Yutaka Suzuki

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. pmc Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach
    Marty Kwok Shing Wong
    Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
    BMC Genomics 15:1134. 2014
  2. pmc Dengue transmission model by means of viremic adult immuno-competent mouse
    Lucky Ronald Runtuwene
    Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879 5593, Japan
    Parasit Vectors 7:143. 2014
  3. pmc The Babesia bovis gene and promoter model: an update from full-length EST analysis
    Junya Yamagishi
    National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada cho west 2 13, Obihiro, Hokkaido 080 8555, Japan
    BMC Genomics 15:678. 2014
  4. pmc High-resolution characterization of Toxoplasma gondii transcriptome with a massive parallel sequencing method
    Junya Yamagishi
    1National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
    DNA Res 17:233-43. 2010
  5. pmc Massive transcriptional start site analysis of human genes in hypoxia cells
    Katsuya Tsuchihara
    Cancer Physiology Project, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
    Nucleic Acids Res 37:2249-63. 2009
  6. pmc Intrinsic promoter activities of primary DNA sequences in the human genome
    Yuta Sakakibara
    Graduate School of Frontier Sciences, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    DNA Res 14:71-7. 2007
  7. pmc RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks
    Jun Kitano
    Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, Japan
    BMC Genomics 14:214. 2013
  8. pmc Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
    Marilyn B Renfree
    The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
    Genome Biol 12:R81. 2011
  9. pmc Profiling ascidian promoters as the primordial type of vertebrate promoter
    Kohji Okamura
    Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    BMC Genomics 12:S7. 2011
  10. pmc Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation
    Kahori Hara
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
    BMC Genomics 13:119. 2012

Collaborators

Detail Information

Publications83

  1. pmc Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach
    Marty Kwok Shing Wong
    Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
    BMC Genomics 15:1134. 2014
    ..Regulatory genes for transforming intestinal function have not been identified. A transcriptomic approach was used to search for such genes in the intestine of euryhaline medaka...
  2. pmc Dengue transmission model by means of viremic adult immuno-competent mouse
    Lucky Ronald Runtuwene
    Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879 5593, Japan
    Parasit Vectors 7:143. 2014
    ..Here, we report a method for creating artificial viremia in immuno-competent mice, and further demonstrate the use of viremic mice to simultaneously infect a large number of Aedes aegypti...
  3. pmc The Babesia bovis gene and promoter model: an update from full-length EST analysis
    Junya Yamagishi
    National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada cho west 2 13, Obihiro, Hokkaido 080 8555, Japan
    BMC Genomics 15:678. 2014
    ..Therefore, we validated a preproposed gene model of B. bovis and extended the associated annotations on the basis of experimentally obtained full-length expressed sequence tags (ESTs)...
  4. pmc High-resolution characterization of Toxoplasma gondii transcriptome with a massive parallel sequencing method
    Junya Yamagishi
    1National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
    DNA Res 17:233-43. 2010
    ..This encyclopaedic analysis also suggested that the TATA box, and the other well-known core promoter elements were hardly utilized...
  5. pmc Massive transcriptional start site analysis of human genes in hypoxia cells
    Katsuya Tsuchihara
    Cancer Physiology Project, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
    Nucleic Acids Res 37:2249-63. 2009
    ..The novel dynamic figure of the human gene transcriptome will deepen our understanding of the transcriptional program of the human genome as well as bringing new insights into the biology of cancer cells in hypoxia...
  6. pmc Intrinsic promoter activities of primary DNA sequences in the human genome
    Yuta Sakakibara
    Graduate School of Frontier Sciences, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    DNA Res 14:71-7. 2007
    ....
  7. pmc RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks
    Jun Kitano
    Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, Japan
    BMC Genomics 14:214. 2013
    ..Although the biological functions of the different small RNAs have been elucidated in several laboratory animals, little is known regarding naturally occurring variation in small RNA transcriptomes among closely related species...
  8. pmc Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
    Marilyn B Renfree
    The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
    Genome Biol 12:R81. 2011
    ..Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development...
  9. pmc Profiling ascidian promoters as the primordial type of vertebrate promoter
    Kohji Okamura
    Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    BMC Genomics 12:S7. 2011
    ..However, the limited annotation of these genes has impeded the large-scale analysis of their promoters...
