-61.

  The cell cycle is driven by the activity of cyclin-dependent kinase (CDK)-cyclin complexes. Therefore, internal and external signals converge on the regulation of CDK-cyclin activity to modulate cellThe cell cycle is driven by the activity of cyclin-dependent kinase (CDK)-cyclin complexes. Therefore, internal and external signals converge on the regulation of CDK-cyclin activity to modulate cell proliferation in specific developmental processes and under various environmental conditions. CDK-cyclin activity is fine-tuned by multiple mechanisms, for example, transcriptional control, protein degradation, phosphorylation, and binding to CDK inhibitor. These molecular mechanisms underlie the regulation of the entry into or the exit from the cell cycle, the rate of cell cycle, or the transition from the mitotic cell cycle to the endocycle. The multiple mechanisms regulating CDK-cyclin activity coordinately enable the elaborate control of cell cycle by various upstream signals. Here, we review the molecular mechanisms that regulate the cell cycle and the endocycle in plants. We also introduce the recent progress in elucidating the regulatory mechanisms underlying plant development and the stress response in terms of cell-cycle control.

• Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.

  Authors: Soichi Inagaki, Asuka Miura-Kamio, Yasukazu Nakamura, Falong Lu, Xia Cui, Xiaofeng Cao, Hiroshi Kimura, Hidetoshi Saze, Tetsuji Kakutani

  The EMBO journal. 10/2010; 29(20):3496-506.

  In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical forIn diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical for maintaining genome integrity, mechanisms to exclude H3K9me from active genes remain largely unexplored. Here, we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation). Loss-of-function ibm1 mutation results in ectopic H3K9me and non-CG methylation in thousands of genes. The ibm1-induced genic H3K9me depends on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks--H3K9me and non-CG methylation. Notably, IBM1 enhances loss of H3K9me in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induces ectopic non-CG methylation, which mimics the loss of IBM1 function. We propose that active chromatin is stabilized by an autocatalytic loop of transcription and H3K9 demethylation. This process counteracts a similarly autocatalytic accumulation of silent epigenetic marks, H3K9me and non-CG methylation.

• Control of genic DNA methylation in Arabidopsis.

  Authors: Soichi Inagaki, Tetsuji Kakutani

  Journal of plant research. 04/2010; 123(3):299-302.

  Detailed features of genomic DNA methylation have been revealed by recent genome-wide analyses on several model organisms. An unexpected feature conserved among plants and some animals is theDetailed features of genomic DNA methylation have been revealed by recent genome-wide analyses on several model organisms. An unexpected feature conserved among plants and some animals is the presence of DNA methylation within transcribed genes. For understanding the controlling mechanisms of the enigmatic genic methylation, genetic and genomic approaches using Arabidopsis may be effective.

• A link among DNA replication, recombination, and gene expression revealed by genetic and genomic analysis of TEBICHI gene of Arabidopsis thaliana.

  Authors: Soichi Inagaki, Kenzo Nakamura, Atsushi Morikami

  PLoS genetics. 09/2009; 5(8):e1000613.

  Spatio-temporal regulation of gene expression during development depends on many factors. Mutations in Arabidopsis thaliana TEBICHI (TEB) gene encoding putative helicase and DNA polymeraseSpatio-temporal regulation of gene expression during development depends on many factors. Mutations in Arabidopsis thaliana TEBICHI (TEB) gene encoding putative helicase and DNA polymerase domains-containing protein result in defects in meristem maintenance and correct organ formation, as well as constitutive DNA damage response and a defect in cell cycle progression; but the molecular link between these phenotypes of teb mutants is unknown. Here, we show that mutations in the DNA replication checkpoint pathway gene, ATR, but not in ATM gene, enhance developmental phenotypes of teb mutants, although atr suppresses cell cycle defect of teb mutants. Developmental phenotypes of teb mutants are also enhanced by mutations in RAD51D and XRCC2 gene, which are involved in homologous recombination. teb and teb atr double mutants exhibit defects in adaxial-abaxial polarity of leaves, which is caused in part by the upregulation of ETTIN (ETT)/AUXIN RESPONSIVE FACTOR 3 (ARF3) and ARF4 genes. The Helitron transposon in the upstream of ETT/ARF3 gene is likely to be involved in the upregulation of ETT/ARF3 in teb. Microarray analysis indicated that teb and teb atr causes preferential upregulation of genes nearby the Helitron transposons. Furthermore, interestingly, duplicated genes, especially tandemly arrayed homologous genes, are highly upregulated in teb or teb atr. We conclude that TEB is required for normal progression of DNA replication and for correct expression of genes during development. Interplay between these two functions and possible mechanism leading to altered expression of specific genes will be discussed.

• An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites.

  Authors: Asuka Miura, Miyuki Nakamura, Soichi Inagaki, Akie Kobayashi, Hidetoshi Saze, Tetsuji Kakutani

  The EMBO journal. 04/2009;

  Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non-CG sites,Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non-CG sites, whereas the non-CG methylation is rarely found in active genes. Our previous genetic analysis suggested that a jmjC domain-containing protein IBM1 (increase in BONSAI methylation 1) prevents ectopic deposition of non-CG methylation, and this process is necessary for normal Arabidopsis development. Here, we directly determined the genomic targets of IBM1 through high-resolution genome-wide analysis of DNA methylation. The ibm1 mutation induced extensive hyper-methylation in thousands of genes. Transposons were unaffected. Notably, long transcribed genes were most severely affected. Methylation of genes is limited to CG sites in wild type, but CHG sites were also methylated in the ibm1 mutant. The ibm1-induced hyper-methylation did not depend on previously characterized components of the RNAi-based DNA methylation machinery. Our results suggest novel transcription-coupled mechanisms to direct genic methylation not only at CG but also at CHG sites. IBM1 prevents the CHG methylation in genes, but not in transposons.

