Research Topics
Genomes and Genes | Takashi ItoSummaryAffiliation: Kanazawa University Country: Japan Publications
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Publications
A comprehensive two-hybrid analysis to explore the yeast protein interactomeT Ito
Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920 0934, Japan
Proc Natl Acad Sci U S A 98:4569-74. 2001..Our data would thus significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system...- Novel modular domain PB1 recognizes PC motif to mediate functional protein-protein interactionsT Ito
Division of Genome Biology, Cancer Research Institute, Kanazawa University, 13 1 Takaramachi, Kanazawa 920 0934, Japan
EMBO J 20:3938-46. 2001..This domain-swapping experiment demonstrates that Bem1p function requires interaction with Cdc24p, in which the PB1 domain and the PC motif participate as responsible modules... - [Exploring interaction networks of the yeast proteins]Takashi Ito
Tanpakushitsu Kakusan Koso 47:898-905. 2002 - Roles for the two-hybrid system in exploration of the yeast protein interactomeTakashi Ito
Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920 0934, Japan
Mol Cell Proteomics 1:561-6. 2002.... - A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q: comparison with chromosome 21qYoichi Yamada
Department of Information and Systems Engineering, Faculty of Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
DNA Seq 17:300-6. 2006..Thus, methylation status of CGIs may substantially differ from one chromosome to another... - Analysis of gene network regulating yeast multidrug resistance by artificial activation of transcription factors: involvement of Pdr3 in salt toleranceMiyuki Onda
Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-0934, Japan
Gene 332:51-9. 2004..The strategy would thus contribute not only to identify target genes but to reveal redundancy and specificity in complex gene regulatory networks... - A yeast one-hybrid system to detect methylation-dependent DNA-protein interactionsShu-Ying Feng
Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-0934, Japan
Biochem Biophys Res Commun 313:922-5. 2004..This methylation-dependent one-hybrid system would provide a versatile tool for the search and analysis of proteins that recognize methylated DNA to participate in epigenetic regulation... - A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21qYoichi Yamada
Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-0934, Japan
Genome Res 14:247-66. 2004..Thus, the cell seems to have a broader repertoire of methylating CGIs than previously thought, and our approach may contribute to uncover novel modes of allelic methylation... - Rapamycin-induced translational derepression of GCN4 mRNA involves a novel mechanism for activation of the eIF2 alpha kinase GCN2Hiroyuki Kubota
Division of Genome Biology, Cancer Research Institute, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-0934, Japan
J Biol Chem 278:20457-60. 2003..However, in contrast with amino acid starvation, rapamycin activates GCN2 without increasing the amount of uncharged tRNAs, but presumably by modifying the tRNA binding affinity of GCN2... - Regulation of N-cadherin-based cell-cell interaction by JSAP1 scaffold in PC12h cellsMunkhuu Bayarsaikhan
Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920 0934, Japan
Biochem Biophys Res Commun 353:357-62. 2007..Taken together, these results suggest that JSAP1 regulates cell-cell interactions in PC12h cells specifically in the NGF-induced signaling pathway, and does so by modulating N-cadherin... - Identification of a five-pass transmembrane protein family localizing in the Golgi apparatus and the ERAbbas Shakoori
Division of Molecular Membrane Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-0934, Japan
Biochem Biophys Res Commun 312:850-7. 2003..These results suggest that FinGERs function in maintenance of the Golgi structure and/or transport between the ER and the Golgi apparatus... - Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplificationYoichi Yamada
School of Electrical and Computer Engineering, College of Science and Engineering, Kanazawa University, Kanazawa 920 1192, Japan
BMC Res Notes 4:179. 2011..abstract:.. - OPR, PC and AID: all in the PB1 familyChris P Ponting
Trends Biochem Sci 27:10. 2002 - Transcriptomic and proteomic analysis of a 14-3-3 gene-deficient yeastTohru Ichimura
Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji shi, Tokyo 192 0397, Japan
Biochemistry 43:6149-58. 2004..This study presents the first comprehensive overview of the genes and proteins that are affected by the depletion of Bmh1/2p and extends the scope of knowledge of the regulatory roles of Bmh1/2p in S. cerevisiae... - A large-scale full-length cDNA analysis to explore the budding yeast transcriptomeFumihito Miura
