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Transcriptome analysis using full-length enriched cDNA library and technology develop ment

Research Project

Project/Area Number 17020002
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

SUGANO Sumio  The University of Tokyo, 大学院・新領域創成科学研究科, 教授 (60162848)

Co-Investigator(Kenkyū-buntansha) NAKAI Kenta  東京大学, 医科学研究所, 教授 (60217643)
HASHIMOTO Shinichi  東京大学, 大学院・新領域創成科学研究科, 特任准教授 (00313099)
YAMADA Tomoyuki  東京大学, 大学院・新領域創成科学研究科, 助教 (50376604)
土井 晃一郎  東京大学, 大学院・情報理工系研究科, 科学技術振興特任教員 (10345126)
Project Period (FY) 2005 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥617,900,000 (Direct Cost: ¥617,900,000)
Fiscal Year 2009: ¥121,200,000 (Direct Cost: ¥121,200,000)
Fiscal Year 2008: ¥125,600,000 (Direct Cost: ¥125,600,000)
Fiscal Year 2007: ¥124,200,000 (Direct Cost: ¥124,200,000)
Fiscal Year 2006: ¥123,700,000 (Direct Cost: ¥123,700,000)
Fiscal Year 2005: ¥123,200,000 (Direct Cost: ¥123,200,000)
Keywordsゲノム / 発現制御 / バイオテクノロジー / 蛋白質 / 生体分子
Research Abstract

Using full-length cDNA library made by our Oligo-capping method as the technological base, we made large cDNA resource as well as transcriptome map of various organism with the collaboration with the Priority area of "Systems Genomics" and "Comparative Genomics". At the same time, we developed a method for genome wide identification of the transcriptional start sites and for measurement of it strength in semi-quantitative manner, by combining Oligo-capping method with second generation sequencers.

Report

(6 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • Research Products

    (54 results)

All 2010 2009 2008 2007 2006 2005 Other

All Journal Article (44 results) (of which Peer Reviewed: 34 results) Presentation (3 results) Remarks (7 results)

  • [Journal Article] DBTSS provides a tissue specific dynamic view of Transcription Start Sites2010

    • Author(s)
      Yamashita, ら
    • Journal Title

      Nucleic Acids Res 38

      Pages: 98-104

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 20092009

    • Author(s)
      Wakaguri H, Suzuki Y, Katayama T, Kawashima S, Kibukawa E, Hiranuka K, Sasaki M, Sugano S, Watanabe J.
    • Journal Title

      Nucleic Acids Res 37

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer2009

    • Author(s)
      Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K.
    • Journal Title

      PLoS ONE 4

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mapping human genetic diversity in Asia2009

    • Author(s)
      HUGO Pan-Asian SNP Consortium, ら
    • Journal Title

      Science 326

      Pages: 1541-1545

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs2009

    • Author(s)
      Wakaguri, ら
    • Journal Title

      BMC Genomic 10

      Pages: 312-312

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer2009

    • Author(s)
      Hashimotoら
    • Journal Title

      PLoS ONE 4

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transcriptome analysis and identification of regulators for long-term plasticity in Aplysia kurodai.2008

    • Author(s)
      Lee YS, Choi SL, Kim TH, Lee JA, Kim HK, Kim H, Jang DJ, Lee JJ, Lee S, Sin GS, Kim CB, Suzuki Y, Sugano S, Kubo T, Moroz LL, Kandel ER, Bhak J, Kaang BK
    • Journal Title

      Proc Natl Acad Sci USA 105

      Pages: 18602-18607

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.2008

    • Author(s)
      Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T, Imanishi T.
    • Journal Title

      Nucleic Acids Res 36

      Pages: 6386-6395

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.2008

    • Author(s)
      Osada N, Hashimoto K, Kameoka Y, Hirata M, Tanuma R, Uno Y, Inoue I, Hida M, Suzuki Y, Sugano S, Terao K, Kusuda J, Takahashi I.
    • Journal Title

      BMC Genomics 9

      Pages: 90-90

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The functional consequences of alternative promoter use in mammalian genomes.2008

    • Author(s)
      Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang TH.
    • Journal Title

      Trends Genet. 24

      Pages: 167-177

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics2008

    • Author(s)
      Yamashita R, Suzuki Y, Takeuchi N, Wakaguri H, Ueda T, Sugano S, Nakai K.
    • Journal Title

      Nucleic Acids Res.

