Yoshihide Hayashizaki

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. ncbi Antisense transcripts with rice full-length cDNAs
    Naoki Osato
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045
    Genome Biol 5:R5. 2003
  2. ncbi Dynamic usage of transcription start sites within core promoters
    Hideya Kawaji
    NTT Software Corporation, 209 Yamashita cho Nakak ku, Yokohama, Kanagawa, 231 8551, Japan
    Genome Biol 7:R118. 2006
  3. ncbi SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    BMC Bioinformatics 10:133. 2009
  4. ncbi Constructing ORFeome resources with removable termination codons
    Masayoshi Itoh
    RIKEN DRI, Wako, RIKEN GSC, Yokohama, Japan
    Biotechniques 41:44, 46, 48 passim. 2006
  5. ncbi Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis
    Takeya Kasukawa
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    Genomics 84:913-21. 2004
  6. ncbi In vitro pull-down assay without expression constructs
    Harukazu Suzuki
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama, Kanagawa, Japan
    Biotechniques 37:918, 920. 2004
  7. ncbi Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR
    Harukazu Suzuki
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    FEBS Lett 573:214-8. 2004
  8. ncbi Tagging mammalian transcription complexity
    Piero Carninci
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2 1 Hirosawa, Wako, Saitama 351 0198 Japan
    Trends Genet 22:501-10. 2006
  9. ncbi Multifaceted mammalian transcriptome
    Piero Carninci
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Curr Opin Cell Biol 20:274-80. 2008
  10. ncbi Reversible hydrogel formation driven by protein-peptide-specific interaction and chondrocyte entrapment
    Fuyu Ito
    CREST, Japan Science and Technology Agency, 4 1 8 Honcho, Kawaguchi, Saitama 332 0012, Japan
    Biomaterials 31:58-66. 2010

Collaborators

Detail Information

Publications130 found, 100 shown here

  1. ncbi Antisense transcripts with rice full-length cDNAs
    Naoki Osato
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045
    Genome Biol 5:R5. 2003
    ..On the basis of our results, experiments should be carried out to analyze the function of plant antisense transcripts...
  2. ncbi Dynamic usage of transcription start sites within core promoters
    Hideya Kawaji
    NTT Software Corporation, 209 Yamashita cho Nakak ku, Yokohama, Kanagawa, 231 8551, Japan
    Genome Biol 7:R118. 2006
    ..We previously characterized the static structures of transcription start site usage within promoters at the base pair level, based on large-scale sequencing of transcript 5' ends...
  3. ncbi SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    BMC Bioinformatics 10:133. 2009
    ..While the format provides an explicit framework to describe experiments, increase of experimental steps makes it less obvious to understand the content of the SDRF files...
  4. ncbi Constructing ORFeome resources with removable termination codons
    Masayoshi Itoh
    RIKEN DRI, Wako, RIKEN GSC, Yokohama, Japan
    Biotechniques 41:44, 46, 48 passim. 2006
  5. ncbi Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis
    Takeya Kasukawa
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045, Japan
    Genomics 84:913-21. 2004
    ..RTPSs of human, mouse, and rat have been produced by this method and used for validation. Their comprehensiveness and quality are discussed by comparison with other clustering approaches. The RTPSs are available at ...
  6. ncbi In vitro pull-down assay without expression constructs
    Harukazu Suzuki
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama, Kanagawa, Japan
    Biotechniques 37:918, 920. 2004
  7. ncbi Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR
    Harukazu Suzuki
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    FEBS Lett 573:214-8. 2004
    ..These results provide unique molecular markers that may account for the molecular basis of the unique functions of specific brain regions...
  8. ncbi Tagging mammalian transcription complexity
    Piero Carninci
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2 1 Hirosawa, Wako, Saitama 351 0198 Japan
    Trends Genet 22:501-10. 2006
    ..The next few years will see efforts to identify novel transcripts systematically and decipher their function. A deeper understanding of transcriptional complexity might even lead us to redefine what we mean by the term 'gene'...
  9. ncbi Multifaceted mammalian transcriptome
    Piero Carninci
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Curr Opin Cell Biol 20:274-80. 2008
    ..Here, we focus on various aspects of the diversity of the biological role of these nonprotein-coding RNAs (ncRNAs), with emphasis on functional mechanisms recently elucidated...