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8561, Japan
Proc Natl Acad Sci U S A 103:17846-51. 2006..The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies... - A novel Cdc42-interacting domain of the yeast polarity establishment protein Bem1. Implications for modulation of mating pheromone signalingYoshihiro Yamaguchi
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa 277 8561, Japan
J Biol Chem 282:29-38. 2007..Intriguingly, Cdc42 can mediate an indirect interaction of the SH3b-CI to the CRIB domain of Ste20. These results suggest that the SH3b and the CI collaborate in tethering of Ste20 to Bem1 to ensure efficient mating pheromone signaling... - Dual roles of p300 in chromatin assembly and transcriptional activation in cooperation with nucleosome assembly protein 1 in vitroHiroshi Asahara
Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
Mol Cell Biol 22:2974-83. 2002..As p300 acted cooperatively with NAP-1 in stimulating transcription from a chromatin template in vitro, our results suggest a dual role of NAP-1-p300 complexes in promoting chromatin assembly and transcriptional activation... - [Trends in interactomics]Takashi Ito
Tanpakushitsu Kakusan Koso 50:2263-8. 2005 - Transcriptional activators in yeastBjörn Titz
Institut fur Genetik, Forschungszentrum Karlsruhe, Box 3640, D 76021 Karlsruhe, Germany
Nucleic Acids Res 34:955-67. 2006.... - The PB1 domain and the PC motif-containing region are structurally similar protein binding modulesSosuke Yoshinaga
Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo 060-0812, Japan
EMBO J 22:4888-97. 2003..Based on the structural information, we group the PB1 domains and the PCCRs into a novel family, named the PB1 family. Thus, the PB1 family proteins form a specific dimer with each other... - Molecular recognition in dimerization between PB1 domainsYukiko Noda
Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
J Biol Chem 278:43516-24. 2003..Thus the PB1 domain appears to be a protein module that fully exploits its two mutually interacting elements in molecular recognition to expand its repertoire of protein-protein interactions... - Proteomic analysis of in vivo 14-3-3 interactions in the yeast Saccharomyces cerevisiaeKazue Kakiuchi
Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192 0397, Japan
Biochemistry 46:7781-92. 2007.... - Structure and function of the PB1 domain, a protein interaction module conserved in animals, fungi, amoebas, and plantsHideki Sumimoto
Medical Institute of Bioregulation, Kyushu University, Maidashi, Higashi ku, Fukuoka, Japan
Sci STKE 2007:re6. 2007..This Review describes various aspects of PB1 domains at the molecular and cellular levels... - Regulation of histone acetylation and nucleosome assembly by transcription factor JDP2Chunyuan Jin
Gene Engineering Division, Dept. of Biological Systems, BioResource Center, RIKEN (The Institute of Physical and Chemical Research, Tsukuba Science City, Ibaraki 305-0074, Japan
Nat Struct Mol Biol 13:331-8. 2006..These results suggest that the sequence-specific DNA-binding protein JDP2 may control transcription via direct regulation of the modification of histones and the assembly of chromatin... - The yeast eIF4E-associated protein Eap1p attenuates GCN4 translation upon TOR-inactivationRyu Matsuo
Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
FEBS Lett 579:2433-8. 2005.... - High-throughput fluorescence labelling of full-length cDNA products based on a reconstituted translation systemYuko Kawahashi
Department of Biosciences and Informatics, Keio University, Yokohama, Japan
J Biochem 141:19-24. 2007..These methods yielded large numbers of labelled proteins from cDNA sets of various organisms, such as mouse, yeast and Escherichia coli... - Marked strain differences in the pharmacokinetics of an alpha4beta1 integrin antagonist, 4-[1-[3-Chloro-4-[N-(2-methylphenyl)-ureido]phenylacetyl]-(4S)-fluoro-(2S)-pyrrolidine-2-yl]-methoxybenzoic Acid (D01-4582), in Sprague-Dawley rats are associated witTakashi Ito
Drug Metabolism and Physicochemistry Research Laboratory, R and D Division, Daiichi Pharmaceutical Co, Ltd, Tokyo, Japan
J Pharmacol Exp Ther 320:124-32. 2007..In conclusion, the strain differences in D01-4582 pharmacokinetics were suggested to be caused by an alteration in Kd, associated with albumin genetic polymorphism... - Rac1 activity is required for cardiac myocyte alignment in response to mechanical stressMasako Yamane
Department of Clinical Pharmacology and Pharmacogenomics, Graduate School of Pharmaceutical Sciences, Osaka University, 1 6 Yamadaoka, Suita City, Osaka 565 0871, Japan
