Large-scale DNA sequencing for comparative systems biology

• Project/Area Number: 17020009
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: National Institute of Genetics
• Principal Investigator: KOHARA Yuji National Institute of Genetics, 所長 (70135292)
• Project Period (FY): 2005 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥751,600,000 (Direct Cost: ¥751,600,000); Fiscal Year 2009: ¥151,200,000 (Direct Cost: ¥151,200,000); Fiscal Year 2008: ¥150,100,000 (Direct Cost: ¥150,100,000); Fiscal Year 2007: ¥150,000,000 (Direct Cost: ¥150,000,000); Fiscal Year 2006: ¥150,100,000 (Direct Cost: ¥150,100,000); Fiscal Year 2005: ¥150,200,000 (Direct Cost: ¥150,200,000)
• Keywords: 胚発生 / 母性遺伝子 / mRNA局在化 / UTR(非翻訳領域) / トランスクリプトーム / in situハイブリダイゼーション / 転写調節領域 / 多光子共焦点顕微鏡 / 線虫C.elegans / 遺伝子発現 / mRNA局在 / RNAi / モチーフ探索 / EST解析 / 全ゲノムショットガン / whole mount in situハイブリダイゼーション / 計算機モデル / whole genome shotgun sequencing

Research Abstract

We performed cDNA analysis of the nematode C.elegans thouroughly. ESTs of about 150,000 full-length cDNA clones that had been made by the V-capping method were obtained to produce 4,909 new cDNA species. Altogether 11,309 cDNA species have been analysed for their expression patterns by the whole mount in situ hybridization. The mRNAs for the cDNA libraries were analysed by the next generation DNA sequencer to obtain the whole transriptome information. These data were integrated in NEXTDB, which were linked with the C.elegans central database WormBase. As to the studies for gene expression regulation network, we identified 1) the stage-specific cis-regulatory sequences and their trans-factors in the early intestine lineage, and 2) the regulatory sequence for the expression in the thermo-sensory neuron AFD and its ragulatory genes. As to the studies for mRNA localization mechanisms, we identified 1) cis-element in its 3`-UTR for pos-1 mRNA localization and its trans-factor, and 2) cis-element for mex-3 mRNA localization. We developed a semi-automatic system for the creation of cell shape models in C. elegans embryogenesis. We carried out whole genome sequencing of a nematode D. cronatus by the hybrid method using the Sanger method and the new generation sequencer.