  10. pmc Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation
    Kahori Hara
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
    BMC Genomics 13:119. 2012
    ..A recent study has identified a novel mutant silkworm line called KG, whose mutation in the W chromosome causes severe female masculinization. However, the molecular nature of KG line has not been well characterized yet...
  11. pmc Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
    Wei Qu
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277 0882, Japan
    Genome Res 22:1419-25. 2012
    ..This is the first report of findings showing that the CpG methylation state is significantly correlated with the characteristics of evolutionary change in neighboring DNA...
  12. pmc Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
    Riu Yamashita
    Frontier Research Initiative, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Res 21:775-89. 2011
    ..The collected integrative information should provide a useful basis for future biological characterization of TSCs...
  13. pmc DBTSS provides a tissue specific dynamic view of Transcription Start Sites
    Riu Yamashita
    Frontier Research Initiative, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
    Nucleic Acids Res 38:D98-104. 2010
    ..Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated. DBTSS can be accessed at http://dbtss.hgc.jp/...
  14. ncbi request reprint Diverse DNA methylation statuses at alternative promoters of human genes in various tissues
    Jieun Cheong
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba, Japan
    DNA Res 13:155-67. 2006
    ..DNA methylation appears to play a significant role in differential usage of alternative promoters and may be related to functional diversification between CpG-island-containing promoters and CpG-island-less promoters...
  15. pmc Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer
    Nuankanya Sathira
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa shi, Chiba 277 8568, Japan
    DNA Res 17:169-83. 2010
    ....
  16. pmc Characterization of STAT6 target genes in human B cells and lung epithelial cells
    Akinori Kanai
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwashi, Chiba 277 8562, Japan
    DNA Res 18:379-92. 2011
    ..The rough landscape of STAT6-responsive sites was found to be shaped by chromatin structure, but distinct cellular responses were mainly mediated by distinct sets of transcription factors...
  17. pmc Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes
    Katsuki Tsuritani
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minatoku, Tokyo 108 8639, Japan
    Genome Res 17:1005-14. 2007
    ..Taken together, our data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution...
  18. pmc Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs
    Hiroyuki Wakaguri
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
    BMC Genomics 10:312. 2009
    ..To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites...
  19. pmc DBTSS: database of transcription start sites, progress report 2008
    Hiroyuki Wakaguri
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 36:D97-101. 2008
    ..With the expanded dataset and the enhanced functionalities, DBTSS provides a unique platform that enables in-depth transcriptome analyses. DBTSS is accessible at http://dbtss.hgc.jp/...
  20. pmc Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009
    Hiroyuki Wakaguri
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo 4 6 1, Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D520-5. 2009
    ..Full-Malaria/Parasites and Full-Arthropods are accessible from http://fullmal.hgc.jp/...
  21. pmc Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions
    Yutaka Suzuki
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
    Genome Res 14:1711-8. 2004
    ....
  22. pmc Predicting promoter activities of primary human DNA sequences
    Takuma Irie
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwashi, Chiba 277 8562, Japan
    Nucleic Acids Res 39:e75. 2011
    ..Furthermore, we found that nucleosomes occasionally formed open chromatin structures with RNA polymerase II recruitment where the program predicted significant promoter activities, although no transcripts were observed...
  23. pmc Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs
    Junichi Watanabe
    Department of Parasitology, Institute of Medical Science, Graduate School of Frontier Sciences, University of Tokyo, 4 6 1, Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Nucleic Acids Res 35:D431-8. 2007
    ..Our full-length cDNA databases and Comparasite are accessible from http://fullmal.ims.u-tokyo.ac.jp...
  24. doi request reprint A single female-specific piRNA is the primary determiner of sex in the silkworm
    Takashi Kiuchi
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    Nature 509:633-6. 2014
    ..Our study characterizes a single small RNA that is responsible for primary sex determination in the WZ sex determination system. ..
  25. pmc Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance
    Sho Maekawa
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba, 277 8562, Japan
    BMC Genomics 16:154. 2015
    ....
  26. pmc Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species
    Yoichiro Nakatani
    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277 0882, Japan
    BMC Genomics 16:978. 2015
    ..Transcription start sites (TSSs) with pronounced and phased nucleosome arrays downstream and nucleosome-depleted regions upstream of TSSs are observed in various species...
  27. ncbi request reprint Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokane dai Minato ku, Tokyo 108 8639, Japan
    Gene 350:129-36. 2005
    ....