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.2008

    • Author(s)
      Rensing SA, Sugano S, et al
    • Journal Title

      Science 319

      Pages: 64-69

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Physcomitrella genome reveals evolutionary insights into the conquest of land by plants2008

    • Author(s)
      Rensingら
    • Journal Title

      Science 319

      Pages: 64-69

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics2008

    • Author(s)
      Yamashitaら
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 3707-3715

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.2007

    • Author(s)
      Yamamoto YY, Ichida H, Abe T, Suzuki Y, Sugano S, Obokata J.
    • Journal Title

      Nucleic Acids Res. 35

      Pages: 6219-6226

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Distinct class of putative non-conserved promoters in humans: Comparative studies of alternative promoters of human and mouse genes.2007

    • Author(s)
      Tsuritani K, Irie T, Yamashita R, Sakakibara Y, Wakaguri H, Kanai A, Mizushima-Sugano J, Sugano S, Nakai K, Suzuki Y.
    • Journal Title

      Genome Res. 17

      Pages: 1005-1014

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The medaka draft genome and insights into vertebrate genome evolution.2007

    • Author(s)
      Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Sugano S, et al
    • Journal Title

      Nature 447

      Pages: 714-719

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome.2007

    • Author(s)
      Sakakibara Y, Irie T, Suzuki Y, Yamashita R, Wakaguri H, Kanai A, Chiba J, Takagi T, Mizushima-Sugano J, Hashimoto SI, Nakai K, Sugano S.
    • Journal Title

      DNA Res. 14

      Pages: 71-77

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational.2007

    • Author(s)
      Takeda JI, Suzuki Y, Nakao M, Kuroda T, Sugano S, Gojobori T, Imanishi T.
    • Journal Title

      Nucleic Acids Res. 35(1)

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.2007

    • Author(s)
      Watanabe J, Wakaguri H, Sasaki M, Suzuki Y, Sugano S.
    • Journal Title

      Nucleic Acids Res. 35

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The medaka draft genome and insights into vertebrate genome evolution.2007

    • Author(s)
      Kasahara, ら
    • Journal Title

      Nature 447

      Pages: 714-719

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Distinct class of putative "non-conserved" promoters in humans: Compazative studies of altemative promoters of human and mouse genes2007

    • Author(s)
      Tsuritani, ら
    • Journal Title

      Genome Res 17

      Pages: 1005-1014

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome2007

    • Author(s)
      Sakakibara
    • Journal Title

      DNA Res 14

      Pages: 71-77

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Deletion of angiotensin-converting enzyme 2 accelerates pressure overload-induced cardiac dysfunction by increasing local angiotensin II.2006

    • Author(s)
      Yamamoto K, Ohishi M, Katsuya T, Ito N, Ikushima M, Kaibe M, Tatara Y, Shiota A, Sugano S, Takeda S, Rakugi H, Ogihara T.
    • Journal Title

      Hypertension. 47

      Pages: 718-726

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Activation of genes for growth factor and cytokine pathways late in chondrogenic differentiation of ATDC5 cells.2006

    • Author(s)
      Osawa A, Kato M, Matsumoto E, Iwase K, Sugimoto T, Matsui T, Ishikura H, Sugano S, Kurosawa H, Takiguchi M, Seki N.
    • Journal Title

      Genomics. 88(1)