  10. ncbi Reversible hydrogel formation driven by protein-peptide-specific interaction and chondrocyte entrapment
    Fuyu Ito
    CREST, Japan Science and Technology Agency, 4 1 8 Honcho, Kawaguchi, Saitama 332 0012, Japan
    Biomaterials 31:58-66. 2010
    ..The potential use of such a shear-sensitive hydrogel for injectable cell delivery into diseased or lost cartilage tissue is discussed...
  11. ncbi Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell
    Hiromi Nishida
    Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Yokohama, Japan
    Chromosome Res 14:203-11. 2006
    ..Our results imply that the relative nucleosome depletion in the vicinity of TSS is not necessarily associated with active transcription, but with histone H3 K9 acetylation in promoter...
  12. ncbi Constructing the landscape of the mammalian transcriptome
    Piero Carninci
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, Wako, Saitama, Japan
    J Exp Biol 210:1497-506. 2007
    ..Recent experimental evidence suggests that the list of non-protein coding RNAs is still largely incomplete and that transcription is substantially more complex even than currently thought...
  13. ncbi Noncoding RNA transcription beyond annotated genes
    Piero Carninci
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Curr Opin Genet Dev 17:139-44. 2007
    ..Although the function of the majority of noncoding RNAs has yet to be discovered, many of them are transcribed from both strands of the genome, and evidence points towards a regulatory function for many noncoding RNAs in mammalian cells...
  14. ncbi Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs
    Norihiro Maeda
    Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
    PLoS Genet 2:e62. 2006
    ....
  15. ncbi 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...
  16. ncbi The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho Tsurumi ku Yokohama, Kanagawa, 230 0045 Japan
    Genome Biol 10:R40. 2009
    ..In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource...
  17. ncbi Structural and functional differences of SWIRM domain subtypes
    Misao Yoneyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Mol Biol 369:222-38. 2007
    ..We also solved the structure of the SANT domain of MYSM1, and demonstrated that it bound DNA with a similar mode to that of the c-Myb DNA-binding domain...
  18. ncbi Unamplified cap analysis of gene expression on a single-molecule sequencer
    Mutsumi Kanamori-Katayama
    Omics Science Center, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Japan
    Genome Res 21:1150-9. 2011
    ..Finally, although the majority of tags are 5' associated, we also observe a low level of signal on exons that is useful for defining gene structures...
  19. ncbi Solution structure of the mouse enhancer of rudimentary protein reveals a novel fold
    Hua Li
    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Yokohama, Tsurumi, 230-0045, Japan
    J Biomol NMR 32:329-34. 2005
  20. ncbi Effect of thiazole orange doubly labeled thymidine on DNA duplex formation
    Yasumasa Kimura
    RIKEN Omics Science Center OSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Yokohama, Kanagawa 230 0045, Japan
    Biochemistry 51:6056-67. 2012
    ..gsc.riken.jp/echo/thermodynamics/. It provides reliable thermodynamic data for using the unique features of ECHOs in fluorescence-based experiments...
  21. ncbi Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia
    Piero Carninci
    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 13:1273-89. 2003
    ..Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete...
  22. ncbi Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode
    Hua Li
    Systems and Structural Biology Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 283:27165-78. 2008
    ..The extensive binding features of the PID domain of Fe65L1 with the cytoplasmic domain of APP provide a framework for further understanding of the function, trafficking, and processing of APP modulated by adapter proteins...
  23. ncbi Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling
    Itoshi Nikaido
    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 13:1402-9. 2003
    ..These data provide a major resource for understanding the role of imprinting in mammalian inherited traits...
  24. ncbi Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode
    Kanako Kuwasako
    Protein Research Group, Genomic Sciences Center, Yokohama Institute, RIKEN, Tsurumi ku, Yokohama 230 0045, Japan
    Biochemistry 47:6437-50. 2008
    ..An investigation of the chemical shift perturbation revealed similarity in the RNA recognition modes between the TIA-1 and U2AF65 RRMs...
  25. ncbi Gene expression during liver regeneration after partial hepatectomy in mice lacking type 1 tumor necrosis factor receptor
    Tetsuya Shimizu
    Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
    J Surg Res 152:178-88. 2009
    ..To investigate the function of tumor necrosis factor-alpha (TNF-alpha) during hepatocyte proliferation, we studied liver regeneration following partial hepatectomy in mice lacking type 1 TNF receptor (TNFR-1)...
  26. ncbi Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3
    Naoya Tochio
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Protein Sci 15:2534-43. 2006
    ..This concave surface includes the highly conserved Glu-Leu-Lys-Leu motif at the C terminus, indicating that it is important for the function of the KA1 domain...
