論文

• Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA.
• • Hisano, O., Ito, T. & Miura, F. (2021)
  • BMC Biol., 19, 225.

• Neuronal activation modulates enhancer activity of genes for excitatory synaptogenesis through de novo DNA methylation.
• • Kameda, T., Nakashima, H., Takizawa, T., Miura, F., Ito, T., Nakashima, K. & Imamura, T. (2021)
  • J. Reprod. Dev., in press.
    

• Simple-to-use CRISPR-SpCas9/SaCas9/AsCas12a vector series for genome editing in Saccharomyces cerevisiae.
• • Okada, S., Doi, G., Nakagawa, S., Kusumoto, E. & Ito, T. (2021)
  • G3 (Bethesda) 11, jkab304.

• The evolving genomic landscape of esophageal squamous cell carcinoma under chemoradiotherapy.
• • Hirat, H., Niida, A., Kakiuchi, N., Uchi, R., Sugimachi, K., Masuda, T., Saito, T., Kageyama, SI., Motomura, Y., Ito, S., Yoshitake, T., Tsurumaru, D., Nishimuta, Y., Yokoyama, A., Hasegawa, T., Chiba, K., Shiraishi, Y., Du, J., Miura, F., Morita, M., Toh, Y., Hirakawa, M., Shioyama, Y., Ito, T., Akimoto, T., Miyano, S., Shibata, T., Mori, M., Suzuki, Y., Ogawa, S., Ishigami, K. & Mimori K. (2021)
  • Cancer Res. 81, 4926-4938

• Transcriptome dynamics during cholesterol-induced transdifferentiation of human coronary artery smooth muscle cells: a gene ontology-centric clustering approach.
• • Inoue, K., Araki, H., Miura, F. & Ito, T. (2021)
  • Biochem. Biophys. Rep. 27, 101061.

• Hoxa10 mediates positional memory to govern stem cell function in adult skeletal muscle.
• • Yoshioka, K., Nagahisa, H., Miura, F., Araki, H., Kamei, Y., Kitajima, Y., Seko, D., Nogami, J., Tsuchiya, Y., Okazaki, N., Yonekura, A., Ohba, S., Sumita, Y., Chiba, K., Ito, K., Asahina, I., Ogawa, Y., Ito, T., Ohkawa, Y. & Ono, Y. (2021)
  • Sci. Adv. 7, eabd7924.

• Maintenance DNA methylation in pre-meiotic germ cells regulates meiotic prophase by facilitating homologous chromosome pairing.
• • Takada, Y., Yaman-Deveci, R., Shirakawa, T., Sharif, J., Tomizawa, S.I., Miura, F., Ito, T., Ono, M., Nakajima, K., Koseki, Y., Shiotani, F., Ishiguro, K.I., Ohbo, K. & Koseki, H. (2021)
  • Development 148, dev194605.

• Catalytically inactive Cas9 impairs DNA replication fork progression to induce focal genomic instability.
• • Doi, G., Okada, S., Yasukawa, T., Sugiyama, Y., Bala, S., Miyazaki, S., Kang, D & Ito, T. (2021)
  • Nucleic Acids Res. 49, 954-968.

• Reconstitution of the oocyte transcriptional network with transcription factors.
• • Hamazaki, N., Kyogoku, H., Araki, H., Miura, F., Horikawa, C., Hamada, N., Shimamoto, S., Hikabe, O., Nakashima, K., Kitajima, T. S., Ito, T., Leitch, H.G. & Hayashi, K. (2021)
  • Nature 589, 264-269.

• Identification of genes associated with endometrial cell ageing.
• • Kawamura, T., Tomari, H., Onoyama, I., Araki, H., Yasunaga, M., Lin, C., Kawamura, K., Yokota, N., Yoshida, S., Yagi, H., Asanoma, K., Sonoda, K., Egashira, K., Ito, T. & Kato, K. (2021)
  • Mol. Hum. Reprod. 27, gaaa078.

• Limited rejuvenation of aged hematopoietic stem cells in young bone marrow niche.
• • Kuribayashi, W., Oshima, M., Itokawa, N., Koide, S., Nakajima-Takagi, Y., Yamashita, M., Yamazaki, S., Rahmutulla, B., Miura, F., Ito, T., Kaneda, A. & Iwama, A. (2021)
  • J. Exp. Med. 218, e20192283.

