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10 Years at GSC (Genomic Sciences Center)

From sequencing to the elucidation of life phenomena, to the full picture of life strategies

We have succeeded in deepening the understanding of various life processes by viewing an organism from a molecular biology viewpoint as a "dynamic molecular device". However, the rapid development of genomic science in the 1990s changed the style of biological investigation, and generated a new trend of research. In other words, a paradigm shift has occurred away from the inductive approach, which tries to conjecture the whole system based on the understanding of individual life processes, toward the deductive approach, which understands individual phenomenon by observing the whole configuration that provides the basic design of life, such as a genome. GSC was established in 1998 as the implementing center for this type of genome science research. Since then, we have made numerous accomplishments, known internationally, that have become milestones in life science research, such as complete sequencing of the human genome, completing the mouse gene encyclopedia project, discovering the RNA continent, and completing the Protein 3000 Project. We have also conducted systematic development of the mutant resources of experimental organisms such as the mouse (Mus musculus) and Arabidopsis thaliana. Moreover, we have continued the challenge of working toward establishing a technology base for computational biology, which is important for understanding life as a system.

Click on each year to display its details.

  1. 1998
    GSC was started
  2. 1999
    Partial base sequence data of 20,000 mouse gene were made publically available
    Mechanisms of a base-specific protein binding to a single-stranded RNA unveiled
    Mouse gene data (180,000 pieces) were disclosed in collaboration with the National Institute of Genetics

    High-speed large-capacity sequencer "RISA"
    Completion of the large-capacity DNA sequencer, the RIKEN Integrated Sequence Analyzer (RISA) Construction of the high-speed large capacity sequencer RISA was completed. This analyzer has a processing capacity four times that of a conventional high-speed large-capacity sequencer, making it possible to analyze approximately 600,000 base pairs of DNA in 8 hours.
  3. 2000

    The article detailing the complete sequencing of human chromosome 21 was published in Nature journal
    Complete sequencing of human chromosome 21 sets a precedent for the world The international team, mainly consisting of GSC, completed the sequencing of human chromosome 21 as part of the International Genome Project. GSC was responsible for 50% of approximately 34,000,000 bases.
    In addition to the discovery of 98 new genes, characteristic repeat configurations in the adjacent centromere and telomeres were elucidated for the very first time.
    The International Human Genome Sequence Consortium, including GSC, declared the completion of the draft sequencing of the human genome
    The human genome draft sequence integrated database was jointly created and made publicly available in public by GSC and the Human Genome Center, Institute of Medical Science, University of Tokyo
    All genomes of the symbiotic microbe "Buchnera" were sequenced as a world-first
  4. 2001

    An article with functional annotations of mouse full-length cDNA was published by Nature journal
    Disclosure of mouse cDNA annotation information

    Press release of the human genome draft sequence
    Publication of an article about the human genome draft sequence analysis Publication of an article on the human genome draft sequence analysis by the "International Human Genome Sequence Determination Consortium", comprised of the 6 countries of Japan, the United States, the UK, France, China, and Germany, and 20 research centers. GSC acquired and analyzed about 203 Mb of the sequence data.
    Elucidation of the part of the Mechanism about the Internalization of Extracellular Molecules into Cells
    Started the development of a large-scale high-throughput discovery system for the N-ethyl-N-nitrosourea (ENU) induced mutation
    Established the International Structural Genomics Organization (ISGO)
  5. 2002

    Total imaging of the chimpanzee genome fragment,
    arranged on the human chromosome
    Publication of the world's first human/chimpanzee genome comparison map Terminal sequences of approximately 64,000 kinds of DNA fragment of the chimpanzee genome were determined and the world's first genome map comparing the human and chimpanzee was accomplished. Results of the analysis clearly showed that the difference in genomes was only 1.23% (approximately 37,000,000 bases).

    A. thaliana
    Identified approximately 14,600 kinds of A. thaliana full-length cDNA Developed the "RIKEN Arabidopsis Genome Encyclopedia", we analyzed approximately 14,600 A. thaliana full-length cDNAs, leading the way for this kind of analysis, and attached functional explanatory notes. Confirmed approximately 2,400 new genes and clarified control region information for 14,000 genes.
    Started the National Project on Protein Structural and Functional Analysis (Protein 3000) and the National BioResource Project
    National BioResource Project

    We have been collecting, maintaining, and offering the biological resources of 24 species under the "TNational BioResource Project"T, a five-year national project that started in 2002. Toshihiko Shiroishi, Project Director of the Functional Genomics Research Group which is the core agency for "Tmouse mutagenesis"T, was in charge of developing the mouse mutant strains. We have developed various mutants that can be used as models of human disease including adult diseases, and are making them available to the global research community. These mutants were developed by our unique methodology, the systematic phenotype screening of mouse mutants induced by chemical mutagen, ENU.

