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Research Output 1987 2019

2019

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., Oct 8 2019, In : Stem Cell Reports. 13, 4, p. 761-774 14 p.

Research output: Contribution to journalArticle

Open Access
Induced Pluripotent Stem Cells
Retinal Pigments
Autologous Transplantation
Stem cells
Epithelial Cells
Open Access
Single-Stranded DNA
Ligation
Genome
Libraries
DNA Nucleotidylexotransferase
8 Citations (Scopus)

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., Feb 6 2019, In : Neuron. 101, 3, p. 472-485.e7

Research output: Contribution to journalArticle

Microglia
Epigenomics
Neurons
Transcription Factors
Genes
2018

DMS-seq for In Vivo Genome-Wide Mapping of Protein-DNA Interactions and Nucleosome Centers

Umeyama, T. & Ito, T., Jul 1 2018, In : Current Protocols in Molecular Biology. 123, 1, e60.

Research output: Contribution to journalArticle

Nucleosomes
Chromosome Mapping
DNA
Genome
Proteins
7 Citations (Scopus)

Epigenetic landscape influences the liver cancer genome architecture

Hama, N., Totoki, Y., Miura, F., Tatsuno, K., Saito-Adachi, M., Nakamura, H., Arai, Y., Hosoda, F., Urushidate, T., Ohashi, S., Mukai, W., Hiraoka, N., Aburatani, H., Ito, T. & Shibata, T., Dec 1 2018, In : Nature communications. 9, 1, 1643.

Research output: Contribution to journalArticle

genome
Liver Neoplasms
liver
Epigenomics
Liver

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., Jul 2018, In : Epigenomics. 10, 7, p. 955-979 25 p.

Research output: Contribution to journalArticle

Methylation
Hepatocytes
Histone Code
Genome
RNA Sequence Analysis
8 Citations (Scopus)

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., Dec 1 2018, In : Nature communications. 9, 1, 3885.

Research output: Contribution to journalArticle

spermatozoa
nuclease
genes
Histones
Spermatozoa

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., Oct 5 2018, In : Nutrients. 10, 10, 1436.

Research output: Contribution to journalArticle

Receptors, Prostaglandin E, EP1 Subtype
DNA methylation
DNA Methylation
prostaglandins
kidneys
1 Citation (Scopus)

Post-bisulfite adaptor tagging for PCR-free whole-genome bisulfite sequencing

Miura, F. & Ito, T., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 123-136 14 p. (Methods in Molecular Biology; vol. 1708).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome
Polymerase Chain Reaction
Genomic Library
DNA
hydrogen sulfite
2 Citations (Scopus)

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., Sep 19 2018, In : Nucleic acids research. 46, 16, p. e95

Research output: Contribution to journalArticle

Open Access
Triazoles
Azides
Single-Stranded DNA
Ligation
Alkynes
2017
4 Citations (Scopus)

DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers

Umeyama, T. & Ito, T., Oct 3 2017, In : Cell Reports. 21, 1, p. 289-300 12 p.

Research output: Contribution to journalArticle

Nucleosomes
Chromosome Mapping
Genes
DNA
Proteins
10 Citations (Scopus)

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. C., Igarashi, K., Ideta-Otsuka, M., Miura, F., Ito, T., Fujii, N., Ikeo, K. & Nakashima, K., Sep 19 2017, In : Cell Reports. 20, 12, p. 2992-3003 12 p.

Research output: Contribution to journalArticle

Neural Stem Cells
Stem cells
Epigenomics
Mental Competency
Neurons
6 Citations (Scopus)

Mediator cyclin-dependent kinases upregulate transcription of inflammatory genes in cooperation with NF-κB and C/EBPβ on stimulation of Toll-like receptor 9

Yamamoto, S., Hagihara, T., Horiuchi, Y., Okui, A., Wani, S., Yoshida, T., Inoue, T., Tanaka, A., Ito, T., Hirose, Y. & Ohkuma, Y., Mar 1 2017, In : Genes to Cells. 22, 3, p. 265-276 12 p.

