Functional analysis of the C. elegansgenome by a systematic gene knock-down

• Project/Area Number: 15011261
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: RIKEN
• Principal Investigator: SUGIMOTO Asako RIKEN, Laboratory for Developmental Genomics, Team Leader, 発生ゲノミクス研究チーム, チームリーダー (80281715)
• Co-Investigator(Kenkyū-buntansha): MITANI Shohei Tokyo Women's Medical University, School of Medicine, Associate Professor, 医学部, 助教授 (90192757)
• Project Period (FY): 2003 – 2004
• Project Status: Completed (Fiscal Year 2004)
• Budget Amount: ¥24,000,000 (Direct Cost: ¥24,000,000); Fiscal Year 2004: ¥12,000,000 (Direct Cost: ¥12,000,000); Fiscal Year 2003: ¥12,000,000 (Direct Cost: ¥12,000,000)
• Keywords: nematode / C. elegans / RNAi / deletion mutant / functional genomics / C. elegans

Research Abstract

In this study, we aimed to understand the framework of genetic cascades and networks that regulate the development and behavior of multicellular organisms, using the nematode C. elegans as a model system. To this end, we performed systematic analyses of loss-of-function phenotypes caused by either RNAi or deletion mutations.
1. A general phenotype analysis was performed for〜6000 genes by an RNAi-by-soaking method, and 30% of them were shown to be essential for developmental processes. We further performed embryonic phenotype profiling of the 833 embryonic lethal genes identified in this screen. A cluster analysis of the phenotypic profiles successfully grouped the gene sets that were known to function in the same developmental/biological processes. Thus, this method will be useful to predict gene functions of uncharacterized genes. We compiled these data and established "A C. elegans RNAi phenome database" accessible via Web. We also performed the post-embryonic functions of the embryonic lethal genes by a developmental stage-specific RNAi method.
2. Systematic screening for deletion mutants of transcription factors in C. elegans was conducted. We have isolated mutants corresponding to 437 genes, which are more than two thirds of whole transcription factors. We are also isolating many other mutants and simultaneously use them to reveal gene function. Among the mutants, we found that ags-3 mutants show abnormal chemosensory perception, body size and moving activity. We found that ags-3 phenotypes are suppressed by an egl-4 (PKG) mutant. AGS-3 is known to play an important role in cocaine addiction. We found that AGS-3 and PKG from both nematode and mouse interact with each other.