• Base-resolution methylomes of gliomas bearing histone H3.3 mutations reveal a G34 mutant-specific signature shared with bone tumors
• • Sangatsuda, Y., Miura, F., Araki, H., Mizoguchi, M., Hata, N., D., Hatae, R., Akagi, Y., Amemiya, T., Fujioka, Y., Arai, Y., Yoshida, A., Shibata, T., Yoshimoto, K., Iihara, K. & Ito, T. (2020)
  • Sci. Rep. 10, 16162.

• NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing
• • Shirane, K., Miura, F., Ito, T. & Lorincz, M.C. (2020)
  • Nat. Genet. 52, 1088-1098.

• DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem
• • Higo, A., Saihara, N., Miura, F., Higashi, Y., Yamada, M., Tamaki, S., Ito, T., Tarutani, Y., Sakamoto, T., Fujiwara, M., Kurata, T., Fukao, Y., Moritoh, S., Terada, R., Kinoshita, T., Ito, T., Kakutani, T., Shimamoto, K. & Tsuji, H. (2020)
  • Nat. Commun. 11, 4079.

• Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity
• • Tanaka, S., Ise, W., Inoue, T., Ito, A., Ono, C., Shima, Y., Sakakibara, S., Nakayama, M., Fujii, K., Miura, I., Sharif, J., Koseki, H., Koni, P.A., Raman, I., Li, Q.-Z., Kubo, M., Fujiki, K., Nakato, R., Shirahige, K., Araki, H., Miura, F., Ito, T., Kawakami, E., Baba, Y. & Kurosaki, T.
  • Nat. Immunol. 21, 950-961.

• ATF7-Dependent Epigenetic Changes Are Required for the Intergenerational Effect of a Paternal Low-Protein Diet
• • Yoshida, K., Maekawa, T., Ly, N.H., Fujita, S., Muratani, M., Ando, M., Katou, Y., Araki, H., Miura, F., Shirahige, K., Okada, M., Ito, T., Chatton, B. & Ishii, S. (2020)
  • Mol. Cell 78, 445-458.

• Base-resolution methylome of retinal pigment epithelial cells used in the first trial of human induced pluripotent stem cell-based autologous transplantation.
• • Araki, H., Miura, F., Watanabe, A., Morinaga, C., Kitaoka, F., Kitano, Y., Sakai, N., Shibata, Y., Terada, M., Goto, S., Yamanaka, S., Takahashi, M. & Ito, T. (2019)
  • Stem Cell Reports 13, 761-774.

• Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
• • Miura, F., Shibata, Y., Miura, M., Sangatsuda, Y., Hisano, O., Araki, H. & Ito, T. (2019)
  • Nucleic Acids Res. 47, e85.

• Pioneer factor NeuroD1 rearranges transcriptional and epigenetic profiles to execute microglia-neuron conversion.
• • Matsuda, T., Irie, T., Katsurabayashi, S., Hayashi, Y., Nagai, T., Hamazaki, N., Adefuin, A.M.D., Miura, F., Ito, T., Kimura, H., Shirahige, K., Takeda, T., Iwasaki, K., Imamura, T. & Nakashima, K. (2019)
  • Neuron 101, 472-485.

• Triazole linking for preparation of a next-generation sequencing library from single-stranded DNA.
• • Miura, F., Fujino, T., Kogashi, K., Shibata, Y., Miura, M., Isobe, H. & Ito, T. (2018)
  • Nucleic Acids Res. 46, e95.

• Maternal protein restriction alters the renal Ptger1 DNA methylation state in SHRSP offspring.
• • Miyoshi, M., Sato, M., Saito, K., Otani, L., Shirahige, K., Miura, F., Ito, T., Jia, H. & Kato, H. (2018)
  • Nutrients 10, 1436.

• Mapping of histone-binding sites in histone replacement-completed spermatozoa.
• • Yoshida, K., Muratani, M., Araki, H., Miura, F., Suzuki, T., Dohmae, N., Katou, Y., Shirahige, K., Ito, T. & Ishii, S. (2018)
  • Nat. Commun. 9, 3885.

• Epigenome mapping of human normal purified hepatocytes: personal epigenome variation and genome-epigenome correlation.
• • Arai, E., Miura, F., Totoki, Y., Yamashita, S., Tian, Y., Gotoh, M., Ojima, H., Nakagawa, H., Takahashi, Y., Nakamura, H., Hama, N., Kato, M., Kimura, H., Suzuki, Y., Ito, T., Shibata, T. & Kanai, Y. (2018)
  • Epigenomics 10, 955-979.