Biochem Biophys Res Commun 353:1023-7. 2007..The transfection with adenovirus vector expressing dnRac1, but not dnRhoA, inhibited stretch-induced cell alignment. In conclusion, Rac1 activity is necessary for cardiomyocyte alignment in response to directional stretch... - Proteolytic cleavage of high mobility group box 1 protein by thrombin-thrombomodulin complexesTakashi Ito
Laboratory and Vascular Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
Arterioscler Thromb Vasc Biol 28:1825-30. 2008..We previously reported that thrombomodulin (TM), an endothelial thrombin-binding protein, bound to HMGB1, thereby protecting mice from lethal endotoxemia. However, the fate of HMGB1 bound to TM remains to be elucidated... - Peroxisomal metabolism is regulated by an oxygen-recognition system through organelle crosstalk between the mitochondria and peroxisomesShuki Fujimura
Department of Food Science and Technology, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan
Yeast 24:491-8. 2007.... - Dorfin-CHIP chimeric proteins potently ubiquitylate and degrade familial ALS-related mutant SOD1 proteins and reduce their cellular toxicityShinsuke Ishigaki
Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya 466 8500, Japan
Neurobiol Dis 25:331-41. 2007..Furthermore, Dorfin-CHIP(L) rescued neuronal cells from mutant SOD1-associated toxicity and reduced the aggresome formation induced by mutant SOD1 more effectively than did Dorfin(WT)... - Distribution, diversity and regulation of alcohol oxidase isozymes, and phylogenetic relationships of methylotrophic yeastsTakashi Ito
Department of Food Science and Technology, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan
Yeast 24:523-32. 2007.... - Molecular characterization of the PEX5 gene encoding peroxisomal targeting signal 1 receptor from the methylotrophic yeast Pichia methanolicaTakashi Ito
Department of Food Science and Technology, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido 099 2493, Japan
Yeast 24:589-97. 2007..methanolica, including methanol metabolism, and in peroxisomal localization and activation of methanol-metabolizing enzymes, e.g. AOD isozymes, DHAS and CTA... - DNA damage-dependent acetylation and ubiquitination of H2AX enhances chromatin dynamicsTsuyoshi Ikura
Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryoumachi 2 1, Aobaku Sendai 980 8575, Japan
Mol Cell Biol 27:7028-40. 2007..We conclude that the sequential acetylation and ubiquitination of H2AX by TIP60-UBC13 promote enhanced histone dynamics, which in turn stimulate a DNA damage response... - Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomicsKeiji Kito
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
Proteomics 8:2366-70. 2008..We successfully applied this strategy to analyze two yeast protein complexes, eIF2B-eIF2 and cyclin-Cdc28... - Crystal structure of aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli and conformational change of methionine 260 involved in substrate recognitionKiyoshi Ito
Graduate School of Biomedical Sciences, Nagasaki University, 1 14 Bunkyo machi, Nagasaki 852 8521, Japan
J Biol Chem 281:33664-76. 2006.... - ACT domain repeat protein 7, ACR7, interacts with a chaperone HSP18.0-CII in rice nucleiToshihiko Hayakawa
Graduate School of Agricultural Science, Tohoku University, 1 1 Tsutsumidori Amamiyamachi, Aoba ku, Sendai, 981 8555 Japan
Plant Cell Physiol 47:891-904. 2006..0-CII in vivo. The potential ability of nuclear protein ACR7 to bind Gln and the possibility of the protein acting as a Gln sensor in rice leaves is discussed... - A functional single-nucleotide polymorphism in the human cytidine deaminase gene contributing to ara-C sensitivityLijie Yue
Division of Cardiovascular Medicine, Vascular Medicine, Angiogenesis and Vascular Development, Department of Pediatrics, Kanazawa University Graduate School of Medical Science, Ishikawa, Japan
Pharmacogenetics 13:29-38. 2003.... - Phosphorylation of p47phox directs phox homology domain from SH3 domain toward phosphoinositides, leading to phagocyte NADPH oxidase activationTetsuro Ago
Medical Institute of Bioregulation, Kyushu University, and Department of Molecular and Structural Biology, Kyushu University Graduate School of Medicine, Fukuoka 812 8582, Japan
Proc Natl Acad Sci U S A 100:4474-9. 2003.... - Dorfin localizes to Lewy bodies and ubiquitylates synphilin-1Takashi Ito
Department of Neurology, Nagoya University Graduate School of Medicine, Showa Ku, Nagoya 466 8550, Japan
J Biol Chem 278:29106-14. 2003.... - The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndromeHirochika Kitagawa
Institute of Molecular and Cellular Biosciences, University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, 113 0032, Tokyo, Japan