      Pages: 52-64

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii.2006

    • Author(s)
      Khan A, Bohme U, Kelly KA, Adlem E, Brooks K, Simmonds M, Mungall K, Quail MA, Arrowsmith C, Chillingworth T, Churcher C, Harris D, Collins M, Fosker N, Fraser A, Hance Z, Jagels K, Moule S, Murphy L, O'Neil S, Rajandream MA, Saunders D, Seeger K, Whitehead S, Mayr T, Xuan X, Watanabe J, Suzuki Y, Wakaguri H, Sugano S, Sugimoto C, Paulsen I, Mackey AJ, Roos DS, Hall N, Berriman M, Barrell B, Sibley LD, Ajioka JW.
    • Journal Title

      Genome Res. 16

      Pages: 1119-1125

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56, 419 completely sequenced and manually annotated full-length cDNAs.2006

    • Author(s)
      Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T.
    • Journal Title

      Nucleic Acids Res. 34

      Pages: 3917-3928

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Diverse DNA methylation statuses at alternative promoters of human genes in various tissues.2006

    • Author(s)
      Cheong J, Yamada Y, Yamashita R, Irie T, Kanai A, Wakaguri H, Nakai K, Ito T, Saito I, Sugano S, Suzuki Y.
    • Journal Title

      DNA Res. 13

      Pages: 155-167

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transcriptome analyses of human genes and applications for proteome analyses.2006

    • Author(s)
      Suzuki Y, Sugano S.
    • Journal Title

      Curr Protein Pept Sci. 7

      Pages: 147-163

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Restoration of transforming growth factor-beta type II receptor reduces tumorigenicity in the human adrenocortical carcinoma SW-13 cell line.2006

    • Author(s)
      Yamamoto N, Imai J, Watanabe M, Hiroi N, Sugano S, Yoshino G.
    • Journal Title

      Horm Metab Res. 38

      Pages: 159-166

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Diversification of transcriptional modulation: large-scale identification and characterization of purative alternative promoters of human genes2006

    • Author(s)
      Yamamoto N, Imai J, Watanabe M, Hiroi N, Sugano S, Yoshino G
    • Journal Title

      Genome Res. 16

      Pages: 55-65

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Diverse DNA methylation statuses at alternative promoters of human genes in various tissues.2006

    • Author(s)
      Cheong J, et al.
    • Journal Title

      DNA Res. 13

      Pages: 155-167

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.2006

    • Author(s)
      Takeda J
    • Journal Title

      Nucleic Acids Res. 34

      Pages: 3917-3928

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii2006

    • Author(s)
      Khan A
    • Journal Title

      Genome Res. 16

      Pages: 1119-1125

    • Related Report
      2006 Annual Research Report
  • [Journal Article] DBTSS : DataBase of Human Transcription Start Sites, progress report 2006.2006

    • Author(s)
      Yamashita R
    • Journal Title

      Nucleic Acids Res 34

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Transcriptome analyses of human genes and applications for proteome analyses.2006

    • Author(s)
      Suzuki Y, Sugano S
    • Journal Title

      Curr Protein Pept Sci. 7

      Pages: 147-163

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Signal Sequence and Keyword Trap in silico for Selection of Full-Length Human cDNAs Encoding Secretion or Membrane Proteins from Oligo-Capped cDNA Libraries.2005

    • Author(s)
      Kimura, K., Watanabe, A., Suzuki, Y., Ota, T., Nishikawa, T., Yamashita, R., Yamamoto, J., Sekine,M., Tsuritani, K., Ishii, S., Sugiyama, T., Saito, K., Isono, Y., Irie, R., Kushida, N., Yoneyama,T., Otsuka, R., Kanda, K., Yokoi, T., Kondo, H., Wagatsuma, M., Murakawa, K., Ishida, S., Ishibashi,T., Takahashi-Fujii, A., Tanase, T., Nagai, K., Kikuchi, H., Nakai, K., Isogai, T., Sugano, S.
    • Journal Title

      DNA Res. 12

      Pages: 117-126

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Substitution Rate and Structural Divergence of 5'UTR Evolution: Comparative Analysis Between Human and Cynomolgus Monkey cDNAs2005

    • Author(s)
      Osada N, Hirata M, Tanuma R, Kusuda J, Hida M, Suzuki Y, Sugano S, Gojobori T, Shen CK, Wu CI, Hashimoto K.
    • Journal Title