  27. ncbi 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...
  28. ncbi Development of a spot reliability evaluation score for DNA microarrays
    Yonehiro Matsumura
    Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
    Gene 350:149-60. 2005
    ..This score was applied to approximately 1,500,000 points of the expression profile in the RIKEN Expression Array Database...
  29. ncbi 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
    ....
  30. ncbi 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...
  31. ncbi The PDZ protein tax-interacting protein-1 inhibits beta-catenin transcriptional activity and growth of colorectal cancer cells
    Mutsumi Kanamori
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    J Biol Chem 278:38758-64. 2003
    ..These data suggest that TIP-1 may represent a novel regulatory element in the Wnt/beta-catenin signaling pathway...
  32. ncbi 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
    ....
  33. ncbi 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...
  34. ncbi CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis
    Hideya Kawaji
    NTT Software Corporation, Teisan Kannai Building 209, Yamashita-cho Naka-ku, Yokohama, Kanagawa, 231-8551, Japan
    Nucleic Acids Res 34:D632-6. 2006
    ..Now access is free for all users through the World Wide Web at http://fantom3.gsc.riken.jp/...
  35. ncbi FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions
    Jessica Severin
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho Tsurumi ku Yokohama, Kanagawa, 230 0045 Japan
    Genome Biol 10:R39. 2009
    ..This is an important resource for gene regulation in acute myeloid leukemia, monocyte/macrophage differentiation and human transcriptional networks...
  36. ncbi FREP: a database of functional repeats in mouse cDNAs
    Takeshi Nagashima
    Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
    Nucleic Acids Res 32:D471-5. 2004
    ....
  37. ncbi Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)
    Takeshi Maeda
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 279:13174-82. 2004
    ..On the other hand the tissue tumor marker MUC1 has a SEA domain belonging to another subfamily, and its GSVVV motif for proteolytic cleavage is located in the short loop connecting beta2 and beta3...
  38. ncbi Ligand-specific sequential regulation of transcription factors for differentiation of MCF-7 cells
    Yuko Saeki
    Cellular Systems Modeling Team, Computational Systems Biology Research Group, Advanced Computational Sciences Department, RIKEN Advanced Science Institute, 1 7 22 Suehiro cho Tsurumi ku Yokohama, Kanagawa 230 0045, Japan
    BMC Genomics 10:545. 2009
    ....
  39. ncbi Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts
    Takahiro Suzuki
    Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    PLoS ONE 7:e33474. 2012
    ....
  40. ncbi Crystal structure analysis of the PHD domain of the transcription co-activator Pygopus
    Yoshihiro Nakamura
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Mol Biol 370:80-92. 2007
    ..These results suggest that the Pygo1 PHD dimerization is functionally important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway...
  41. ncbi Rapid screening assay for KRAS mutations by the modified smart amplification process
    Kenji Tatsumi
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    J Mol Diagn 10:520-6. 2008
    ..The PNA-clamp SMAP-2 method is a rapid, simple, and highly sensitive detection assay for cancer mutations...
  42. ncbi Dynamic force spectroscopy of the specific interaction between the PDZ domain and its recognition peptides
    Tei Maki
    Core Research for Evolutional Science and Technology CREST, Japan Science and Technology Agency, 4 1 8 Honcho, Saitama 332 0012, Japan
    Langmuir 23:2668-73. 2007
    ..The reason for such topographic differences in the energy landscape is discussed in relation to the differences in the pathways of forced unbinding and spontaneous dissociation...
  43. ncbi Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns
    Anton Kratz
    Keiko University, Graduate School of Media and Governance, Kanagawa, Japan
    BMC Genomics 11:257. 2010
    ..The promoter classes were analyzed for association with relevant genomic sequence features...
  44. ncbi Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas
    Akira Watahiki
    Genome Science Laboratory, RIKEN, Wako Main Campus, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
    Nat Methods 1:233-9. 2004
    ..Thus, the ASL approach proved effective in identifying splicing events, which suggest that alternative splicing is important in melanoma development...
  45. ncbi Discrimination of non-protein-coding transcripts from protein-coding mRNA
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Kanagawa, Japan
    RNA Biol 3:40-8. 2006
    ..Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts...