Research output: Contribution to journalArticle

Toll-Like Receptor 9
Cyclin-Dependent Kinases
Up-Regulation
Cyclins
Genes
7 Citations (Scopus)

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., Jan 5 2017, In : BMC Genomics. 18, 1, 31.

Research output: Contribution to journalArticle

Software
Genome
Methylation
Libraries
DNA
10 Citations (Scopus)

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., Dec 1 2017, In : Scientific reports. 7, 1, 17402.

Research output: Contribution to journalArticle

Th17 Cells
Transcription Factor AP-1
Cell Differentiation
Helper-Inducer T-Lymphocytes
Autoimmune Experimental Encephalomyelitis
2016
6 Citations (Scopus)

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., May 1 2016, In : Proteomics. 16, 10, p. 1457-1473 17 p.

Research output: Contribution to journalArticle

Proteome
Mass spectrometry
Mass Spectrometry
Peptides
Proteins
6 Citations (Scopus)

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., Jun 1 2016, In : Biology of Reproduction. 94, 6, 128.

Research output: Contribution to journalArticle

DNA Methylation
Germ Cells
Spermatozoa
Genome
Epigenomics
1 Citation (Scopus)

Erratum: The adaptor protein p40phox as a positive regulator of the superoxide-producing phagocyte oxidase (EMBO Journal (2002) 21 (6312-6320) DOI 10.1093/emboj/cdf642)

Kuribayashi, F., Nunoi, H., Wakamatsu, K., Tsunawaki, S., Sato, K., Ito, T. & Sumimoto, H., Feb 1 2016, In : EMBO Journal. 35, 3, p. 369-370 2 p.

Research output: Contribution to journalComment/debate

Phagocytes
Superoxides
Oxidoreductases
Proteins
neutrophil cytosol factor 40K
2015
3 Citations (Scopus)

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., Aug 12 2015, In : BMC Genomics. 16, 1, 594.

Research output: Contribution to journalArticle

Methylation
Genome
Cell Lineage
Neoplasms
hydrogen sulfite
12 Citations (Scopus)

DNA methylation and gene expression in Mimulus guttatus

Colicchio, J. M., Miura, F., Kelly, J. K., Ito, T. & Hileman, L. C., Jul 7 2015, In : BMC Genomics. 16, 1, 507.

Research output: Contribution to journalArticle

Mimulus
DNA Methylation
Methylation
Gene Expression
Cytosine Nucleotides
22 Citations (Scopus)

Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging

Miura, F. & Ito, T., Jan 1 2015, In : DNA Research. 22, 1, p. 13-18 6 p.

Research output: Contribution to journalArticle

DNA
Genome
Costs and Cost Analysis
Firearms
hydrogen sulfite
2014
3 Citations (Scopus)

Detecting protein – DNA interactions using a modified yeast one-hybrid system

Ota, K., Feng, S. Y. & Ito, T., Jan 1 2014, In : Methods in Molecular Biology. 1164, p. 39-50 12 p.

Research output: Contribution to journalArticle

Reporter Genes
Yeasts
DNA
DNA-Binding Proteins
DNA Methylation
2013
150 Citations (Scopus)

High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice

Kobayashi, H., Sakurai, T., Miura, F., Imai, M., Mochiduki, K., Yanagisawa, E., Sakashita, A., Wakai, T., Suzuki, Y., Ito, T., Matsui, Y. & Kono, T., Apr 1 2013, In : Genome Research. 23, 4, p. 616-627 12 p.

Research output: Contribution to journalArticle

Germ Cells
Methylation
DNA
Epigenomics
Genome
145 Citations (Scopus)

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., Apr 1 2013, In : PLoS genetics. 9, 4, e1003439.

Research output: Contribution to journalArticle

methyltransferases
Methyltransferases
methylation
DNA Methylation
Methylation
14 Citations (Scopus)

Regional 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., Jul 1 2013, In : Journal of Human Genetics. 58, 7, p. 446-454 9 p.