  28. pmc Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
    Shin Sasaki
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, 277 0882, Japan
    Science 323:401-4. 2009
    ..These data exemplify the potential for genetic activity (transcription) and chromatin structure to contribute to molding the DNA sequence on an evolutionary time scale...
  29. doi request reprint Characterization of a novel chromodomain-containing gene from the silkworm, Bombyx mori
    Keisuke Shoji
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    Gene 527:649-54. 2013
    ..siRNA-mediated knockdown of BmCdp1 in BmN4 cells and early embryos did not affect the expression of the gene located close to the BmCdp1-bound locus...
  30. pmc The silkworm W chromosome is a source of female-enriched piRNAs
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
    RNA 17:2144-51. 2011
    ..Collectively, we revealed the nature of the silkworm W chromosome as a source of piRNAs...
  31. pmc Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins
    Natsuko Izumi
    Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    RNA 19:896-901. 2013
    ..Our data highlight a role of Hsp90 in accurate loading of precursor piRNAs into PIWI proteins...
  32. pmc Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 36:3707-15. 2008
    ....
  33. pmc Silkworm HP1a transcriptionally enhances highly expressed euchromatic genes via association with their transcription start sites
    Keisuke Shoji
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    Nucleic Acids Res 42:11462-71. 2014
    ..These results demonstrate that BmHP1a binds near TSSs of highly expressed euchromatic genes and positively regulates their expression. Our study revealed a novel mode of transcriptional regulation mediated by HP1 proteins. ..
  34. pmc Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly
    Reginaldo M Kuroshu
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
    PLoS ONE 5:e10517. 2010
    ..However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded...
  35. doi request reprint Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance
    Sho Maekawa
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba, 277 8562, Japan
    BMC Genomics 16:1358. 2015
    ....
  36. pmc DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
    Riu Yamashita
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 34:D86-9. 2006
    ..Third, DBTSS provides detailed sequence comparisons of user-specified TSSs. Finally, we have added TSS information for zebrafish, malaria and schyzon (a red algae model organism). DBTSS is accessible at http://dbtss.hgc.jp...
  37. pmc Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species
    Junichi Watanabe
    Department of Parasitology, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1, Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Nucleic Acids Res 32:D334-8. 2004
    ....
  38. doi request reprint Construction and analysis of full-length cDNA library of Cryptosporidium parvum
    Junya Yamagishi
    National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
    Parasitol Int 60:199-202. 2011
    ..parvum as prospective candidates for addable genes. These observations should improve the reliability of C. parvum transcriptome and provide a versatile resource for further studies...
  39. ncbi request reprint Transcriptome analyses of human genes and applications for proteome analyses
    Yutaka Suzuki
    Laboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Curr Protein Pept Sci 7:147-63. 2006
    ..Rapidly accumulating genome data as well as versatile use of the transcriptome information will shortly lay a firm foundation for proteome-level understanding of human gene networks...
  40. pmc Zygotic amplification of secondary piRNAs during silkworm embryogenesis
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    RNA 17:1401-7. 2011
    ..These results provide on-site evidence for the ping-pong cycle...
  41. pmc Coordinated changes in DNA methylation in antigen-specific memory CD4 T cells
    Shin Ichi Hashimoto
    Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113 0033, Japan
    J Immunol 190:4076-91. 2013
    ..By comparing DMRs between naive and Ag-specific memory T cells, this study provides new insights into the functional status of memory T cells...
  42. pmc Identification and characterization of cancer mutations in Japanese lung adenocarcinoma without sequencing of normal tissue counterparts
    Ayako Suzuki
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
    PLoS ONE 8:e73484. 2013
    ....
  43. doi request reprint Sexually biased transcripts at early embryonic stages of the silkworm depend on the sex chromosome constitution
    Munetaka Kawamoto
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    Gene 560:50-6. 2015
    ..Our analysis has drawn a picture of a global landscape of sexually biased transcriptome during early B. mori embyogenesis and has suggested for the first time that most sexually biased embryonic transcripts depend on sex chromosomes...
  44. doi request reprint Analysis of changes in transcription start site distribution by a classification approach
    Kuo Ching Liang
    Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Gene 537:29-40. 2014
    ..We use a set of time-course TSS data from mouse dendritic cells stimulated with lipopolysaccharide (LPS) to demonstrate the usefulness of our method. ..