Research Products

• [Journal Article] Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. (2006)
  • Author(s): Duchaine T, Wohlshlegel JA, Kennedy S, Bei Y, Conte D, Pang K, Brownell DR, Harding S, Mitani S, Ruvkun G, Yates IIIJr, Mello C
  • Journal Title: Cell 124 Pages: 343-354
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. (2006)
  • Author(s): Duchaine TF, Wohlshlegel JA, Kennedy S, Bei Y, Conte D, Pang K, Brownell DR, Harding S, Mitani S, Ruvkun G, Yates III JR, Mello CC
  • Journal Title: Cell 124 Pages: 343-354
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Caenorhabditis elegans DAZ-1 is expressed in proliferating germ cells and directs proper nuclear organization and cytoplasmic core formation during oogenesis. (2005)
  • Author(s): Maruyama, R., Endo, S., Sugimoto, A., Yamamoto, M.
  • Journal Title: Dev Biol 277 Pages: 142-154
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] C.elegans ced-13 can promote apoptosis and is induced in response to DNA damage. (2005)
  • Author(s): Schumacher, B., Schertel, C., Wittenburg, N., Mitani, S.
  • Journal Title: Cell Death Differ 12 Pages: 153-161
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Caenorhabditis elegans geminin homologue participates in cell cycle regulation and germ line development. (2005)
  • Author(s): Yanagi, K., Mizuno, T., Tsuyama, T., Tada, S., Iida, Y., Sugimoto, A., Eki, T., Enomoto, T., Hanaoka, F.
  • Journal Title: J Biol Chem 280 Pages: 19689-19694
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The C.elegans eyes absent ortholog EYA-1 is required for tissue differentiation and plays partially redundant roles with PAX-6. (2005)
  • Author(s): Furuya, M., Qadota, H., Chisholm, A.D., Sugimoto, A.
  • Journal Title: Dev Biol 286 Pages: 452-463
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Control of body size by SMA-5, a homolog of MAP kinase BMK1/ERK5 in C.elegans. (2005)
  • Author(s): Watanabe N, Nagamatsu Y, Gengyo-Ando K, Mitani S, Ohshima Y
  • Journal Title: Development 132 Pages: 3175-3184
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A Runx family transcription factor RNT-1/MAB-2 is required for asymmetric cell division in Caenorhabditis elegans. (2005)
  • Author(s): Kagoshima H, Sawa H, Mitani S, Burglin TR, Shigesada K, Kohara Y
  • Journal Title: Dev Biol 287 Pages: 262-273
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] C. elegans ced-13 can promote apoptosis and is induced in response to DNA damage. (2005)
  • Author(s): Schumacher, B., Schertel, C., Wittenburg, N., Mitani, S.
  • Journal Title: Cell Death Differ 12 Pages: 153-161
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The C. elegans eyes absent ortholog EYA-1 is required for tissue differentiation and plays partially redundant roles with PAX-6. (2005)
  • Author(s): Furuya, M., Qadota, H., Chisholm, A.D., Sugimoto, A.
  • Journal Title: Dev Biol 286 Pages: 452-463
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Control of body size by SMA-5, a homolog of MAP kinase BMK1/ERK5 in C. elegans. (2005)
  • Author(s): Watanabe N, Nagamatsu Y, Gengyo-Ando K, Mitani S, Ohshima Y
  • Journal Title: Development 132 Pages: 3175-3184
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A Runx family transcription factor RNT-1/MAB-2 is required for asymmetric cell division in Caenorhabditis elegans. (2005)
  • Author(s): Kagoshima H, Sawa H, Mitani S, B_rglin TR, Shigesada K, Kohara Y
  • Journal Title: Dev. Bio1. 287 Pages: 262-273
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] High-throughput RNAi in Caenorhabditis elegans : genome-wide screens and functional genomics. (2004)
  • Author(s): Sugimoto, A.
  • Journal Title: Differentiation 72 Pages: 81-91
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Type II platelet-activating factor-acetylhydrolase is essential for epithelial morphogenesis in Caenorhabditis elegans. (2004)
  • Author(s): Inoue, T., Sugimoto, A., Suzuki, Y., Yamamoto, M.
  • Journal Title: Proc Natl Acad Sci U S A 101 Pages: 13233-13238
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The Caenorhabditis elegans eukaryotic initiation factor 5A homologue, IFF-1 is required for germ cell proliferation, gametogenesis and localization of the P-granule component PGL-l. (2004)
  • Author(s): Hanazawa, M., Kawasaki, I., Kunitomo, H., Mitani, S.
  • Journal Title: Mech Dev 121 Pages: 213-224
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Nematode chondroitin polymerizing factor showing cell-/organ-specific expression is indispensable for chondroitin synthesis and embryonic cell division. (2004)
  • Author(s): Izumikawa, T., Kitagawa, H., Mizuguchi, S., Mitani, S.
  • Journal Title: J Biol Chem 279 Pages: 53755-53761
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Type II platelet-activating factor-acetylhydrolase isessential for epithelial morphogenesis in Caenorhabditis elegans. (2004)
  • Author(s): Inoue, T., Sugimoto, A., Suzuki, Y., Yamamoto, M.
  • Journal Title: Proc Natl Acad Sci U S A 101 Pages: 13233-13238
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] The Caenorhabditis elegans eukaryotic initiation factor 5A homologue, IFF-1 is required for germ cell proliferation, gametogenesis and localization of the P-granule component PGL-1. (2004)
  • Author(s): Hanazawa, M., Kawasaki, I., Kunitomo, H., Mitani, S.
  • Journal Title: Mech Dev 121 Pages: 213-224
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Type II platelet-activating factor-acetylhydrolase is essential for epithelial morhogenesis in Caenorhabditis elegans. (2004)