• DMS-seq for in vivo genome-wide mapping of protein-DNA interactions and nucleosome centers.
• • Umeyama, T. & Ito, T. (2018)
  • Curr. Protoc. Mol. Biol. 123, e60.

• Epigenetic landscape influences the liver cancer genome architecture.
• • Hama, N., Totoki, Y., Miura, F., Tatsuno, K., Adachi, M., Nakamura, H., Arai, Y., Hosoda, F., Urushidate, T., Ohashi, S., Mukai, W., Hiraoka, N., Aburatani, H., Ito, T. & Shibata, T. (2018)
  • Nat. Commun. 9, 1643.

• Post-bisulfite adaptor tagging for PCR-free whole-genome bisulfite sequencing.
• • Miura, F. & Ito, T. (2018)
  • Methods Mol. Biol. 1708, 123-136.

• The AP-1 transcription factor JunB is required for Th17 cell differentiation.
• • Yamazaki, S., Tanaka, Y., Araki, H., Kohda, A., Sanematsu, F., Arasaki, T., Duan, X., Miura, F., Katagiri, T., Shindo, R., Nakano, H., Ito, T., Fukui, Y., Endo, S. & Sumimoto, H. (2017)
  • Sci. Rep. 7, 17402.

• DMS-seq for in vivo genome-wide mapping of protein-DNA interactions and nucleosome centers.
• • Umeyama, T. & Ito, T. (2017)
  • Cell Rep. 21, 289-300.

• DNA methylome analysis identifies transcription factor-based epigenomic signatures of multilineage competence in neural stem/progenitor cells.
• • Sanosaka, T., Imamura, T., Hamazaki, N., Chai, M., Igarashi, K., Ideta-Otsuka, M., Miura, F., Ito, T., Fujii, N., Ikeo, K. & Nakashima, K. (2017)
  • Cell Rep. 20, 2992-3003.

• Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.
• • Toh, H., Shirane, K., Miura, F., Kubo, N., Ichiyanagi, K., Hayashi, K., Saitou, M., Suyama, M., Ito, T. & Sasaki, H. (2017)
  • BMC Genomics 18, 31.

• The International Human Epigenome Consortium: A blueprint for scientific collaboration and discovery.
• • Stunnenberg, H.G., International Human Epigenome Consortium. & Hirst, M. (2016)
  • Cell 167, 1145–1149.

• DNA methylation errors in cloned mouse sperm by germ line barrier evasion.
• • Koike, T., Wakai, T., Jincho, Y., Sakashita, A., Kobayashi, H., Mizutani, E., Wakayama, S., Miura, F., Ito, T. & Kono, T. (2016)
  • Biol. Reprod. 94, 128.

• A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards.
• • Kito, K., Okada, M., Ishibashi, Y., Okada, S. & Ito T. (2016)
  • Proteomics 16, 1457-1473.

• Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape.
• • Yokoyama, T., Miura, F., Araki, H., Okamura, K. & Ito, T. (2015)
  • BMC Genomics 16, 594.

• DNA methylation and gene expression in Mimulus guttatus.
• • Colicchio, J.M., Miura, F., Kelly, J.K., Ito, T. & Hileman, L.C. (2015)
  • BMC Genomics 16, 507.

• Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging.
• • Miura, F. & Ito, T. (2015)
  • DNA Res. 22, 13-18.

• Detecting protein-DNA interactions using a modified yeast one-hybrid system.
• • Ota, K., Feng, S.Y. & Ito, T. (2014)
  • Methods Mol. Biol. 1164, 39-50.

• DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes.
• • Fukuda, K., Ichiyanagi, K., Yamada, Y., Go, Y., Udono, T., Wada, S., Maeda, T., Soejima, H., Saitou, N., Ito, T. & Sasaki, H. (2013)
  • J. Hum. Genet. 58, 446-454.

• Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases.
• • Shirane, K., Toh, H., Kobayashi, H., Miura, F., Chiba, H., Ito, T., Kono, T. & Sasaki, H. (2013)
  •  PLoS Genet. 9, e1003439.

• High resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice.  
• • Kobayashi, H., Sakurai, T., Miura, F., Imai, M., Mochizuki, K., Yanagisawa, E., Sakashita, A., Wakai, T., Suzuki, Y., Ito, T., Matsui, Y. & Kono, T. (2013)
  • Genome Res. 23, 616-627.

• The WD40 protein Morg1 facilitates Par6-aPKC binding to Crb3 for apical identity in epithelial cells.  
• • Hayase, J., Kamakura, S., Iwakiri, Y., Yamaguchi, Y., Izaki, T., Ito, T. & Sumimoto, H. (2013)
  • J. Cell Biol. 200, 635-650.