  45. pmc DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
    Yutaka Suzuki
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 30:328-31. 2002
    ....
  46. ncbi request reprint Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries
    Tetsuji Otsuki
    Helix Research Institute, Yana, Kisarazu shi, Chiba, Japan
    DNA Res 12:117-26. 2005
    ..Thus, an efficient method of selecting secretion or membrane protein-encoding cDNAs was developed by combining the above four procedures...
  47. pmc CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes
    Hikari Yoshitane
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    Mol Cell Biol 34:1776-87. 2014
    ..Collectively, CLOCK-dependent direct transactivation through multiple E-boxes and indirect regulations polyphonically orchestrate dynamic circadian outputs. ..
  48. doi request reprint Integrated molecular analysis of clear-cell renal cell carcinoma
    Yusuke Sato
    Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    Nat Genet 45:860-7. 2013
    ..This integrated molecular analysis unmasked new correlations between DNA methylation, gene mutation and/or gene expression and copy number profiles, enabling the stratification of clinical risks for patients with ccRCC. ..
  49. pmc A role for transcription from a piRNA cluster in de novo piRNA production
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo, Japan
    RNA 18:265-73. 2012
    ..Bioinformatic analyses suggest that the fusion transcript is a source of GFP primary piRNAs. Our data implicate a role for transcription from a piRNA cluster in initiating de novo piRNA production against a new insertion...
  50. pmc DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
    Yutaka Suzuki
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Nucleic Acids Res 32:D78-81. 2004
    ....
  51. pmc DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data
    Ayako Suzuki
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
    Nucleic Acids Res 43:D87-91. 2015
    ..Consequently, DBTSS is no longer a mere storage site for TSS information but has evolved into an integrative platform of a variety of genome activity data. ..
  52. pmc The Endosymbiotic Bacterium Wolbachia Selectively Kills Male Hosts by Targeting the Masculinizing Gene
    Takahiro Fukui
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    PLoS Pathog 11:e1005048. 2015
    ..Our study also shows a novel strategy by which a pathogen hijacks the host sex determination cascade. ..
  53. pmc Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment
    Ayako Suzuki
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277 8562, Japan
    Genome Biol 16:66. 2015
    ..Recent advances in next-generation sequencing-related technologies have enabled us to conduct a single-cell RNA-Seq analysis of a series of lung adenocarcinoma cell lines...
  54. doi request reprint Screening for possible miRNA-mRNA associations in a colon cancer cell line
    Sotaro Kanematsu
    Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562, Japan
    Gene 533:520-31. 2014
    ....
  55. ncbi request reprint Molecular cloning, mRNA expression and chromosomal localization of mouse angiotensin-converting enzyme-related carboxypeptidase (mACE2)
    Takami Komatsu
    Laboratory of Genome Structure Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    DNA Seq 13:217-20. 2002
    ..Mouse ACE2 showed 83% identity with human ACE2. Northern blot analysis revealed that 2.8- and 2.0-kb transcripts were expressed mainly in the kidney and the lungs. The mouse ACE2 gene was mapped to chromosome X 70.5 cM...
  56. pmc Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing
    J Fah Sathirapongsasuti
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562, Japan
    Nucleic Acids Res 39:1967-79. 2011
    ..The discovery of UCSs shed new light on the multifaceted, fine-tuned and tight post-transcriptional regulation of gene families as conserved through the majority of the mammalian lineage...
  57. doi request reprint Expressed sequence tags from cynomolgus monkey (Macaca fascicularis) liver: a systematic identification of drug-metabolizing enzymes
    Yasuhiro Uno
    Division of Genetic Diagnosis, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, Japan
    FEBS Lett 582:351-8. 2008
    ..Our comparative genomics approach identified nine lineage-specific candidate ESTs, including three drug-metabolizing enzymes, which could be important for understanding the physiological differences between monkeys and humans...
  58. doi request reprint BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells
    Naoto Imamachi
    Radioisotope Center, The University of Tokyo, 2 11 16 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Methods 67:55-63. 2014
    ..Here, we describe a detailed protocol and provide tips for BRIC-seq, followed by computational analysis. ..