Research Products

• [Journal Article] The Landscape of C. elegans 3'UTRs. (2010)
  • Author(s): Mangone, M., Manoharan, A.P., Thierry-Mieg, D., Thierry-Mieg, J., Han, T., Mackowiak, S., Mis, E., Zegar, C., Gutwein, M.R., Khivansara, V., Attie, O., Chen, K., Salehi-Ashtiani, K., Vidal, M., Harkins, T.T., Bouffard, P., Suzuki, Y., Sugano, S., Kohara, Y., Rajewsky, N., Piano, F., Gunsalus, K.C., Kim, J.K.
  • Journal Title: Science Published Online
• [Journal Article] Protein phosphatase 2A cooperates with the autophagy-related kinase UNC-51 to regulate axon guidance in Caenorhabditis elegans. (2010)
  • Author(s): Ogura, K., Okada, T., Mitani, S., Gengyo-, o, K., Baillie, D.L., Kohara, Y., Goshima, Y.
  • Journal Title: Development 137 Pages: 1657-1667
• [Journal Article] Protein phosphatase 2A cooperates with the autophagy-related kinase UNC-51 to regulate axon guidance in Caenorhabditis elegans (2010)
  • Author(s): Ken-ichi Ogura
  • Journal Title: Development 137 Pages: 1657-1667
  • Peer Reviewed
• [Journal Article] Latrophilin signalling links anterior-posterior tissue polarity and oriented cell divisions in the C (2009)
  • Author(s): Langenhan, T., Promel, S., Mestek, L., Esmaeili, B., Waller-Evans, H., Hennig, C., Kohara, Y., Avery, L., Vakonakis, I., Schnabel, R.,, Russ, A.P.
  • Journal Title: elegans embryo. Developmental Cell 17(4) Pages: 494-504
• [Journal Article] C. elegans mig-6 encodes papilin isoforms that affect distinct aspects of DTC migration, and interacts genetically with mig-17 and collagen IV. (2009)
  • Author(s): Kawano T, Zheng H, Merz DC, Kohara Y, Tamai KK, Nishiwaki K, Culotti JG.
  • Journal Title: Development. 136 Pages: 1433-1442
• [Journal Article] ELT-2 Is the Predominant Transcription Factor Controlling Differentiation and Function of the C. elegans Intestine, from Embryo to Adult. (2009)
  • Author(s): J.D. McGhee; T. Fukushige; M.W. Krause; S.E. Minnema; B. Goszczynski; J. Gaudet; Y. Kohara; O. Bossinger; Y. Zhao; J. Khattra; M. Hirst; S.J. Jones; M.A. Marra; P. Ruzanov; A. Warner; R. Zapf; D.G. Moerman; J.M. Kalb
  • Journal Title: Developmental Biology 327 Pages: 551-565
• [Journal Article] Latrophilin signalling links anterior-posterior tissue polarity and oriented cell divisions in the C.elegans embryo (2009)
  • Author(s): Tobias Langenhan
  • Journal Title: Developmental Cell 17(4) Pages: 494-504
  • Peer Reviewed
• [Journal Article] ELT-2 Is the Predominant Transcription Factor Controlling Differentiation and Function of the C. elegans Intestine, from Embryo to Adult (2009)
  • Author(s): James Douglas McGhee
  • Journal Title: Developmental Biology 327 Pages: 551-565
  • Peer Reviewed
• [Journal Article] C. elegans mig-6 encodes papilin isoforms that affect distinct aspects of DTC migration, and interacts genetically with mig-17 and collagen IV (2009)
  • Author(s): Kawano T
  • Journal Title: Development 136 Pages: 1433-1442
  • Peer Reviewed
• [Journal Article] Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE (2009)
  • Author(s): Xin Wang
  • Journal Title: BMC Genomics 10 Pages: 213-213
  • Peer Reviewed
• [Journal Article] The C. elegans CBFb homologue BRO-1 interacts with the Runx factor, RNT-1, to promote stem cell proliferation and self-renewal. (2007)
  • Author(s): H. Kagoshima, R. Nimmo, N. Saad, J. Tanaka, Y. Miwa, S. Mitani, Y. Kohara, A. Woollard
  • Journal Title: Development 134 Pages: 3905-3915
• [Journal Article] RUNX regulates stem cell proliferation and differentiation: Insights from studies of C. elegans. (2007)
  • Author(s): Kagoshima H, Shigesada K, Kohara Y
  • Journal Title: J Cell Biochem. 100(5) Pages: 1119-30
• [Journal Article] The ELT-2 GATA-Factor and the Global Regulation of Transcription in the C. elegans (2007)
  • Author(s): J.D. McGhee, M.C. Sleumer; M. Bilenky; K. Wong; S.J. McKay; B. Goszczynski; H. Tian; N.D. Krich; J. Khattra; R.A. Holt; D.L. Baillie; Y. Kohara; M.A. Marra; S.J.M. Jones; D.G. Moerman; A.G. Robertson
  • Journal Title: Intestine. Developmental Biology 302 Pages: 627-645
• [Journal Article] The C. elegans CBFb homologue BRO-1 interacts with the Runx factor, RNT-1, to promote stem cell proliferation and self-renewal. (2007)
  • Author(s): Hiroshi Kagoshima
  • Journal Title: Development 134 Pages: 3905-3915
  • Peer Reviewed
• [Journal Article] RUNX regulates stem cell proliferation and differentiation: Insights from studies of C. elegans. (2007)
  • Author(s): Kagoshima H
  • Journal Title: Journal of Cell Biochemistry Apr 1;100(5) Pages: 1119-30
  • Peer Reviewed
• [Journal Article] The ELT-2 GATA-Factor and the Global Regulation of Transcription in the C. elegans Intestine. (2007)
  • Author(s): James Douglas McGhee
  • Journal Title: Developmental Biology 302 Pages: 627-645
• [Journal Article] RUNX regulates stem cell proliferation and differentiation : Insights from studies of C. elegans. (2007)
  • Author(s): Kagoshima H
  • Journal Title: J Cell Biochem. Apr1;10(5) Pages: 1119-1130
• [Journal Article] nfi-1 affects behavior and life-span in C. elegans but is not essential for DNA replication or survival. (2005)
  • Author(s): E. Lazakovitch, J. M Kalb, R. Matsumoto, K. Hirono, Y. Kohara, R.M. Gronostajski
  • Journal Title: BMC Developmental Biology 5 Pages: 24-24
• [Journal Article] The C. elegans RUNX transcription factor MAB-2/RNT-1 is required for asymmetrical cell division of the T blast cell. (2005)
  • Author(s): H. Kagoshima, H. Sawa, S. Mitani, T.R. Burglin, K. Shigesada, Y. Kohara