• Synthetic gene circuit-mediated monitoring of endogenous metabolites: identification of GAL11 as a novel multicopy enhancer of S-adenosylmethionine level in yeast.  
• • Umeyama, T., Okada, S. & Ito, T. (2013)
  • ACS Synth. Biol., 2, 425-430.

• Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.  
• • Miura, F., Enomoto, Y., Dairiki, R. & Ito, T. (2012)
  • Nucleic Acids Res. 40, e136.

• Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae.  
• • Xia, X., MacKay, V., Yao, X., Wu, J., Miura, F., Ito, T. & Morris, D.R. (2011)
  • Genetics 189, 469-478.

• Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification.
• • Yamada, Y. & Ito, T. (2011)
  • BMC Res. Notes 4, 179.

• A yeast one-hybrid system to screen for methylated DNA-binding proteins.
• • Feng, S.-Y., Ota, K. & Ito, T. (2010)
  • Nucleic Acids Res. 38, e189.

• MafB protein stability is regulated by the JNK and ubiquitin-proteasome pathways.
• • Tanahashi, H., Kito, K., Ito, T. & Yoshioka, K. (2010)
  • Arch. Biochem. Biophys. 494, 94-100.

• Remodeling of the SCF complex-mediated ubiquitination system by compositional alteration of incorporated F-box proteins.
• • Kato, M., Kito, K., Ota, K. & Ito, T. (2010)
  • Proteomics 10, 115-123.

• Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor.
• • Okada, S., Ota, K. & Ito, T. (2009)
  • Protein Sci. 18, 2518-2527.

• NMR structure of the heterodimer of Bem1 and Cdc24 PB1 domains from Saccharomyces cerevisiae.
• • Ogura, K., Tandai, T., Yoshinaga, S., Kobashigawa, Y., Kumeta, H., Ito, T., Sumimoto, H. & Inagaki, F. (2009)
  • J. Biochem.146, 317-325.

• Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs.
• • Miura, F., Kawaguchi, N., Yoshida, M., Uematsu, C., Kito, K., Sakaki, Y. & Ito, T. (2008)
  • BMC Genomics 9, 574.

• A proteomic screen reveals the mitochondrial outer membrane protein Mdm34p as an essential target of the F-box protein Mdm30p.
• • Ota, K., Kito, K., Okada, S. & Ito, T. (2008)
  • Genes Cells 13, 1075-1085.

• Unexpected complexity of the budding yeast transcriptome.
• • Ito, T., Miura, F. & Onda, M. (2008)
  • IUBMB Life 60, 775-781.

• A parallel affinity purification method for selective isolation of polyubiquitinated proteins.
• • Ota, K., Kito, K., Iemura, S., Natsume, T. & Ito, T. (2008)
  • Proteomics 8, 3004-3007.

• Mass spectrometry-based approaches toward absolute quantitative proteomics.
• • Kito, K. & Ito, T. (2008)
  • Curr. Genomics 9, 263-274.

• Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics.
• • Kito, K., Kawaguchi, N., Okada, S. & Ito, T. (2008)
  • Proteomics 8, 2366-2370.

• Structure and function of the PB1 domain, a protein interaction module conserved in animals, fungi, amoebas, and plants.
• • Sumimoto, H., Kamakura, S. & Ito, T. (2007)
  • Sci. STKE 2007, re6.

• Methods for protein-protein interaction analysis.
• • Kito, K. & Ito, T. (2007)
  • In Introduction to Systems Biology (ed. Choi, S), Humana Press, pp.160-182.

• Proteomic analysis of in vivo 14-3-3 interactions in the yeast Saccharomyces cerevisiae.
• • Kakiuchi, K., Yamauchi, Y., Taoka, M., Iwago, M., Fujita, T., Ito, T., Song, S.Y., Sakai, A., Isobe, T. & Ichimura, T. (2007)
  • Biochemistry 46, 7781-7792.

• A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes.
• • Kito, K., Ota, K., Fujita, T. & Ito, T. (2007)
  • J. Proteome Res. 6, 792-800.

• Regulation of N-cadherin-based cell-cell interaction by JSAP1 scaffold in PC12h cells.
• • Bayarsaikhan, M., Takino, T., Gantulga, D., Sato, H., Ito, T. & Yoshioka, K. (2007)
  • Biochem. Biophys. Res. Commun. 353, 357-362.