    DNA repair revealed by the crystal structure of the human recombination protein Rad52
    Revealed novel mechanism of signal transduction from extracellular signal
    Constructed a new system for comprehensive study of protein structure prediction
    Published the world's largest scale gene information demonstrating that the large amount of non-protein code region is transcribed, a finding that may dramatically advance the functional analysis of genes
  6. 2003
    Developed MDGRAPE-2A

    Dr. Sakaki, Director of GSC, presents 24 CD-ROMs containing the complete sequence data of the human genome to Prime Minister Koizumi.
    Declaration of the completion of sequencing the human genome
    Declaration of the completion of sequencing of the human genome

    In April 2003, the International Human Genome Sequencing Consortium (IHGSC), comprising 6 countries (Japan, the US, the UK, France, Germany, and China) with 18 research centers including GSC, jointly declared with the leaders of the 6 countries, the successful completion of the sequencing of the human genome with more than 99.99% accuracy. Sequencing was started in 1991, and continued after the completion of the sequencing of chromosome 22 (December 1999) and chromosome 21 (May 2000); and thereafter, in February 2001, the IHGSC and Celera Genomics Co., Ltd., respectively, published the draft sequence (accuracy: 99.9% or more; non-sequenced sequence: 10% or more) of each chromosome. The characteristics of the human genome, one of which the total number of human genes for coding protein was relatively small at approximately 22,000 were discovered.


    Trial Version of the DNA Book
    Announcement regarding the trial version of the DNA Book "The DNA Book", printed cDNA by the original technology, was completed. Approximately 60,000 cDNA clones can be easily distributed as books and used by researchers worldwide.Press Release
    Analysis of rice full-length cDNAPress Release
    Ultra-high sensitivity NMR data measurement of protein was realized by the world's highest magnetic field (920 MHz) NMR systemPress Release
    Elucidated the repair mechanism for abnormality in the replication of genetic informationPress Release
    Released a mutant database of A. thalianaPress Release
    Created a plant gene expression map of the world's highest-densityPress Release
  7. 2004
    Commenced a homology search service for grid technologyPress Release

    National simultaneous use of OBIYagns
    Succeeded in developing the next-generation cell simulator on the grid Developed the next-generation cell simulator "OBIYagns" (Yet Another Gene Network Simulator) that uses grid technology. In addition to reducing computing time, simultaneous use of multiple users became possible through the internetPress Release
    Started the Genome Network Project
    Structure of the human DNA recombinase revealed a double ringPress Release
    Succeeded in sequencing chimpanzee chromosome 22Press Release
    Elucidated the molecular structure of important proteins in the gene translation systemPress Release
    Succeeded in understanding the activity of the essential protein "cohesin" (chromosome adhesion factor) in cell divisionPress Release
    Released an analysis system for disease/phenotype mappingPress Release
    Succeeded in developing the fastest high-speed LSI in the worldPress Release
    Molecular mechanisms of the tumor necrosis factor signaling revealed by NMRPress Release
    Discovered a chemical compound, a candidate for an anti-SARS corona virus drugPress Release
    The International Human Genome Sequence Consortium, which includes GSC, published the results of the high-precision analysis of the human genomePress Release
    Published "a DNA book" of the A. thaliana transcription factorPress Release
  8. 2005
    Established the RTK Consortium
    The atomic structure determination of the enzyme that can produce a new protein including a heavy atomPress Release
    Development of the unnatural-amino-acid based method to search for unidentified proteinsPress Release
    Released a search system for the DNA Book databasePress Release
    Estimated unknown gene structures using gene expression information (tiling array)Press Release
    Published an article detailing the discovery of a "new RNA continent" following large-scale Transcriptome analysis
    The New RNA Continent

    Through the comprehensive collection of mouse full-length cDNAs, Yoshihide Hayashizaki, Project Director of the Genome Exploration Research Group, studied the role of those RNAs in protein synthesis. The results showed, in fact, that 53% or more of the RNA were transcribed as ncRNA, which is not usually used for protein synthesis. The ncRNAs identified during the study are drawing attention as a new continent of genomics due to its various functions, such as those associated with cell differentiation by taking the role of regulating gene expression.

    New RNA Continent
    Discovered the existence of a large number of RNAs that are not used for protein synthesis (ncRNA)
    Further suggested that such ncRNAs have various functions including regulation of gene expression, and thus this was a great discovery disproving an established theory.Press Release
    Determination of protein structure constituting the genetic code of lifePress Release
    Completion of the Rice Full-Length cDNA Encyclopedia DNA Book containing 30,000 completely sequenced genes of the rice genomePress Release
    Introduction of a high throughput computational environment system for protein analysisPress Release
  9. 2006

    Gon, the chimpanzee
    The article announced the sequencing of the base sequence of the chimpanzee Y-chromosome and comparative analysis results of the DNA sequences of human and chimpanzee. Succeeded in sequencing the chimpanzee Y-chromosome. Showed that the rate of evolution was faster in the chimpanzee Y-chromosome than in the human Y-chromosome.
    Public release of the protein structure database against new type of influenza in the world for drug discovery accelerationPress Release
    Created the gene catalog of human chromosome 11Press Release
    Captured the moment of RNA unwinding of RNA by a proteinPress Release
    Discovered the regulatory region of "broad type" promoters for a new mechanism of gene regulationPress Release