Research output: Contribution to journalArticle

Pan troglodytes
Hominidae
DNA Methylation
Methylation
Gene Expression
18 Citations (Scopus)
Synthetic Genes
S-Adenosylmethionine
Gene Regulatory Networks
Metabolites
Yeast
21 Citations (Scopus)

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., Mar 1 2013, In : Journal of Cell Biology. 200, 5, p. 635-650 16 p.

Research output: Contribution to journalArticle

Epithelial Cells
Proteins
Tight Junctions
Cysts
Madin Darby Canine Kidney Cells
2012
156 Citations (Scopus)

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

Miura, F., Enomoto, Y., Dairiki, R. & Ito, T., Sep 1 2012, In : Nucleic acids research. 40, 17, p. e136

Research output: Contribution to journalArticle

Genome
Epigenomics
DNA
hydrogen sulfite
5-Methylcytosine
2011
2 Citations (Scopus)

Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification

Yamada, Y. & Ito, T., Jun 14 2011, In : BMC Research Notes. 4, 179.

Research output: Contribution to journalArticle

DNA Methylation
Amplification
Assays
Genes
Genome
21 Citations (Scopus)

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., Oct 1 2011, In : Genetics. 189, 2, p. 469-478 10 p.

Research output: Contribution to journalArticle

Poly A
Codon
Saccharomyces cerevisiae
Untranslated Regions
Yeasts
2010
8 Citations (Scopus)

A yeast one-hybrid system to screen for methylated DNA-binding proteins

Feng, S. Y., Ota, K. & Ito, T., Nov 1 2010, In : Nucleic acids research. 38, 20, p. e189

Research output: Contribution to journalArticle

DNA-Binding Proteins
Clone Cells
Yeasts
DNA Methylation
Gene Library
8 Citations (Scopus)

MafB protein stability is regulated by the JNK and ubiquitin-proteasome pathways

Tanahashi, H., Kito, K., Ito, T. & Yoshioka, K., Feb 1 2010, In : Archives of Biochemistry and Biophysics. 494, 1, p. 94-100 7 p.

Research output: Contribution to journalArticle

MafB Transcription Factor
Protein Stability
Proteasome Endopeptidase Complex
Ubiquitin
Phosphorylation
6 Citations (Scopus)

Remodeling of the SCF complex-mediated ubiquitination system by compositional alteration of incorporated F-box proteins

Kato, M., Kito, K., Ota, K. & Ito, T., Jan 1 2010, In : Proteomics. 10, 1, p. 115-123 9 p.

Research output: Contribution to journalArticle

SKP Cullin F-Box Protein Ligases
F-Box Proteins
Ubiquitination
Substrates
Isotope Labeling
2009
25 Citations (Scopus)

Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor

Okada, S., Ota, K. & Ito, T., Dec 1 2009, In : Protein Science. 18, 12, p. 2518-2527 10 p.

Research output: Contribution to journalArticle

Periplasmic Binding Proteins
Nanosensors
Fluorescence Resonance Energy Transfer
Ligands
Proteins
11 Citations (Scopus)

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., Jan 1 2009, In : Journal of biochemistry. 146, 3, p. 317-325 9 p.

Research output: Contribution to journalArticle

Cell Polarity
Saccharomycetales
Static Electricity
Hydrophobic and Hydrophilic Interactions
Isotopes
2008
48 Citations (Scopus)

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., Nov 29 2008, In : BMC Genomics. 9, 574.

Research output: Contribution to journalArticle

Saccharomycetales
Transcriptome
Complementary DNA
Polymerase Chain Reaction
Messenger RNA
10 Citations (Scopus)

A parallel affinity purification method for selective isolation of polyubiquitinated proteins

Ota, K., Kito, K., Iemura, S. I., Natsume, T. & Ito, T., Aug 1 2008, In : Proteomics. 8, 15, p. 3004-3007 4 p.