  46. ncbi Structure of the UNC5H2 death domain
    Noriko Handa
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Acta Crystallogr D Biol Crystallogr 62:1502-9. 2006
    ..In the death-domain dimer, residues in alpha3 and the 3(10)-helix preceding alpha3 and the residues in alpha4 make significant contacts, mainly by hydrophobic and van der Waals interactions...
  47. ncbi Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
    Jasmina Ponjavic
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230 0045, Japan
    Genome Biol 7:R78. 2006
    ..The lack of precise transcription start site (TSS) locations linked with expression information has impeded genome-wide characterization of the interaction between TATA and the pre-initiation complex...
  48. ncbi Genome-wide analysis of abnormal H3K9 acetylation in cloned mice
    Takahiro Suzuki
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    PLoS ONE 3:e1905. 2008
    ....
  49. ncbi Hidden layers of human small RNAs
    Hideya Kawaji
    Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    BMC Genomics 9:157. 2008
    ....
  50. ncbi Large-scale clustering of CAGE tag expression data
    Kazuro Shimokawa
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    BMC Bioinformatics 8:161. 2007
    ..The standard hierarchical clustering algorithm, which gives us easily understandable graphical tree images, has difficulties in processing such huge amounts of TSS data and a better method to calculate and display the results is needed...
  51. ncbi 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...
  52. ncbi Sensitive detection of EGFR mutations using a competitive probe to suppress background in the SMart Amplification Process
    Yuki Kawai
    Genome Exploration Research Group Genome Network Project Core Group, Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Biologicals 36:234-8. 2008
    ..The CP approach is another tool enhancing the effectiveness and versatility of SMAP 2 assays, expanding its potential applications, and reinforcing its position as a highly effective technology for molecular diagnostics...
  53. ncbi LRRN4 and UPK3B are markers of primary mesothelial cells
    Mutsumi Kanamori-Katayama
    Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    PLoS ONE 6:e25391. 2011
    ..Once diagnosed there is a very poor prognosis with a median survival rate of 9 months. Considering this the development of early pre clinical diagnostic markers may help improve clinical outcomes...
  54. ncbi Integrated analysis of the genome and the transcriptome by FANTOM
    Shintaro Katayama
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Brief Bioinform 5:249-58. 2004
    ..Categorised annotation, which refers to transcript grouping, not only helps naming of unknown transcripts, but will be the most utilised method for integration of the genome and the transcriptome from now on...
  55. ncbi 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...
  56. ncbi Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
    Hideya Kawaji
    RIKEN Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama City, Kanagawa 230 0045, Japan
    Nucleic Acids Res 39:D856-60. 2011
    ..gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial release...
  57. ncbi 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...
  58. ncbi NMR solution structures of actin depolymerizing factor homology domains
    Alexander K Goroncy
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    Protein Sci 18:2384-92. 2009
    ..The G-actin binding site of the ADF-H domain of human HIP-55-drebrin-like protein is absent and distorted in mouse GMF beta and GMF gamma...
  59. ncbi Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3
    Kengo Usui
    CREST, Japan Science and Technology Agency, 4 1 8 Honcho, Kawaguchi, Saitama 332 0012, Japan
    Genome Biol 6:R98. 2005
    ....
  60. ncbi Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags
    Rimantas Kodzius
    Genome Science Laboratory, RIKEN, Wako Main Campus, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
    FEBS Lett 559:22-6. 2004
    ..These experiments confirmed the great significance of the absolute expression values within the improved READ database. The new Absolute READ database on absolute expression data is available under...
  61. ncbi Splicing bypasses 3' end formation signals to allow complex gene architectures
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Centre GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Gene 403:188-93. 2007
    ..This bypassing mechanism permits nested and interleaved gene architectures, as well as fusion transcripts that combine exons from adjacent genes...
  62. ncbi CDS annotation in full-length cDNA sequence
    Masaaki Furuno
    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 13:1478-87. 2003
    ....
  63. ncbi Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
    Toshiyuki Shiraki
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
    Proc Natl Acad Sci U S A 100:15776-81. 2003
    ..The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression...
  64. ncbi Optimization of turn-back primers in isothermal amplification
    Yasumasa Kimura
    RIKEN Omics Science Center OSC, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230 0045, Japan
    Nucleic Acids Res 39:e59. 2011
    ..Our computer script is freely available at: http://gerg.gsc.riken.jp/TP_optimization/...
  65. ncbi Generation of full-length cDNA libraries: focus on plants
    Motoaki Seki
    Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, Yokohama, Japan
    Methods Mol Biol 533:49-68. 2009
    ..We have constructed full-length cDNA libraries from various plants and animals using this method. The protocol of the method is described in this chapter...
