Diane Jofuku Okamuro
IOS Division of Integrative Organismal Systems
BIO Directorate for Biological Sciences
Start Date:
September 1, 2004
Expires:
August 31, 2009 (Estimated)
Awarded Amount to Date:
$2474014
Investigator(s):
Xing-Wang Deng xingwang.deng@yale.edu (Principal Investigator)
Pamela Ronald (Co-Principal Investigator) Mark Gerstein (Co-Principal Investigator)
Sponsor:
Yale University
P.O. Box 208337
NEW HAVEN, CT 06520 203/432-2460
NSF Program(s):
PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):
BIOT, 9251, 9232, 9109
Program Element Code(s):
1329
ABSTRACT
As the international effort to sequence the rice genome is completed, it becomes essential to define each and every transcriptional unit (or gene) encoded in the rice genome. Computer assisted genome annotation suggests that there may be about 60,000 genes in the rice genome. However, it is estimated that the combination of all experimental data available provides expression validation for only approximately half of the predicted genes. Further, due to the high GC content in rice gene coding regions, existing gene prediction program will likely miss a significant fraction of the active genes. Thus there is an urgent need for experimental verification of all predicted genes and discovery of rice genes that were missed by current prediction programs.
This project will attempt to discover all possible transcription units of the just completely sequenced Japonica rice. A high-density genome tiling oligonucleotide array produced with the Maskless Array Synthesizer (MAS) technology will be used, which permits reiteration of the oligo design for each subsequent array slide production. The workflow will be optimized first with rice chromosome 10 and then applied to all remaining chromosomes. Pooled probes derived from representative RNA samples from both normal grown rice and those subjected to various inductive treatments will be included to maximize transcription unit discovery. The data will be integrated into the current and ongoing genome annotation to test predicted gene models and to define structures of the novel transcription units. The raw data will be deposited in the MIAME compliant GEO database as soon as the results are subject to quality control. All the original data, including raw hybridization data as well as gene models, will be made available to the public through a project web site (www.plantgenomics.yale.edu) once they are quality controlled and verified. This web site will be online at the end of this first funding year (August 30, 2005) and the last data set will be made available by August 30, 2007. All the new or improved rice gene models created from this work be posted on our project web site and will also be forwarded to the NSF-supported rice genome annotation group at The Institute for Genome Research at bimonthly intervals for their incorporation into their public rice gene annotation web site. The full data set will be made available to TIGR and the public by the end of this project (August, 2007).
Broader Impacts:
The experimental identification of all Japonica rice transcription units will provide an essential foundation for rice functional genomics and proteomics research in the future and provide useful comparative data for other cereals. In the process of our proposed studies, a number of postdoctoral researchers and students (both graduate and undergraduate) will obtain training in plant genomics and informatics. The project will work with the Peabody Museum at Yale University to teach the general public and school children about the role of rice cultivation in cultures around the world, and on the potential benefits of rice genomic advances for society.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Jiao, YL; Deng, XW. "A genome-wide transcriptional activity survey of rice transposable element-related genes," GENOME BIOLOGY, v.8, 2007.
Lei Li, Hang He, Juan Zhang, Xiangfeng Wang, Sulan Bai, Viktor Stolc, Waraporn Tongprasit, Nevin D Young, Oliver Yu and Xing-Wang Deng. "Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays," Genome Biology, v.9, 2008, p. R57.
Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Gerstein M, Deng XW. "Global identification and characterization of transcriptionally active regions in the rice genome," PLoS ONE, v.2 (3), 2007, p. e294.
Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Gerstein M, Deng XW. "Global identification and characterization of transcriptionally active regions in the rice genome," PLoS ONE, v.2(3), 2007, p. e294.
Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW.. "Genome-wide transcription analyses in rice using tiling microarrays," Nature Genetics, v.38, 2006, p. 124.
Li, L., Wang, X, Xia, M., Stolc, V., Su, N., Peng, Z., Li, S., Wang, J., Wang, X., and Deng, X.W.. "Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture," Genome Biology, v.6, 2005, p. R52.
Su, N; He, K; Jiao, YL; Chen, C; Zhou, JL; Li, L; Bai, SL; Li, XY; Deng, XW. "Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice," PLANT MOLECULAR BIOLOGY, v.63, 2007, p. 337-349.
Viktor Stolc, Lei Li, Xiangfeng Wang, Xueyong Li, Ning Su, et al., Mark Gerstein, and Xing Wang Deng. "A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray," Plant Molecular Biology, v.59, 2005, p. 137.
Wang, XF; He, H; Li, L; Chen, RS; Deng, XW; Li, SG. "NMPP: a user-customized NimbleGen microarray data processing pipeline," BIOINFORMATICS, v.22, 2006, p. 2955-2957.
Xueyong Li, Xiangfeng Wang, Kun He, Yeqin Ma, Ning Su, Hang He, Viktor Stolc, Waraporn Tongprasit, Weiwei Jin, Jiming Jiang, William Terzaghi, Songgang Li, and Xing Wang Deng. "Global high resolution mapping of epigenetic modifications of the rice genome uncovers combinatorial interplay between DNA methylation, and histone H3 Lysine 4 di- and tri- methylation and in association with gene expression," The Plant Cell, v.20, 2008, p. 259.
Yuling Jiao, Peixin Jia, Xiangfeng Wang, et al. , and Xing Wang Deng. "A tiling microarray expression analysis of rice chromosome 4 suggests a chromosomal level regulation of transcription," Plant Cell, v.17, 2005, p. 1641.
