Summary of Research Project Results under JSPS FY2004
"Research for the Future Program"

1. Research Institution   National Institutes of Natural Sciences
2. Research Area Life Sciences
3. Research Field Development, Differentiation, and Regeneration
4. Term of Project FY 2000 - FY 2004
5. Project Number 00L01506
6. Title of Project Elucidation of the Principles of Development and Regeneration by Systematic Analysis of Genes

7. Project Leader

Name Institution, Department Title of Position
Naoto, Ueno National Institutes of Natural Sciences, National Institute for Basic Biology Professor

8. Core Members

Names Institution, Department Title of Position
Makoto, Mochii University of Hyogo, Graduate School of Life Science Associate Professor
Kiyokazu, Agata RIKEN, Center for Developmental Biology Group Director

9. Summary of Research Results

In this project, Ueno's group at National Institute for Basic Biology attempted to establish a comprehensive and versatile platform of functional genomics using an amphibian Xenopus laevis that provides unique and advantageous experimental systems for functional analyses. We collected over 200,000 ESTs from normalized Xenopus laevis cDNA libraries derived form stage 10.5, 15, and 25 embryos which Dr. Mochii constructed and grouped them into approximately 10,000 unique gene sets and contributed to promote functional genomics using Xenopus not only by providing the sequence information to public databases but also by distributing the cDNAs to the world-wide community upon request. The "sequenced" cDNA sets were also provided for the fabrication of microarray chips. Among the unique genes, nearly 3,000 genes that are predicted to encode full-length clone were selected for further functional analyses. For those 3,000 genes, the spatio-temporal gene expression during early development of the Xenopus was examined using whole-mount in situ hybridization, which constitutes one of the best recognized resources of vertebrate developmental gene expression patterns. The expression patterns are documented and organized into our own database XDB ( and currently viewable through the web site in direct association with gene/gene product information. Images are also browsable according to developmental stages, direction of photographs taken and clone name. The large numbers of image data highlight synexpression groups representing genes with shared, complex expression pattern that predict molecular pathways involved in development and regeneration, and thus promise the powerful aid for functional annotation of genes. In fact, we have succeeded to identify several important genes regulating gastrulation, regeneration.
In addition, the systematic and comprehensive approach promoted regeneration biology and Dr. Agata in this project identified an essential gene for planarian regeneration.

10. Key Words

( 1 ) early development ( 2 ) regeneration ( 3 ) morphogenesis
( 4 ) genome reading ( 5 ) functional genomics ( 6 ) Xenopus laevis
( 7 ) planaria ( 8 ) microarray ( 9 ) stem cells