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  • 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-Otuka, M., Miura, F., Ito, T., FUjii, N., Ideo, 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.
    • Ago, T., Takeya, R., Kuribayashi, F., Hiroaki, H., Ito, T., Kohda, D. & Sumimoto, H. (2001)
    • Biochem. Biophys. Res. Commun. 287, 733-738.
  • Exploring the protein interactome using comprehensive two-hybrid projects.
    • Ito, T., Chiba, T. & Yoshida, M. (2001)
    • Trends Biotechnol. 19, S23-S27.
  • Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast.
    • Miura, F., Yada, T., Nakai, K., Sakaki, Y. & Ito, T. (2001)
    • FEBS Lett. 505, 103-108.
  • Multiplex polymerase chain reaction (PCR) with color-tagged module-shuffling primers for comparing gene expression levels in various cells.
    • Uematsu, C., Nishida, J., Okano, K., Miura, F., Ito, T., Sakaki, Y. & Kambara, H. (2001)
    • Nucleic Acids Res. 29, e84.
  • Discovery of a novel compound: insight into mechanisms for acrylamide-induced axonopathy and colchicine-induced apoptotic neuronal cell death.
    • Nakagawa-Yagi, Y., Choi, D.-K., Ogane, N., Shimada, S., Seya. M., Momoi, T., Ito, T. & Sakaki, Y. (2001)
    • Brain Res. 909, 8-19.
  • Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif.
    • Terasawa, H., Noda, Y., Ito, T., Hatanaka, H., Ichikawa, S., Ogura, K., Sumimoto, H. & Inagaki, F. (2001)
    • EMBO J. 20, 3947-3956.
  • Novel modular domain PB1 recognizes PC motif to mediate functional protein-protein interactions.
    • Ito, T., Matsui, Y., Ago, T., Ota, K. & Sumimoto, H. (2001)
    • EMBO J. 20, 3938-3946.
  • Solution structure of the PX domain, a target of the SH3 domain.
    • Hiroaki, H., Ago, T., Ito, T., Sumimoto, H. & Kohda, D. (2001)
    • Nature Struct. Biol. 8, 526-530
  • Budding yeast GCN1 binds the GI domain to activate the eIF2α kinase GCN2.
    • Kubota, H., Ota, K., Sakaki, Y. & Ito, T. (2001)
    • J. Biol. Chem. 276, 17591-17596.
  • A comprehensive two-hybrid analysis to explore the yeast protein interactome.
    • Ito, T., Chiba, T., Ozawa, T., Yoshida, M., Hattori, M. & Sakaki, Y. (2001)
    • Proc. Natl. Acad. Sci. USA 98, 4569-4574.
  • Human homologues of the Caenorhabditis elegans cell polarity protein PAR6 as an adaptor that links the small GTPases Rac and Cdc42 to atypical protein kinase C.
    • Noda, Y., Takeya, R., Ohno, S., Naito, S., Ito, T. & Sumimoto, H. (2001)
    • Genes Cells 6, 107-119.
  • Comparative genome analysis of the mouse imprinted gene Impact and its nonimprinted human homolog IMPACT: toward the structural basis for species-specific imprinting.
    • Okamura, K., Hagiwara-Takeuchi, Y., Li, T., Vu, T. H., Hirai, M., Hattori, M., Sakaki, Y., Hoffman, A. R. & Ito, T. (2000)
    • Genome Res. 10, 1878-1889.
  • A novel G-protein coupled receptor gene expressed in striatum.
    • Mizushima, K., Miyamoto, Y., Tsukahara, F., Hirai, M., Sakaki, Y. & Ito, T. (2000)
    • Genomics 69, 314-321.
  • GI domain-mediated association of the eukaryotic initiation factor 2α kinase GCN2 with its activator GCN1 is required for general amino acid control in budding yeast.
    • Kubota, H., Sakaki, Y. & Ito, T. (2000)
    • J. Biol. Chem. 275, 20243-20246.
  • 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.
    • Iijima, Y., Ito, T., Oikawa, T., Eguchi, M., Eguchi-Ishimae, M., Kamada, N., Kishi, K., Asano, S., Sakaki, Y. & Sato, Y. (2000)
    • Blood 95, 2126-2131.
  • Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins.
    • Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S. & Sakaki, Y. (2000)
    • Proc. Natl. Acad. Sci. USA 97, 1143-1147.
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