• Arabidopsis TEBICHI, with helicase and DNA polymerase domains, is required for regulated cell division and differentiation in meristems.

  Authors: Soichi Inagaki, Takamasa Suzuki, Masa-aki Ohto, Hiroko Urawa, Takashi Horiuchi, Kenzo Nakamura, Atsushi Morikami

  The Plant cell. 05/2006; 18(4):879-92.

  In plant meristems, each cell divides and differentiates in a spatially and temporally regulated manner, and continuous organogenesis occurs using cells derived from the meristem. We report theIn plant meristems, each cell divides and differentiates in a spatially and temporally regulated manner, and continuous organogenesis occurs using cells derived from the meristem. We report the identification of the Arabidopsis thaliana TEBICHI (TEB) gene, which is required for regulated cell division and differentiation in meristems. The teb mutants show morphological defects, such as short roots, serrated leaves, and fasciation, as well as defective patterns of cell division and differentiation in the meristem. The TEB gene encodes a homolog of Drosophila MUS308 and mammalian DNA polymerase theta, which prevent spontaneous or DNA damage-induced production of DNA double strand breaks. As expected from the function of animal homologs, teb mutants show constitutively activated DNA damage responses. Unlike other fasciation mutants with activated DNA damage responses, however, teb mutants do not activate transcriptionally silenced genes. teb shows an accumulation of cells expressing cyclinB1;1:GUS in meristems, suggesting that constitutively activated DNA damage responses in teb lead to a defect in G2/M cell cycle progression. Furthermore, other fasciation mutants, such as fasciata2 and tonsoku/mgoun3/brushy1, also show an accumulation of cells expressing cyclinB1;1:GUS in meristems. These results suggest that cell cycle progression at G2/M is important for the regulation of the pattern of cell division and of differentiation during plant development.

• TONSOKU is expressed in S phase of the cell cycle and its defect delays cell cycle progression in Arabidopsis.

  Authors: Takamasa Suzuki, Sakiko Nakajima, Soichi Inagaki, Makiko Hirano-Nakakita, Ken Matsuoka, Taku Demura, Hiroo Fukuda, Atsushi Morikami, Kenzo Nakamura

  Plant & cell physiology. 06/2005; 46(5):736-42.

  TONSOKU(TSK)/MGOUN3/BRUSHY1 of Arabidopsis thaliana encodes a nuclear leucine-glycine-aspargine (LGN) domain protein implicated to be involved in genome maintenance, and mutants with defects in TSKTONSOKU(TSK)/MGOUN3/BRUSHY1 of Arabidopsis thaliana encodes a nuclear leucine-glycine-aspargine (LGN) domain protein implicated to be involved in genome maintenance, and mutants with defects in TSK show a fasciated stem with disorganized meristem structures. We identified a homolog of TSK from tobacco BY-2 cells (NtTSK), which showed high sequence conservation both in the LGN domain and in leucine-rich repeats with AtTSK. The NtTSK gene was expressed during S phase of the cell cycle in tobacco BY-2 cells highly synchronized for cell division. The tsk mutants of Arabidopsis contained an increased proportion of cells with 4C nuclei and cells expressing cyclin B1 compared with the wild type. These results suggest that TSK is required during the cell cycle and defects of TSK cause the arrest of cell cycle progression at G2/M phase.

• A novel Arabidopsis gene TONSOKU is required for proper cell arrangement in root and shoot apical meristems.

  Authors: Takamasa Suzuki, Soichi Inagaki, Sakiko Nakajima, Takafumi Akashi, Masa-aki Ohto, Masatomo Kobayashi, Motoaki Seki, Kazuo Shinozaki, Tomohiko Kato, Satoshi Tabata, Kenzo Nakamura, Atsushi Morikami

  The Plant journal : for cell and molecular biology. 06/2004; 38(4):673-84.

  Root apical meristem (RAM) and shoot apical meristem (SAM) are vital for the correct development of the plant. The direction, frequency, and timing of cell division must be tightly controlled inRoot apical meristem (RAM) and shoot apical meristem (SAM) are vital for the correct development of the plant. The direction, frequency, and timing of cell division must be tightly controlled in meristems. Here, we isolated new Arabidopsis mutants with shorter roots and fasciated stems. In the tonsoku (tsk) mutant, disorganized RAM and SAM formation resulted from the frequent loss of proper alignment of the cell division plane. Irregular cell division also occurred in the tsk embryo, and the size of cells in meristems and embryo in tsk mutant was larger than in the wild type. In the enlarged SAM of the tsk mutant, multiple centers of cells expressing WUSCHEL (WUS) were observed. In addition, expression of SCARECROW (SCR) in the quiescent center (QC) disappeared in the disorganized RAM of tsk mutant. These results suggest that disorganized cell arrangements in the tsk mutants result in disturbed positional information required for the determination of cell identity. The TSK gene was found to encode a protein with 1311 amino acids that possesses two types of protein-protein interaction motif, leucine-glycine-asparagine (LGN) repeats and leucine-rich repeats (LRRs). LGN repeats are present in animal proteins involved in asymmetric cell division, suggesting the possible involvement of TSK in cytokinesis. On the other hand, the localization of the TSK-GFP (green fluorescent protein) fusion protein in nuclei of tobacco BY-2 cells and phenotypic similarity of tsk mutants to other fasciated mutants suggest that the tsk mutation may cause disorganized cell arrangements through defects in genome maintenance.