Cell 113:905-17. 2003..This suggests that WINAC dysfunction contributes to Williams syndrome, which could therefore be considered, at least in part, a chromatin-remodeling factor disease... - Dorfin localizes to the ubiquitylated inclusions in Parkinson's disease, dementia with Lewy bodies, multiple system atrophy, and amyotrophic lateral sclerosisNozomi Hishikawa
Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
Am J Pathol 163:609-19. 2003.... - [Signal transduction and chromatin]Takeya Nakagawa
Tanpakushitsu Kakusan Koso 48:2234-40. 2003 - Identification of Ser-386 of interferon regulatory factor 3 as critical target for inducible phosphorylation that determines activationMitsuaki Mori
Department of Tumor Cell Biology, The Tokyo Metropolitan Institute of Medical Science, Japan
J Biol Chem 279:9698-702. 2004..These results strongly suggest that Ser-386 is the target of the IRF-3 kinase and critical determinant for the activation of IRF-3... - Barrier proteins remodel and modify chromatin to restrict silenced domainsMasaya Oki
Unit on Chromatin and Transcription, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
Mol Cell Biol 24:1956-67. 2004..Our data suggest that multiple overlapping mechanisms were involved in delimiting silenced and active domains in vivo... - Scaffold protein JSAP1 is transported to growth cones of neurites independent of JNK signaling pathways in PC12h cellsShinji Sato
Department of Biosciences, School of Science, Kitasato University, 1 15 1 Kitasato, Sagamihara, Kanagawa 228 8555, Japan
Gene 329:51-60. 2004..Taken together, these results suggest that the proper subcellular localization of JSAP1 along microtubules probably does not require JNK signaling... - Comparative genomics approach toward critical determinants for the imprinting of an evolutionarily conserved gene ImpactKohji Okamura
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
Biochem Biophys Res Commun 329:824-30. 2005..It thus seems that lineage-specific enhancement of gene expression rather than the tandem repeat per se played a critical role in the evolution of imprinting of Impact... - Linker histone variants control chromatin dynamics during early embryogenesisHideaki Saeki
Division of Gene Therapy Science, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
Proc Natl Acad Sci U S A 102:5697-702. 2005..We propose a model that holds that maternally expressed linker histones are key molecules specifying nuclear dynamics with respect to embryonic totipotency... - Taurine prevents the ischemia-induced apoptosis in cultured neonatal rat cardiomyocytes through Akt/caspase-9 pathwayTomoka Takatani
Department of Clinical Evaluation of Medicines and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
Biochem Biophys Res Commun 316:484-9. 2004..These findings provide the first evidence that taurine inhibits ischemia-induced apoptosis in cardiac myocytes with the increase in Akt activities, by inactivating caspase-9... - An evolutionary scenario for genomic imprinting of Impact lying between nonimprinted neighborsKohji Okamura
Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
DNA Res 11:381-90. 2004..This model assumes that segmental duplication followed by enhancement of the promoter activity in the lineage to mouse is responsible for the species-specific imprinting of Impact... - Sox9 and p300 cooperatively regulate chromatin-mediated transcriptionTakayuki Furumatsu
Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
J Biol Chem 280:35203-8. 2005..These findings suggest that Sox9 interacts with chromatin and activates transcription via regulation of chromatin modification... - A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequencesFumihito Miura
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo Kashiwa, Japan
Bioinformatics 21:4363-70. 2005..Thus, the algorithm will be generally useful for improving various PCR-based applications... - Crystallization and preliminary X-ray characterization of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalisYoshitaka Nakajima
Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852 8521, Japan
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:1046-8. 2005..14 A3 Da(-1). Diffraction data were collected to 2.1 A resolution using synchrotron radiation at the BL5 station of the Photon Factory... - The adaptor protein p40(phox) as a positive regulator of the superoxide-producing phagocyte oxidaseFutoshi Kuribayashi
Medical Institute of Bioregulation, Kyushu University, 3 1 1 Maidashi, Higashi ku, Fukuoka 812 8582, Japan
EMBO J 21:6312-20. 2002..Thus p40(phox) participates in activation of the phagocyte oxidase by regulating membrane recruitment of p67(phox) and p47(phox) via the PB1-PC interaction with p67(phox)...