Research Topics
Genomes and Genes | Yasuhiro TomaruSummaryAffiliation: RIKEN Brain Science Institute Country: Japan Publications
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Detail Information
Publications
Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysisYasuhiro 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....- Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiationAtsutaka 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... - Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAiTaku 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.... - Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genesHisashi 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... - The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cellsAtsutaka 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... - Comparative analysis of expression of histone H2a genes in mouseHiromi 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... - Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cellsMisato 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... - Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGEMorana 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... - Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAiYasuhiro 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... - Naturally occurring antisense RNA of histone H2a in mouse cultured cell linesHiromi 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)... - A comprehensive search for HNF-3alpha-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysisYasuhiro 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... - The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell lineHarukazu Suzuki
RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
Nat Genet 41:553-62. 2009.... - Nuclear pore complex protein mediated nuclear localization of dicer protein in human cellsYoshinari 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... - A novel replication-independent histone H2a gene in mouseHiromi 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... - EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genesItoshi 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... - A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectivenessA Maxwell Burroughs
Omics Science Center OSC, RIKEN Yokohama Institute, Tsurumi ku, Yokohama shi, Kanagawa 230 0045, Japan
Genome Res 20:1398-410. 2010.... - Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarraysHidemasa 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... - Identification of genes regulating colorectal carcinogenesis by using the algorithm for diagnosing malignant state methodYasushi 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...