• High-throughput fluorescence labeling of full-length cDNA products based on a reconstituted translation system.
• • Kawahashi, Y., Doi, N., Oishi, Y., Tsuda, C., Takashima, H., Baba, T., Mori, H., Ito, T. & Yanagawa, H. (2007)
  • J. Biochem. 141, 19-24.

• A novel Cdc42-interacting domain of the yeast polarity establishment protein Bem1: implications for modulation of mating pheromone signaling.
• • Yamaguchi, Y., Ota, K. & Ito, T. (2007)
  • J. Biol. Chem. 282, 29-38.

• A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.
• • Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S. & Ito, T. (2006)
  • Proc. Natl. Acad. Sci. USA 103, 17846-17851.

• Diverse DNA methylation status at alternative promoters of human genes in various normal tissues.
• • Cheong, J., Yamada, Y., Yamashita, R., Irie, T., Kanai, A., Wakaguri, H., Nakai, K., Ito, T., Saito, I., Sugano, S. & Suzuki, Y. (2006)
  • DNA Res. 13, 155-167.

• A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q: comparison with chromosome 21q.
• • Yamada, Y., Shirakawa, T., Taylor, T., Okamura, K., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Muramoto, K., Sakaki, Y. & Ito, T. (2006)
  • DNA Seq. 17, 300-306.

• Lessons from comparative analysis of species-specific imprinted genes.
• • Okamura, K. & Ito, T. (2006)
  • Cytogenet. Genome Res. 113, 159-164.

• Transcriptional activators in yeast.
• • Titz, B., Seesandra, T., Rajagopala, S.V., Chiba, T., Ito, T. & Uetz, P. (2006)
  • Nucleic Acids Res. 34, 955-967.

• A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3′-end subsequences.
• • Miura, F., Uematsu, C., Sakaki, Y. & Ito, T. (2005)
  • Bioinformatics 21, 4363-4370.

• The yeast eIF4E-associated protein Eap1p attenuates GCN4 translation upon TOR inactivation.
• • Matsuo, R., Kubota, H., Obata, T., Kito, K., Ota, K., Kitazono, T., Ibayashi, S., Sasaki, T., Iida, M. & Ito, T. (2005)
  • FEBS Lett. 579, 2433-2438.

• Comparative genomics approach toward critical determinants for the imprinting of an evolutionarily conserved gene Impact.
• • Okamura, K., Sakaki, Y. & Ito, T. (2005)
  • Biochem. Biophys. Res. Commun. 329, 824-830.

• An evolutionary scenario for genomic imprinting of Impact lying between nonimprinted neighbors.
• • Okamura, K., Yamada, Y., Sakaki, Y. & Ito, T. (2004)
  • DNA Res. 11, 381-390.

• Mass spectrometry-based proteomics for quantitative description of cellular events.
• • Kito, K. & Ito, T. (2004)
  • Curr. Genomics 5, 629-635.

• Transcriptomic and proteomic analysis of a 14-3-3 gene-deficient yeast.
• • Ichimura, T., Kubota, H., Goma, T., Mizushima, N., Ohsumi, Y., Iwago, M., Kakiuchi, K., Shekhar, H. U., Shinkawa, T., Taoka, M., Ito, T. & Isobe, T. (2004)
  • Biochemistry 43, 6149-6158.

• Analysis of gene network regulating yeast multidrug resistance by artificial activation of transcription factors: involvement of Pdr3 in salt resistance.
• • Onda, M., Ota, K., Chiba, T., Sakaki, Y. & Ito, T. (2004)
  • Gene 332, 51-59.

• Scaffold protein JSAP1 is transported to growth cones of neurites independent of JNK signaling pathways in PC12h cells.
• • Sato, S., Ito, M., Ito, T. & Yoshioka, K. (2004)
  • Gene 329, 51-60.

• SKIP affects gene expression by both affecting transcription and splicing.Biochem.
• • Nagai, K., Yamaguchi, T., Takami, T., Kawasumi, A., Aizawa, M., Masuda, N., Shimizu, M., Tominaga, S., Ito, T., Tsukamoto, T. & Osumi, T. (2004)
  • Biophys. Biochem. Res. Commun. 316, 512-517.

• Barrier proteins remodel and modify chromatin to restrict silenced domains.
• • Oki, M., Valenzuera, L., Chiba, T., Ito, T. & Kamakaka, R. (2004)
  • Mol. Cell. Biol. 24, 1956-1967.

