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

• Project/Area Number: 17020002
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The 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: ¥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.

Research Products

• [Journal Article] DBTSS provides a tissue specific dynamic view of Transcription Start Sites (2010)
  • Author(s): Yamashita, ら
  • Journal Title: Nucleic Acids Res 38 Pages: 98-104
  • Peer Reviewed
• [Journal Article] Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009 (2009)
  • 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
  • Peer Reviewed
• [Journal Article] High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer (2009)
  • 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
  • Peer Reviewed
• [Journal Article] Mapping human genetic diversity in Asia (2009)
  • Author(s): HUGO Pan-Asian SNP Consortium, ら
  • Journal Title: Science 326 Pages: 1541-1545
  • Peer Reviewed
• [Journal Article] Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs (2009)
  • Author(s): Wakaguri, ら
  • Journal Title: BMC Genomic 10 Pages: 312-312
  • Peer Reviewed
• [Journal Article] High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer (2009)
  • Author(s): Hashimotoら
  • Journal Title: PLoS ONE 4
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics (2008)
  • Author(s): Yamashita R, Suzuki Y, Takeuchi N, Wakaguri H, Ueda T, Sugano S, Nakai K.
  • Journal Title: Nucleic Acids Res.
  • 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
  • Peer Reviewed
• [Journal Article] Physcomitrella genome reveals evolutionary insights into the conquest of land by plants (2008)
  • Author(s): Rensingら
  • Journal Title: Science 319 Pages: 64-69
  • Peer Reviewed
• [Journal Article] Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics (2008)
  • Author(s): Yamashitaら
  • Journal Title: Nucleic Acids Res. 36 Pages: 3707-3715
  • 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
  • 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
  • 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
  • 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
  • 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)
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Distinct class of putative "non-conserved" promoters in humans: Compazative studies of altemative promoters of human and mouse genes (2007)
  • Author(s): Tsuritani, ら
  • Journal Title: Genome Res 17 Pages: 1005-1014
  • Peer Reviewed
• [Journal Article] Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome (2007)
  • Author(s): Sakakibara
  • Journal Title: DNA Res 14 Pages: 71-77
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Diversification of transcriptional modulation: large-scale identification and characterization of purative alternative promoters of human genes (2006)
  • Author(s): Yamamoto N, Imai J, Watanabe M, Hiroi N, Sugano S, Yoshino G
  • Journal Title: Genome Res. 16 Pages: 55-65
  • 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
• [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
• [Journal Article] Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii (2006)
  • Author(s): Khan A
  • Journal Title: Genome Res. 16 Pages: 1119-1125
• [Journal Article] DBTSS : DataBase of Human Transcription Start Sites, progress report 2006. (2006)
  • Author(s): Yamashita R
  • Journal Title: Nucleic Acids Res 34
• [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
• [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
  • Peer Reviewed
• [Journal Article] Substitution Rate and Structural Divergence of 5'UTR Evolution: Comparative Analysis Between Human and Cynomolgus Monkey cDNAs (2005)
  • 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
  • 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
  • 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
• [Journal Article] The genome of the social amoeba Dictyostelium discoideum. (2005)
  • Author(s): Eichinger L., et al.
  • Journal Title: Nature 435, Pages: 43-57
• [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
• [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
• [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
• [Presentation] Genome Wide Mapping of Transcriptional Start Sites :Landscape of Gene Expression (2009)
  • Author(s): Sumio Sugano
  • Organizer: The 2009 International Conference on Genomics
  • Place of Presentation: ShenZhen, China
  • Year and Date: 2009-11-03
• [Presentation] Deep sequencing analysis of transcriptional start sites (2008)
  • Author(s): Yutaka Suzuki
  • Organizer: Personal Genomics
  • Place of Presentation: Cold Spring Harbor laboratory, New York, USA
  • Year and Date: 2008-10-11
• [Presentation] Identification and comparative studies of altemative promoters of human genes (2007)
  • 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
• [Remarks] データベース公開(DB名、URL、簡潔な内容紹介)
• [Remarks] DB名:DBTSS
  • URL: http://dbtss.hgc.jp/
• [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。
• [Remarks] DB名:PrimerStation URL:
  • URL: http://ps.cb.k.u-tokyo.ac.jp/index.html
• [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
• [Remarks]
  • URL: http://dbtss.hgc.jp/
• [Remarks]
  • URL: http://dbtss.hgc.jp/