  • Journal Title: Developmental Biol 287 Pages: 262-273
• [Journal Article] The C.elegans RUNX transcription factor MAB-2/RNT-1 is required for asymmetrical cell division of the T blast cell. (2005)
  • Author(s): Hiroshi KAGOSHIMA
  • Journal Title: Developmental Biology 287 Pages: 262-273
• [Journal Article] nfi-1 affects behavior and life-span in C.elegans but is not essential for DNA replication or survival. (2005)
  • Author(s): Elena Lazakovitch
  • Journal Title: BMC Developmental Biology 5 Pages: 24-24
• [Journal Article] Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE.
  • Author(s): X. Wang, Y. Zhao, K. Wong, P. Ehlers, Y. Kohara, S.J. Jones, M.A. Mara, R.A. Holt, D.G. Moerman, D. Hansen
  • Journal Title: BMC Genomics 2009 10 Pages: 213-213
• [Presentation] Systematic analyses of AFD-specific enhancers in C.elegans (2009)
  • Author(s): Hiroshi Kagoshima
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-12
• [Presentation] Computational and experimental studies on cis-regulatory modules in C.elegans embryogenesis (2009)
  • Author(s): Akihiro Mori
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-12
• [Presentation] Semi-automatic system for the creation of cell shape models in C.elegans embryogenesis (2009)
  • Author(s): Hideaki Hiraki
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-11
• [Presentation] Studies on localization mechanisms of the maternal pos-1 mRNA in C.elegans embryos (2009)
  • Author(s): Koki Noguchi
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-11
• [Presentation] 線虫 Caenorhabditis elegans ミトコンドリア電子伝達系複合体IIフラビンタンパク質(Fp)サブユニットの変異による精子機能不全 (2009)
  • Author(s): 網野比佐子
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-11
• [Presentation] Study on localization mechanisms of maternal mex-3 mRNA in C.elegans (2009)
  • Author(s): Hiroyuki Konno
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-10
• [Presentation] Beta-catenin HMP-2 is involved in Src pathway in endoderm induction (2009)
  • Author(s): Eisuke Sumiyoshi
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2009-12-10
• [Presentation] Study on localization mechanisms of maternal mex-3 mRNA in C.elegans (2009)
  • Author(s): Hiroyuki Konno
  • Organizer: 17th International C.elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2009-06-27
• [Presentation] Comparative genomic analysis of the nematodes in Antarctica (2009)
  • Author(s): Hiroshi Kagoshima
  • Organizer: 17th International C.elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2009-06-27
• [Presentation] Combination of cis-regulatory modules for temporal regulation of gene expression in C.elegans : Towards promoter design (2009)
  • Author(s): Akihiro Mori
  • Organizer: 17th International C.elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2009-06-26
• [Presentation] Systematic analyses of AFD-specific enhancers in C.elegans (2009)
  • Author(s): Hiroshi Kagoshima
  • Organizer: 17th International C.elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2009-06-25
• [Presentation] Genome and transcriptome analysis by the next-generation sequencer (2009)
  • Author(s): Tadasu Shin-i
  • Organizer: 17th International C.elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2009-06-25
• [Presentation] Semi-automatic system for the creation of cell shape models in C.elegans embryogenesis (2009)
  • Author(s): Hideaki Hiraki
  • Organizer: 17th International C.elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2009-06-25
• [Presentation] WHOLE TRANSCRIPTOME ANALYSIS OF THE NEMATODEC. ELEGANS (2008)
  • Author(s): Tadasu Shin-i
  • Organizer: Cold Spring Harbor Meeting "The Biology of Genomes"
  • Place of Presentation: Cold Spring Harbor, NY, USA
• [Presentation] 線虫初期胚での腸系譜の時期特異的なシス・エレメントの予測と同定 (2008)
  • Author(s): 森明弘
  • Organizer: 第31回日本分子生物学会年会・第81回日本生化学会大会合同大会
  • Place of Presentation: 神戸
• [Presentation] SRC-1に依存したbeta-カテニンHMP-2のカドヘリンHMR-1からの解離がTcfホモログPOP-1の核局在を阻害する事で内胚葉誘導に寄与する。 (2008)
  • Author(s): 住吉英輔
  • Organizer: 第31回日本分子生物学会年会・第81回日本生化学会大会合同大会
  • Place of Presentation: 神戸
• [Presentation] 線虫C.elegansの温度感受神経AFDでの発現を制御する調節配列の系統的解析 (2008)
  • Author(s): 鹿児島浩
  • Organizer: 第31回日本分子生物学会年会・第81回日本生化学会大会合同大会
  • Place of Presentation: 神戸
• [Presentation] Studies on localization mechanisms of the maternal pos-1 mRNA in Caenorhabditis elegans embryos. (2007)
  • Author(s): 野口 浩毅
  • Organizer: 第30回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜・ヨコハマグランドインターコンチネンタルホテル
  • Year and Date: 2007-12-13
• [Presentation] Beta-catenin HMP-2 is involved in Src pathway in gut induction (2007)
  • Author(s): 住吉 英輔
  • Organizer: 第30回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜・ヨコハマグランドインターコンチネンタルホテル
  • Year and Date: 2007-12-11
• [Presentation] Studies on localization mechanisms of pos-1 mRNA in C. elegans embryos. (2007)
  • Author(s): Kouki Noguchi
  • Organizer: 16th International C. elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2007-06-30
• [Presentation] Beta-catenin HMP-2 is involved in src pathway in endoderm induction (2007)
  • Author(s): Eisuke Sumiyoshi
  • Organizer: 16th International C. elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2007-06-29
• [Presentation] Semi-automatic sysem for the creation of cell shape models in C. elegans embryogenesis (2007)
  • Author(s): Hideaki Hiraki
  • Organizer: 16th International C. elegans Meeting
  • Place of Presentation: UCLA, USA
  • Year and Date: 2007-06-29
• [Remarks] NEXTDB
  • URL: http://nematode.lab.nig.ac.jp