Yasuhiro Tomaru

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. pmc Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis
    Yasuhiro Tomaru
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Biol 10:R121. 2009
  2. pmc Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation
    Atsutaka Kubosaki
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Biol 10:R41. 2009
  3. pmc Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi
    Taku Tanaka
    Division of Genomics, Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tusurumi Ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 32:2740-50. 2004
  4. pmc Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes
    Hisashi Miura
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 37:778-92. 2009
  5. doi request reprint The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells
    Atsutaka Kubosaki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Mol Immunol 47:2295-302. 2010
  6. pmc Comparative analysis of expression of histone H2a genes in mouse
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    BMC Genomics 6:108. 2005
  7. pmc Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells
    Misato Nakanishi
    Laboratory of Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 36:3443-54. 2008
  8. pmc Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
    Morana Vitezic
    Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Nucleic Acids Res 38:8141-8. 2010
  9. pmc Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi
    Yasuhiro Tomaru
    OMICS Sciences Center OSC, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Japan
    Nucleic Acids Res 37:1049-60. 2009
  10. doi request reprint CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication
    Atsutaka Kubosaki
    RIKEN Omics Science Center, 1 7 22 Suehiro cho, Yokohama, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 426:141-7. 2012

Detail Information

Publications21

  1. pmc Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis
    Yasuhiro Tomaru
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Biol 10:R121. 2009
    ....
  2. pmc Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation
    Atsutaka Kubosaki
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Biol 10:R41. 2009
    ..EGR-1 has been thought to work as a modifier of monopoiesis, but the precise function of EGR-1 in monocytic differentiation has not been fully elucidated...
  3. pmc Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi
    Taku Tanaka
    Division of Genomics, Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tusurumi Ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 32:2740-50. 2004
    ....
  4. pmc Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes
    Hisashi Miura
    RIKEN Omics Science Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 37:778-92. 2009
    ..Finally, co-transfection reporter assays with various combinations of expression vectors for these HNF genes demonstrated the transcriptional activation of the CEBPA gene in a combinatorial manner by these TRFs...
  5. doi request reprint The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells
    Atsutaka Kubosaki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Mol Immunol 47:2295-302. 2010
    ..We suggest that IRF8 and PU.1 can have both combined, and independent actions on different promoters in myeloid cells...
  6. pmc Comparative analysis of expression of histone H2a genes in mouse
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    BMC Genomics 6:108. 2005
    ..In addition, we compared histone H3 K9 acetylation levels in the promoter regions of H2a genes by ChIP (chromatin immunoprecipitation)--quantitative PCR (qPCR) analysis...
  7. pmc Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells
    Misato Nakanishi
    Laboratory of Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 36:3443-54. 2008
    ..Finally, 36 transcriptional regulatory edges were validated by chromatin immunoprecipitation. These analyses enabled us to depict a part of the transcriptional regulatory cascades closely linked to ATRA-induced cell growth arrest...
  8. pmc Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE
    Morana Vitezic
    Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Nucleic Acids Res 38:8141-8. 2010
    ..We found a previously described composite motif for PU.1 and IRF8 that explains the overlapping set of transcriptional responses upon knockdown of either factor...
  9. pmc Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi
    Yasuhiro Tomaru
    OMICS Sciences Center OSC, RIKEN Yokohama Institute 1 7 22 Suehiro cho, Japan
    Nucleic Acids Res 37:1049-60. 2009
    ..The resultant significant edges enabled us to depict the inter-TRF TRN forming an apparent regulatory hierarchy of (FOXA1, RXRA) --> TCF1 --> (HNF4A, ONECUT1) --> (RORC, CEBPA) as the main streamline...
  10. doi request reprint CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication
    Atsutaka Kubosaki
    RIKEN Omics Science Center, 1 7 22 Suehiro cho, Yokohama, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 426:141-7. 2012
    ..Since the unmodified MoCEV did not undergo any DNA methylation during cell division, the results strongly suggest that somatic cells undergo hmC to mC specifically at the CpG sites during cell division...
  11. doi request reprint Identification of ZNF395 as a novel modulator of adipogenesis
    Ryota Hasegawa
    Omics Science Center OSC, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, Japan
    Exp Cell Res 319:68-76. 2013
    ..These loss and gain of function experiments firmly establish that ZNF395 coordinate the transcriptional regulatory pathway with PPARG2, which may be necessary for the genesis of adipocytes...
  12. pmc Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    BMC Genet 6:23. 2005
    ..In the present study, we evaluated this transcript by using RT-PCR and compared the expression patterns of the sense and antisense transcripts by using quantitative RT-PCR (qRT-PCR)...
  13. doi request reprint The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
    Harukazu Suzuki
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    Nat Genet 41:553-62. 2009
    ....
  14. ncbi request reprint A comprehensive search for HNF-3alpha-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis
    Yasuhiro Tomaru
    Laboratory of Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Biochem Biophys Res Commun 310:667-74. 2003
    ..The potential usefulness of the present approach to extensive characterization of gene expression framework directed by a specific transcription regulatory factor is discussed...
  15. pmc A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness
    A Maxwell Burroughs
    Omics Science Center OSC, RIKEN Yokohama Institute, Tsurumi ku, Yokohama shi, Kanagawa 230 0045, Japan
    Genome Res 20:1398-410. 2010
    ....
  16. pmc EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes
    Itoshi Nikaido
    Division of Genomic Information Resource Exploration, Science of Biological Supramolecular Systems, Yokohama City University, Graduate School of Integrated Science, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 32:D548-51. 2004
    ..gsc.riken.jp/EICODB/) and the DAS client software. These data and interfaces facilitate understanding of the mechanism of imprinting in mammalian inherited traits...
  17. ncbi request reprint Cancer research with non-coding RNA
    Yasuhiro Tomaru
    RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama City, Kanagawa 230 0045, Japan
    Cancer Sci 97:1285-90. 2006
    ..Here we would like to introduce the latest in cancer research that has emerged from the field of molecular biology research...
  18. pmc A novel replication-independent histone H2a gene in mouse
    Hiromi Nishida
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    BMC Genet 6:10. 2005
    ..The proteins encoded by this transcript and the human H2afj mRNA isoform-2 have the highest amino acid similarity. In this paper, we characterize it from the expression pattern given by quantitative RT-PCR...
  19. pmc Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells
    Yoshinari Ando
    RIKEN Omics Science Center, Yokohama, Kanagawa, Japan
    PLoS ONE 6:e23385. 2011
    ..Additional characterization of the NUP153-DICER1 association suggests NUP153 plays a crucial role in the nuclear localization of the DICER1 protein...
  20. pmc Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays
    Hidemasa Bono
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Res 13:1318-23. 2003
    ..In addition, 1926 clones (70%) of 2768 clones that were categorized as "unknown EST," and 1969 (58%) clones of 3388 clones that were categorized as "unclassifiable" were also shown to be reproducibly expressed...
  21. ncbi request reprint Identification of genes regulating colorectal carcinogenesis by using the algorithm for diagnosing malignant state method
    Yasushi Ichikawa
    Second Department of Surgery, School of Medicine, Yokohama City University, Yokohama, Japan
    Biochem Biophys Res Commun 296:497-506. 2002
    ..Included in the 135 genes were tumor suppressor and growth factor-related genes and were consistent with the literature. ADMS is a reliable means for identifying genes useful for the diagnosis of cancer...