      Mol Biol Evol. 22

      Pages: 1976-1982

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity.2005

    • Author(s)
      Yamashita R, Suzuki Y, Sugano S, Nakai K.
    • Journal Title

      Gene 350

      Pages: 129-136

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] 5'SAGE : 5'-end Serial Analysis of Gene Expression database.2005

    • Author(s)
      Kasai Y, et al.
    • Journal Title

      Nucleic Acids Res. 33

    • Related Report
      2005 Annual Research Report
  • [Journal Article] The genome of the social amoeba Dictyostelium discoideum.2005

    • Author(s)
      Eichinger L., et al.
    • Journal Title

      Nature 435,

      Pages: 43-57

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Substitution Rate and Structural Divergence of 5'UTR Evolution : Comparative Analysis Between Human and Cynomolgus Monkey cDNAs.2005

    • Author(s)
      Osada N., et al.
    • Journal Title

      Mol Biol Evol. 22

      Pages: 1976-1982

    • Related Report
      2005 Annual Research Report
  • [Journal Article] dbQSNP : a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.2005

    • Author(s)
      Tahira T, et al.
    • Journal Title

      Hum Mutat. 226

      Pages: 69-77

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Cell surface labeling and mass spectrometry reveal diversity of cell-surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells.2005

    • Author(s)
      Nunomura K, et al.
    • Journal Title

      Mol Cell Proteomics. 4

      Pages: 1968-1976

    • Related Report
      2005 Annual Research Report
  • [Presentation] Genome Wide Mapping of Transcriptional Start Sites :Landscape of Gene Expression2009

    • Author(s)
      Sumio Sugano
    • Organizer
      The 2009 International Conference on Genomics
    • Place of Presentation
      ShenZhen, China
    • Year and Date
      2009-11-03
    • Related Report
      2009 Annual Research Report
  • [Presentation] Deep sequencing analysis of transcriptional start sites2008

    • Author(s)
      Yutaka Suzuki
    • Organizer
      Personal Genomics
    • Place of Presentation
      Cold Spring Harbor laboratory, New York, USA
    • Year and Date
      2008-10-11
    • Related Report
      2008 Annual Research Report
  • [Presentation] Identification and comparative studies of altemative promoters of human genes2007

    • Author(s)
      Yutaka Suzuki
    • Organizer
      THE BIOLOGY OF GENOMES
    • Place of Presentation
      Cold Spring Harbor labor atory, New York, USA
    • Year and Date
      2007-11-05
    • Related Report
      2007 Annual Research Report
  • [Remarks] データベース公開(DB名、URL、簡潔な内容紹介)

    • Related Report
      2009 Final Research Report
  • [Remarks] DB名:DBTSS

    • URL

      http://dbtss.hgc.jp/

    • Related Report
      2009 Final Research Report
  • [Remarks] 各種生物の転写開始点の情報をデータベースとしたもの。現在は、ヒトとマウスが多いが、今後他の生物を充実。なお、5'SAGEのHEK293とRamosの配列データに関しては、http://5sage.gi.k.u-tokyo.ac.jp/にて、生データを公開している。

    • Related Report
      2009 Final Research Report
  • [Remarks] DB名:PrimerStation URL:

    • URL

      http://ps.cb.k.u-tokyo.ac.jp/index.html

    • Related Report
      2009 Final Research Report
  • [Remarks] PrimerStationは全ヒトゲノムに対して非常に高い特異性を持つ最適なプライマセットを計算するウェブサービス。本設計方法では高い精度を出すためにプライマの溶液中での会合率を用いる。会合率で厳格に計算するのは非常に計算時間がかかるため、これまでこのような物理化学モデルで計算し全ヒトゲノムに対してチェックをするようなウェブサービスはなかった

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://dbtss.hgc.jp/

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://dbtss.hgc.jp/

    • Related Report
      2008 Annual Research Report

URL: 

Published: 2005-04-01   Modified: 2018-03-28  

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