Research output: Contribution to journalArticle

Ubiquitinated Proteins
Purification
Ubiquitin
Bearings (structural)
Ubiquitins
20 Citations (Scopus)

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., Dec 1 2008, In : Genes to Cells. 13, 10, p. 1075-1085 11 p.

Research output: Contribution to journalArticle

F-Box Proteins
Ubiquitinated Proteins
Proteomics
Membrane Proteins
Ubiquitination
13 Citations (Scopus)

Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics

Kito, K., Kawaguchi, N., Okada, S. & Ito, T., Jun 1 2008, In : Proteomics. 8, 12, p. 2366-2370 5 p.

Research output: Contribution to journalArticle

Proteomics
Cyclins
Fungal Proteins
Isotopes
Purification
69 Citations (Scopus)

Mass spectrometry-based approaches toward absolute quantitative proteomics

Kito, K. & Ito, T., Jun 1 2008, In : Current Genomics. 9, 4, p. 263-274 12 p.

Research output: Contribution to journalReview article

Proteome
Proteomics
Mass Spectrometry
Isotope Labeling
Peptides
5 Citations (Scopus)

Unexpected complexity of the budding yeast transcriptome

Ito, T., Miura, F. & Onda, M., Dec 1 2008, In : IUBMB Life. 60, 12, p. 775-781 7 p.

Research output: Contribution to journalReview article

Saccharomycetales
Transcriptome
Yeast
Genes
Genome
2007
27 Citations (Scopus)
Pheromones
Proline
Yeast
Substitution reactions
Yeasts
67 Citations (Scopus)

A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes

Kito, K., Ota, K., Fujita, T. & Ito, T., Feb 1 2007, In : Journal of Proteome Research. 6, 2, p. 792-800 9 p.

Research output: Contribution to journalArticle

Multiprotein Complexes
Stoichiometry
Peptides
Proteins
Eukaryotic Initiation Factor-2B
3 Citations (Scopus)

High-throughput fluorescence labelling 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., Jan 1 2007, In : Journal of biochemistry. 141, 1, p. 19-24 6 p.

Research output: Contribution to journalArticle

Labeling
Complementary DNA
Fluorescence
Throughput
Proteins

Methods for protein-protein interaction analysis

Kito, K. & Ito, T., Dec 1 2007, Introduction to Systems Biology. Humana Press, p. 160-182 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteins
Mass Spectrometry
Mass spectrometry
Protein Interaction Maps
Biological Phenomena
56 Citations (Scopus)

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., Jul 3 2007, In : Biochemistry. 46, 26, p. 7781-7792 12 p.

Research output: Contribution to journalArticle

Cell signaling
Proteomics
Yeast
Saccharomyces cerevisiae
Chitin
9 Citations (Scopus)

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., Feb 9 2007, In : Biochemical and Biophysical Research Communications. 353, 2, p. 357-362 6 p.

Research output: Contribution to journalArticle

Cadherins
Scaffolds
Cell Communication
Nerve Growth Factor
Cells
94 Citations (Scopus)
Protein Interaction Domains and Motifs
Amoeba
Fungi
Animals
NADPH Oxidase
2006
9 Citations (Scopus)

A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 11q: Comparison with chromosome 21q

Yamada, Y., Shirakawa, T., Taylor, T. D., Okamura, K., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Muramoto, K. I., Sakaki, Y. & Ito, T., Aug 1 2006, In : DNA Sequence - Journal of DNA Sequencing and Mapping. 17, 4, p. 300-306 7 p.

Research output: Contribution to journalArticle

CpG Islands
Methylation
Human Chromosomes
Chromosomes
Tandem Repeat Sequences
170 Citations (Scopus)

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., Nov 21 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 47, p. 17846-17851 6 p.

Research output: Contribution to journalArticle

Saccharomycetales
Transcription Initiation Site
Transcriptome
Open Reading Frames
Complementary DNA