  59. doi request reprint Contrasting expression patterns of histone mRNA and microRNA 760 in patients with gastric cancer
    Takeshi Iwaya
    Authors Affiliations Department of Surgery, Kyushu University Beppu Hospital, Beppu Department of Surgery, Iwate Medical University, Morioka Department of Gastric Surgery Division, National Cancer Center Hospital Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa shi, Chiba Department of Surgery, Teikyo University School of Medicine, Tokyo Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka, University, Suita and Department of Digestive Surgery, Hyogo Medical College, Japan
    Clin Cancer Res 19:6438-49. 2013
    ..Here, RNA-seq analysis of bone marrow from gastric cancer patients was performed to identify prognostic markers for gastric cancer...
  60. pmc Giardia lamblia transcriptome analysis using TSS-Seq and RNA-Seq
    Mohammed E M Tolba
    Department of Medical Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan Department of Parasitology, Faculty of Medicine, Assiut University, Assiut, Egypt
    PLoS ONE 8:e76184. 2013
    ..From the 8000 TRs, we were able to identify an AT-rich consensus that includes the transcription initiation site. It is possible that transcription that was previously thought to be bidirectional is actually unidirectional. ..
  61. doi request reprint ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm
    Hideki Terajima
    Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
    Nat Genet . 2016
    ..These phenotypes were associated with abnormal accumulation of CRY2. The present study identifies A-to-I RNA editing as a key mechanism of post-transcriptional regulation in the circadian clockwork...
  62. ncbi request reprint Analysis of transcriptomes of human malaria parasite Plasmodium falciparum using full-length enriched library: identification of novel genes and diverse transcription start sites of messenger RNAs
    Junichi Watanabe
    Department of Parasitology, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo 108 8639, Japan
    Gene 291:105-13. 2002
    ..The transcriptional start sites of all the genes studied were far more diverse than those of human genes. These observations may reflect unique mechanism(s) of gene expression in this organism, which has an extremely AT-rich genome...
  63. pmc High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer
    Shin Ichi Hashimoto
    Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    PLoS ONE 4:e4108. 2009
    ..The high-resolution 5'end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology...
  64. pmc Local potentiation of stress-responsive genes by upstream noncoding transcription
    Naomichi Takemata
    Department of Life Sciences, The University of Tokyo, Meguro ku, Tokyo 153 8902, Japan
    Nucleic Acids Res 44:5174-89. 2016
    ..These results reveal a new mechanism in which upstream noncoding transcription locally magnifies the specific activation of stress-inducible genes via counteraction of corepressors. ..
  65. doi request reprint Comparative Analysis of Genome and Epigenome in Closely Related Medaka Species Identifies Conserved Sequence Preferences for DNA Hypomethylated Domains
    Ayako Uno
    1 Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113 0033, Japan
    Zoolog Sci 33:358-65. 2016
    ..However, we identified short well-conserved motifs that are specifically enriched in HMDs, suggesting that they may play roles in the establishment of HMDs in the medaka genome. ..
  66. ncbi request reprint DKK1, a negative regulator of Wnt signaling, is a target of the beta-catenin/TCF pathway
    Atsushi Niida
    Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Oncogene 23:8520-6. 2004
    ..Our finding suggests the existence of a novel feedback loop in Wnt signaling...
  67. doi request reprint Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates
    Ryohei Nakamura
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113 0033, Japan
    Development 141:2568-80. 2014
    ..We propose that large K27HMDs play a crucial role in pluripotent cells by strictly repressing key developmental genes, whereas their shortening consolidates long-term gene expression in adult differentiated cells. ..
  68. doi request reprint Proteomic identification of differentially expressed genes in neural stem cells and neurons differentiated from embryonic stem cells of cynomolgus monkey (Macaca fascicularis) in vitro
    Kuniko Akama
    Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
    Biochim Biophys Acta 1814:265-76. 2011
    ..RT-PCR results showed that CRMP2 and FABP7 mRNAs were also upregulated in NS cells, while CRABP1 mRNA was unchanged. These results provide insight into the molecular basis of monkey neural differentiation...
  69. pmc Effects of Alu elements on global nucleosome positioning in the human genome
    Yoshiaki Tanaka
    Department of Medical Genome Sciences, University of Tokyo, Minato ku, Japan
    BMC Genomics 11:309. 2010
    ..As a typical example, the 10-bp periodicity of AA/TT and GC dinucleotides has been reported in several species, but it is still unclear whether this feature can be observed in the whole genomes of all eukaryotes...