    MDGRAPE-3 Board

    The MDGRAPE-3 system comprises
    138 servers in a line
    Built an exclusive-use high-speed computer system that was the first to break the Petaflop barrier

    In 2006, Makoto Taiji, Team Leader of the Computational and Experimental Systems Biology Group, completed MDGRAPE-3, the fastest exclusive-use computer system in the world. MDGRAPE-3 is a special-purpose, highly sophisticated computer with 1 Petaflop peak performance specializing in the simulation of molecular dynamics. The completion of MDGRAPE-3 made possible visualization of the movement of molecules in vivo with great accuracy, and it has become feasible to study protein performance and/or the cause of disease at the atomic level. This system is also expected to contribute to new drug development since it can simulate how drug candidates will act when combined with a protein.

    Developed "MDGRAPE-3", a computer exclusively used for molecular dynamics simulation. The theoretical peak performance is 1 Petaflop, or 1 quadrillion operations per second. Press Release

    Unnatural Base Pair "Ds-Pa"
    Creation of a novel unnatural base pair system for the expansion of the genetic alphabet toward future biotechnology
    Artificial Base Pairs

    Ichiro Hirao, Team Leader of the Protein Research Group, and his colleagues developed two kinds of unnatural bases called "TDs"T and "TPa"T. These bases specifically form a pair with each other, like the natural A-T and G-C pairs in DNA. Although the Ds-Pa pair has no hydrogen bonds, found in the natural base pairs, each unnatural base has a specific shape complementation. DNA molecules containing the Ds-Pa pair can be faithfully amplified by PCR and used as templates for making RNA molecules containing extra components by transcription. Thus, the unnatural base pair could open the door to create novel nucleic acids and proteins useful for diagnostics and therapeutics.

    Succeeded in creating the unnatural base pair "Ds-Pa", which is compatible with the natural A-T and G-C base pairs in replication. First in the world to realize unnatural base pair, that can function in replication and transcription. Press Release
    Elucidation of the inhibition mechanism of an antibiotics kasgamycin on protein synthesis
    Open the modeling database of three-dimensional protein structures to the public via the web on a worldwide levelPress Release

    "OmicBrowse" Top Page
    Open access to the search software "OmicBrowse" for the Genome Database Developed and released "OmicBrowse" software, which can search and visualize simultaneously various database groups related to annotation information of genes existing on the genome

    Commensal Bacterium, C. ruddii
    Discovered the smallest ever genome in the living world from the commensal bacterium Carsonella ruddiiPress Release
    Succeeded in high throughput peptide cohesion simulation.
    Peptide cohesion simulation wins the Gordon Bell Prize in 2006.
    Signed an agreement on collaboration with Edinburgh University
    Elucidated the precise control of gene expression of anticancer drug target molecules
    Protein cooperates with RNA to form a pocket that conforms to substrate
  10. 2007
    Discovery of a protein that converts the enzyme peroxisome into a mature form
    Clarification of the structure and function of an oncoprotein involved in lung cancerPress Release

    Reagents used in the SMAP method
    Developed the new gene diagnostic technology, the "SMAP method". Succeeded in developing the rapid isothermal DNA amplification method, "SMAP method" Clinical research was also started in Japan and overseas to investigate the potential technology for determining drug efficacy and for diagnosing side effects within 30 minutes using a drop of blood.
    Structural Basis for interactions of the Ribosome with the Switch Regions of GTP-bound Elongation Factors
    Structure of an archaeal protein referred to as a living fossil in the evolutionary history of the "genetic code dictionary"
    A snapshot of a supramolecular complex at the first step of protein biosynthesis

    Figure shows the structure of proteins.
    The left panel shows a glycosylated protein, human galectin 4, and the right panel shows human ZFAT which is involved in the regulation of autoimmune thyroid desease.
    Completed the Protein 3000 Project
    Finally determined the structure of 2675 proteins
    National Project on Protein Structural and Functional Analysis(Protein 3000)

    The national "TProtein 3000 Project"T led by the Ministry of Education, Culture, Sports, Science and Technology, which targeted the analysis of the 3000 basic structure of proteins within 5 years, was completed in March 2007. Shigeyuki Yokoyama, Director of the project and his colleagues at RIKEN, accomplished 2675 structure determinations and led the project to success. They achieved automation of high-quality sample preparation in large quantities, and were able to improve preparation speed markedly. Their achievement had huge impact on global research and contributed greatly to the development of structural proteomics.

    Completion of the National Bio Resource Project Creation of a total of 399 mutant mice

    A mouse presenting with schizophrenia (left) or depression symptoms (right) showed 13% and 6% decrease in brain volume, respectively.
    Succeeded in developing a mouse model of schizophrenia/depression Developed two mouse lineages having variations in amino acid replacement in the Disc1 gene, which is said to contribute to schizophrenia. It was clarified that this lineage can serve as a mouse model for both depression and schizophrenia.
    Elucidated an endocytosis mechanism, the process in which extra-cellular substances are internalized through the cellular membrane