  • Author(s): Inoue, T., Sugimoto, A., Suzuki, Y., Yamamoto, M.
  • Journal Title: Proc Natl Acad Sci U S A 101 Pages: 13233-13238
• [Journal Article] Distinct developmental function of two Caenorhabditis elegans homologs of the cohesin subunit Sccl/Rad2l. (2003)
  • Author(s): Mito, Y., Sugimoto, A., Yamamoto, M.
  • Journal Title: Mol Biol Cell 14 Pages: 2399-2409
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Essential role of the C.elegans Arp2/3 complex in cell migration during ventral enclosure. (2003)
  • Author(s): Saws, M., Suetsugu, S., Sugimoto, A., Miki, H., Yamamoto, M., Takenawa, T.
  • Journal Title: J Cell Sci 116 Pages: 1505-1518
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Involvement of chondroitin proteoglycans in cytokinesis of embryonic cells of the nematode Caenorhabditis elegans. (2003)
  • Author(s): Mizuguchi, S., Uyama, T., Kitagawa, H., Nomura, K.H., Dejima, K., Gengyo-Ando, K., Mitani, S., Sugahara, K., Nomura, K.
  • Journal Title: Nature 423 Pages: 443-448
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Translational control of maternal glp-1 mRNA by POS-1 and its interacting protein SPN-4 in Caenorhabditis elegans. (2003)
  • Author(s): Ogura, K., Kishimoto, N., Mitani, S., Gengyo-Ando, K., Kohara, Y.
  • Journal Title: Development 130 Pages: 2495-2503
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Cell Corpse Engulfment Mediated by C.elegans Phosphatidylserine Receptor Through CED-5 and CED-12. (2003)
  • Author(s): Wang, X., Wu, Y -C., Fadok, VA., Lee, M-C., Gengyo-Ando, K., Cheng, L-C., Ledwich, D., Hsu, P-K., Chen, J-Y., Chou, B-K., Henson, P., Mitani.S., Xue, D.
  • Journal Title: Science 302 Pages: 1563-1566
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Distinct developmental function of two Caenorhabditis elegans homologs of the cohesin subunit Sccl/Rad21. (2003)
  • Author(s): Mito, Y., Sugimoto, A., Yamamoto, M.
  • Journal Title: Mol Biol Cell 14 Pages: 2399-2409
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Essential role of the C. elegans Arp2/3 complex in cell migration during ventral enclosure. (2003)
  • Author(s): Sawa, M., Suetsugu, S., Sugimoto, A., Miki, H., Yamamoto, M., Takenawa, T.
  • Journal Title: J Cell Sci 116 Pages: 1505-1518
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Cell Corpse Engulfment Mediated by C. elegans Phosphatidylserine Receptor Through CED-5 and CED-12. (2003)
  • Author(s): Wang, X., Wu, Y-C., Fadok, VA., Lee, M-C., Gengyo-Ando, K., Cheng, L-C., Ledwich, D., Hsu, P-K., Chen, J-Y., Chou, B-K., Henson, P., Mitani, S., Xue, D.
  • Journal Title: Science 302 Pages: 1563-1566
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] WormMethod, Reverse genetics : RNAi by soaking. In "WormBook" (2006)
  • Author(s): Sugimoto, A.
  • Publisher: The C.elegans Research Community(印刷中)
  • Description: 「研究成果報告書概要(和文)」より
• [Book] High-throughput RNAi-by-soaking in Caenorhabditis elegans. In RNA interference technology : From basic science to drug development (2005)
  • Author(s): Sugimoto, A.
  • Total Pages: 497
  • Publisher: Cambridge University Press (Ed. Appasani, K)
  • Description: 「研究成果報告書概要(和文)」より
• [Book] High-throughput RNAi-by-soaking in Caenorhabditis elegans. In "RNA interference technology : From basic science to drug development" (Ed. Appasani, K) (2005)
  • Author(s): Sugimoto, A.
  • Total Pages: 497
  • Publisher: Cambridge University Press
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] WormMethod, Reverse genetics : RNAi by soaking. In "WormBook" (2005)
  • Author(s): Sugimoto, A.
  • Publisher: The C. elegans Research Community (In press)
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] High-throughput RNAi-by-soaking in Caenorhabditis elegans. In RNA interference technology : From basic science to drug development (Ed. Appasani, K) (2005)
  • Author(s): Sugimoto, A.
  • Total Pages: 497
  • Publisher: Cambridge University Press
• [Publications] Mito, Y., Sugimoto, A., Yamamoto, M.: "Distinct developmental function of two Caenorhabditis elegans homologs of the cohesin subunit Scc1/Rad2l."Mol Biol Cell. 14. 2399-2409 (2003)
• [Publications] Sawa, M., Suetsugu, S., Sugimoto, A, Miki, H., Yamamoto, M., Takenawa, T.: "Essential role of the C.elegans Arp2/3 complex in cell migration during ventral enclosure."J Cell Sci. 116. 1505-1518 (2003)
• [Publications] Sugimoto, A.: "High-throughput RNAi in Caenorhabditis elegans : genome-wide screens and functional genomics"Differentiation. 印刷中. (2004)
• [Publications] Mizuguchi S., Uyama T., Kitagawa H., Nomura K.H., Dejima K., Gengyo-Ando K., Mitani S., Sugahara K., Nomura K.: "Involvement of chondroitin proteoglycans in cytokinesis of embryonic cells of the nematode Caenorhabditis elegans."Nature. 423. 443-448 (2003)
• [Publications] Ogura K., Kishimoto N., Mitani S., Gengyo-Ando K., Kohara Y.: "Translational control of maternal glp-1 mRNA by POS-1 and its interacting protein SPN-4 in Caenorhabditis elegans."Development. 130. 2495-2503 (2003)
• [Publications] Wang X., Wu Y-C., Fadok VA., Lee M-C., Gengyo-Ando K., Cheng L-C., Ledwich D., Hsu P-K., Chen J-Y., Chou B-K., Henson P., Mitani S., Xue D.: "Cell Corpse Engulfment Mediated by C.elegans Phosphatidylserine Receptor Through CED-5 and CED-12."Science. 302. 1563-1566 (2003)
• [Publications] Sugimoto, A: "'High-throughput RNAi-by-soaking in Caenorhabditis elegans' in "RNA interference technology : From basic science to drug development"(Ed.Appasani, K)"Cambridge University Press(印刷中). (2004)