  70. pmc The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes
    Shinpei Kawaoka
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113 8657, Japan
    RNA 15:1258-64. 2009
    ..Taken together, BmN4 is a unique cell line in which both primary and secondary steps of piRNA biogenesis pathways are active. This cell line would provide useful tools for analysis of piRNA biogenesis and function...
  71. ncbi request reprint Small open reading frames in 5' untranslated regions of mRnas
    Riu Yamashita
    Laboratory of Genome Database, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4 6 1, Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    C R Biol 326:987-91. 2003
    ..They require attention for further analysis to identify their biological role...
  72. ncbi request reprint Database and analysis system for cDNA clones obtained from full-length enriched cDNA libraries
    Tetsuo Nishikawa
    Helix Research Institute, Chiba, Japan
    In Silico Biol 2:5-18. 2002
    ..And various results such as ORF features and database search results can be shown on the same screen by multiple displays. Full-length clones having interesting functions can thus be retrieved efficiently by using this system...
  73. pmc DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
    Riu Yamashita
    Frontier Research Initiative, Institute of Medical Science, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 40:D150-4. 2012
    ..DBTSS can be accessed at http://dbtss.hgc.jp...
  74. pmc Transcriptome analysis of mouse brain infected with Toxoplasma gondii
    Sachi Tanaka
    National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada cho, Obihiro, Hokkaido, Japan
    Infect Immun 81:3609-19. 2013
    ..Our findings may provide insights into the mechanisms underlying neurological changes during T. gondii infection. ..
  75. doi request reprint Bombyx mori nucleopolyhedrovirus actin rearrangement-inducing factor 1 enhances systemic infection in B. mori larvae
    Ryuhei Kokusho
    1Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    J Gen Virol 96:1938-46. 2015
    ..These results indicated that BmNPV ARIF-1 enhanced systemic infection in B. mori larvae. ..
  76. pmc Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines
    Ayako Suzuki
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
    Nucleic Acids Res 42:13557-72. 2014
    ..We also used the multi-omics data to classify the cell lines regarding their hallmarks of carcinogenesis. Our datasets should provide a valuable foundation for biological interpretations of interlaced genomic and epigenomic aberrations. ..
  77. pmc Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
    Hidenori Tani
    Radioisotope Center, The University of Tokyo, 2 11 16 Yayoi, Bunkyo ku, Tokyo, Japan
    Genome Res 22:947-56. 2012
    ..We propose that the strategy of monitoring RNA half-life will provide a powerful tool for investigating hitherto functionally uncharacterized regulatory RNAs...
  78. doi request reprint Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis
    Nicolas Sierro
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Gene 430:44-9. 2009
    ..intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently...
  79. pmc Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs
    Masaaki Oyama
    Human Genome Center, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    Genome Res 14:2048-52. 2004
    ..This investigation provides the first direct evidence of translation of upstream ORFs in human cells, which could greatly change the current outline of the human proteome...
  80. ncbi request reprint SAGE analysis of early oogenesis in the silkworm, Bombyx mori
    Shunsuke Funaguma
    Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
    Insect Biochem Mol Biol 37:147-54. 2007
    ..1-fold enriched) and ATP synthase coupling factor 6 (9.1-fold enriched), suggesting that they are involved in regulation of cell cycle of cystocytes...
  81. pmc A comparison of the rest complex binding patterns in embryonic stem cells and epiblast stem cells
    Masahide Seki
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
    PLoS ONE 9:e95374. 2014
    ..As a result of differences in the components and targets of the Rest complex, its functional roles may differ in ES and EpiS cells. ..
  82. ncbi request reprint OASIS is a transcriptional activator of CREB/ATF family with a transmembrane domain
    Yoshihiro Omori
    Laboratory of Genome Structure Analysis Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Biochem Biophys Res Commun 293:470-7. 2002
    ..Western blot analysis of transfected cells identified OASIS polypeptides of 82 and 66 kDa. These results suggest that the transmembrane domain plays an important role in the regulation of transcriptional activation by OASIS...
  83. doi request reprint Monitoring endoplasmic reticulum stress responsive mRNAs by RNA sequencing
    Tetsuo Okuda
    Department of Medical Genome Sciences, The University of Tokyo, Japan
    Gene 500:63-72. 2012
    ..This was consistent with the concept that the ribosome is the essential site for managing ER stress. DSSR is a useful tool for the search of candidates of ER stress responsive genes...