  66. ncbi Gemin2 plays an important role in stabilizing the survival of motor neuron complex
    Chihiro Ogawa
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    J Biol Chem 282:11122-34. 2007
    ....
  67. ncbi Mammalian RNA polymerase II core promoters: insights from genome-wide studies
    Albin Sandelin
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Nat Rev Genet 8:424-36. 2007
    ..A comprehensive survey of mammalian promoters is a major step towards describing and understanding transcriptional control networks...
  68. ncbi The abundance of short proteins in the mammalian proteome
    Martin C Frith
    Genome Exploration Research Group (Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    PLoS Genet 2:e52. 2006
    ..Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway...
  69. ncbi CAGE: cap analysis of gene expression
    Rimantas Kodzius
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC, Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
    Nat Methods 3:211-22. 2006
  70. ncbi Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing
    Mitsuoki Kawano
    RIKEN Omics Science Center, Yokohama, Japan
    Biotechniques 49:751-5. 2010
    ..This method improves the sequencing yield and efficiency, while simplifying library construction, and makes it easier to perform large-scale small RNA analysis under multiple conditions with next-generation sequencers...
  71. ncbi 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...
  72. ncbi Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
    Charles Plessy
    RIKEN Yokohama Institute, Omics Science Center, Yokohama, Japan
    Nat Methods 7:528-34. 2010
    ..Both of these methods allow further annotation-agnostic studies of the complex human transcriptome...
  73. ncbi Evolutionary turnover of mammalian transcription start sites
    Martin C Frith
    Genome Exploration Research Group, RIKEN Genomic Sciences Centre (GSC, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
    Genome Res 16:713-22. 2006
    ..These findings suggest that the signals encoding transcription start sites are highly flexible and evolvable, and have cautionary implications for the use of sequence-level conservation to detect gene regulatory elements...
  74. ncbi A code for transcription initiation in mammalian genomes
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
    Genome Res 18:1-12. 2008
    ....
  75. ncbi Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts
    Tomoko Hirozane-Kishikawa
    RIKEN Yokohama Institute, Yokohama, Japan
    Biotechniques 35:510-6, 518. 2003
    ..The proportion of full-length cDNAs and the gene discovery rate are high, and library diversity can be validated by in silico randomization...
  76. ncbi Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera
    Atsushi Nakabachi
    Environmental Molecular Biology Laboratory and Genome Science Laboratory, RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Proc Natl Acad Sci U S A 102:5477-82. 2005
    ..Conspicuously high expression of ii and iii shed light on previously unknown aspects of the host-Buchnera interactions in the symbiotic system...
  77. ncbi Genome-wide analysis of mammalian promoter architecture and evolution
    Piero Carninci
    Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
    Nat Genet 38:626-35. 2006
    ..These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them...
  78. ncbi Mapping of 19032 mouse cDNAs on mouse chromosomes
    Itaru Yamanaka
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
    J Struct Funct Genomics 2:23-8. 2002
    ..In the second approach, we related cDNAs to expressed sequence tags (EST) previously mapped in radiation hybrid experiments. We discuss improving the mapping by combining the 2 methods...
  79. ncbi Pseudo-messenger RNA: phantoms of the transcriptome
    Martin C Frith
    Genome Exploration Research Group (Genome Network Project Core Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
    PLoS Genet 2:e23. 2006
    ..Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level...
  80. ncbi Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer
    Norihiro Maeda
    Advanced Science Institute, RIKEN Wako Main Campus, Saitama, Japan
    Biotechniques 45:95-7. 2008
    ..Additionally, this pooled CAGE tag method enables the dynamic changes in promoter usage and gene expression to be monitored...
  81. ncbi A resource for transcriptomic analysis in the mouse brain
    Charles Plessy
    Functional Genomics Technology Team, Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    PLoS ONE 3:e3012. 2008
    ..Studies of sorted cells expressing the same transgene have shown that cell populations can be distinguished according to their transcriptional profile...
  82. ncbi Transcriptomics resources for functional genomics
    Jun Kawai
    Genome Exploration Research Group, Genomic Sciences Center GSC, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Brief Funct Genomic Proteomic 6:171-9. 2007
    ..These transcriptomics resources are providing researchers with essential tools for studies of functional genomics. Here, the importance of quality and availability of these resources is discussed...
