Large-scale DNA sequencing for comparative systems biology

2009 Fiscal Year Final Research Report

• 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
• 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

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 Pages: DOI:10.1126/science.1191244
• [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] 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] 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] 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
• [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] 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
• [Remarks] NEXTDB
  • URL: http://nematode.lab.nig.ac.jp