• A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q.
• • Yamada, Y., Watanabe, H., Miura, F., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Sakaki, Y. & Ito, T. (2004)
  • Genome Res. 14, 247-266.

• A yeast one-hybrid system to detect methylation-dependent DNA-protein interactions.
• • Feng, S.-Y., Ota, K., Yamada, Y., Sawabu, N. & Ito, T. (2004)
  • Biochem. Biophys. Res. Commun. 313, 922-925.

• Identification of a five-pass transmembrane protein family localizing in the Golgi apparatus and the ER.
• • Shakoori, A., Fujii, G., Yoshimura, S., Kitamura, M., Nakayama, K., Ito, T., Ohno, H. & Nakamura, N. (2003)
  • Biochem. Biophys. Res. Commun. 312, 850-857.

• Molecular recognition in dimerization between PB1 domains.
• • Noda, Y., Kohjima, M., Izaki, T., Ota, K., Yoshinaga, S., Inagaki, F., Ito, T. & Sumimoto, H. (2003)
  • J. Biol. Chem. 278, 43516-43524.

• The PB1 domain and the PC motif-containing region are structurally similar protein binding modules.
• • Yoshinaga, S., Kohjima, M., Ogura, K., Yokochi, M., Takeya, R., Ito, T., Sumimoto, H. & Inagaki, F. (2003)
  • EMBO J. 22, 4888-4897.

• Rapamycin-induced translational derepression of GCN4 mRNA involves a novel mechanism for activation of the eIF2α kinase GCN2.
• • Kubota, H., Obata, T., Ota, K., Sasaki, T. & Ito, T. (2003)
  • J. Biol. Chem. 278, 20457-20460.

• Phosphorylation of p47phox directs PX domain from SH3 domain toward phosphoinositides, leading to activation of the phagocyte NADPH oxidase.
• • Ago, T., Kuribayashi, F., Hiroaki, H., Takeya, R., Ito, T., Kohda, D. & Sumimoto, H. (2003)
  • Proc. Natl. Acad. Sci. USA 100, 4474-4479.

• A functional single-nucleotide polymorphism in the human cytidine deaminase gene contributing to ara-C sensitivity.
• • Yue, L., Saikawa, Y., Ota, K., Tanaka, M., Nishimura, R., Uehara, T., Maeba, H., Ito, T., Sasaki, T. & Koizumi, S. (2003)
  • Pharmacogenetics 13, 29-38

• The adaptor protein p40phox as a positive regulator of the superoxide-producing phagocyte oxidase.
• • Kuribayashi, F., Nunoi, H., Wakamatsu, K., Tsunawaki, S., Sato, K., Ito, T. & Sumimoto, H. (2002)
  • EMBO J. 21, 6312-6320.

• Appearance of osteonectin-expressing fibroblastic cells in early rat stomach carcinogenesis and stomach tumors induced with N-methyl-N’-nitro-N-nitrosoguanidine.
• • Maeng, H.-Y., Choi, D.-K., Takeuchi, M., Yamamoto, M., Tomonaga, M., Tsukamoto, T., Tatematsu, M., Ito, T., Sakaki, Y. & Furihata, C.(2002)
  • Jpn. J. Cancer Res. 93, 960-967.

• Roles for the two-hybrid system in exploration of the yeast protein interactome.Mol. Cell.
• • Ito, T., Ota, K., Kubota, H., Yamaguchi, Y., Chiba, T., Sakuraba, K. & Yoshida, M. (2002) 
  • Mol. Cell. Proteomics 1, 561-566.

• Extraction of knowledge on protein-protein interaction by association rule discovery.
• • Oyama, T., Kitano, K., Satou, K. & Ito, T. (2002)
  • Bioinformatics 18, 705-714.

• OPR, PC and AID: all in the PB1 family.
• • Ponting, C. P., Ito, T., Moscat, J., Diaz-Meco, M. T., Inagaki, F. & Sumimoto, H. (2002)
  • Trends Biochem. Sci. 27, 10.

• The PX domain as a novel phosphoinositide-binding module.
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• Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif.
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• Solution structure of the PX domain, a target of the SH3 domain.
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• Budding yeast GCN1 binds the GI domain to activate the eIF2α kinase GCN2.
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• Comparative genome analysis of the mouse imprinted gene Impact and its nonimprinted human homolog IMPACT: toward the structural basis for species-specific imprinting.
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• A new ETV6/TEL partner gene, ARG (ABL related gene or ABL2), identified in an AML-M3 cell line with a t(1;12)(q25;p13) translocation.
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