  83. ncbi Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
    Michiel J L de Hoon
    Omics Science Center, RIKEN Yokohama Institute, Tsurumi, Yokohama 230 0045, Japan
    Genome Res 20:257-64. 2010
    ..Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In contrast to previous reports, our analysis suggests that RNA editing in mature miRNAs is rare in animals...
  84. ncbi Tunable fractionation of nucleic acids
    Md Salimullah
    Functional Genomics Technology Team, Omics Science Center OSC, RIKEN Yokohama Institute, Kanagawa, Japan
    Biotechniques 47:1041-3. 2009
    ..This method could also be applied to the fractionation of nucleic acids generated by other types of reactions...
  85. ncbi Solution structure of the RWD domain of the mouse GCN2 protein
    Nobukazu Nameki
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan
    Protein Sci 13:2089-100. 2004
    ..Thus, it appears that the RWD domain is a novel structural domain for protein-binding that plays specific roles in individual RWD-containing proteins...
  86. ncbi 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
    ....
  87. ncbi Annotating non-coding transcription using functional genomics strategies
    Alistair R R Forrest
    Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230 0045 Japan
    Brief Funct Genomic Proteomic 8:437-43. 2009
    ..g. influencing chromatin structure and epigenetics, translational silencing, transcriptional silencing). Here, we highlight recent functional genomics strategies toward identifying and assigning function to ncRNA transcription...
  88. ncbi A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs
    Naoki Osato
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan
    Genome Res 12:1127-34. 2002
    ..Therefore, our method is useful for the selection of appropriate representative clones for full-length sequencing, thereby greatly reducing the cost, labor, and time necessary for this process...
  89. ncbi High-throughput verification of transcriptional starting sites by Deep-RACE
    Signe Olivarius
    Functional Genomics Technology Team, Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    Biotechniques 46:130-2. 2009
    ..In comparison to the sequencing of RACE PCR products, our approach is more precise and more cost-effective even for batches as small as 17...
  90. ncbi Non-coding RNA transcription: turning on neighbours
    Piero Carninci
    RIKEN Omics Science Center, Yokohama, Japan
    Nat Cell Biol 10:1023-4. 2008
    ..Even though less than 2% of the mammalian genome encodes proteins, a significant fraction can be transcribed into non-coding RNAs. An elegant study identifies a function for non-coding RNA transcription in activating neighbouring genes...
  91. ncbi RNA dust: where are the genes?
    Piero Carninci
    Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    DNA Res 17:51-9. 2010
    ..The emerging hypotheses suggest that the gene regulatory machinery may be deeply interconnected with the world of short RNAs. These RNAs may generally act for fine-tuning of the protein-coding transcriptome...
  92. ncbi [Cap analysis gene expression: CAGE]
    Mari Nakamura
    Tanpakushitsu Kakusan Koso 49:2688-93. 2004
  93. ncbi Whole genome transcriptome analysis
    Alistair R R Forrest
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
    RNA Biol 6:107-12. 2009
    ..We discuss the state of the art as to measuring and identifying these novel RNAs and speculate on whether a universal approach to transcript isoform and expression level measurement is possible in the near future...
  94. ncbi 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...
  95. ncbi CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks
    Hazuki Takahashi
    RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
    Methods Mol Biol 786:181-200. 2012
    ..The protocol takes less than 5 days to complete and presents a notable improvement compared to previously published versions...
  96. ncbi Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Plant J 31:279-92. 2002
    ....
  97. ncbi Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs
    Alka Saxena
    Omics Science Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Bioessays 33:830-9. 2011
    ..Finally, we point to future areas of research and put forward our recommendations for improvements in resources and applications of existing technologies towards targeted outcomes in this active area of research...
  98. ncbi Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library
    Kirk W Beisel
    Department of Biomedical Sciences, Creighton University, 2500 California, Omaha, NE 68178, USA
    Genomics 83:1012-23. 2004
    ..Of these, 59 clusters were found only in our sIEa library and represented approximately 50% of the identified critical regions...
  99. ncbi Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  100. ncbi Functional annotation of a full-length Arabidopsis cDNA collection
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center (GSC, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
    Science 296:141-5. 2002
    ..Furthermore, the full-length cDNAs are useful resources for analyses of the expression profiles, functions, and structures of plant proteins...
  101. ncbi Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis
    Junshi Yazaki
    Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
    Physiol Genomics 17:87-100. 2004
    ..In comparison of cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response as Arabidopsis specific and for protein storage as rice specific...