Plant Cell Advance Online Publication
Published on April 29, 2005; 10.1105/tpc.105.031575
Received February 6, 2005
Returned for revision March 21, 2005
Accepted March 29, 2005
A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription
Yuling Jiao 1, Peixin Jia 2, Xiangfeng Wang 3, Ning Su 4, Shuliang Yu 2, Dongfen Zhang 5, Ligeng Ma 4, Qi Feng 2, Zhaoqing Jin 2, Lei Li 1, Yongbiao Xue 5, Zhukuan Cheng 5, Hongyu Zhao 6, Bin Han 2*, and Xing Wang Deng 1
1 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8014
2 National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
3 National Institute of Biological Sciences, Beijing 102206, China, and Center of Bioinformatics, College of Life Sciences, Peking University, Beijing 100871, China; Peking-Yale Joint Research Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
4 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8014; Peking-Yale Joint Research Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
5 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
6 Division of Biostatistics, Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520
* To whom correspondence should be addressed. E-mail: bhan{at}ncgr.ac.cn.
The complete genome sequence of cultivated rice (Oryza sativa) provides an unprecedented opportunity to understand the biology of this model cereal. An essential and necessary step in this effort is the determination of the coding information and expression patterns of each sequenced chromosome. Here, we report an analysis of the transcriptional activity of rice chromosome 4 using a tiling path microarray based on PCR-generated genomic DNA fragments. Six representative rice organ types were examined using this microarray to catalog the transcribed regions of rice chromosome 4 and to reveal organ- and developmental stage-specific transcription patterns. This analysis provided expression support for 82% of the gene models in the chromosome. Transcriptional activities in 1643 nonannotated regions were also detected. Comparison with cytologically defined chromatin features indicated that in juvenile-stage rice the euchromatic region is more actively transcribed than is the transposon-rich heterochromatic portion of the chromosome. Interestingly, increased transcription of transposon-related gene models in certain heterochromatic regions was observed in mature-stage rice organs and in suspension-cultured cells. These results suggest a close correlation between transcriptional activity and chromosome organization and the developmental regulation of transcription activity at the chromosome level.
This article has been cited by other articles:
|
|
|
|
 
B.-L. Yin, L. Guo, D.-F. Zhang, W. Terzaghi, X.-F. Wang, T.-T. Liu, H. He, Z.-K. Cheng, and X. W. Deng
Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4
Mol Plant,
August 8, 2008;
(2008)
ssn037v1.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
X. Li, X. Wang, K. He, Y. Ma, N. Su, H. He, V. Stolc, W. Tongprasit, W. Jin, J. Jiang, et al.
High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression
PLANT CELL,
February 1, 2008;
20(2):
259 - 276.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
B. Liu, Z. Chen, X. Song, C. Liu, X. Cui, X. Zhao, J. Fang, W. Xu, H. Zhang, X. Wang, et al.
Oryza sativa Dicer-like4 Reveals a Key Role for Small Interfering RNA Silencing in Plant Development
PLANT CELL,
September 1, 2007;
19(9):
2705 - 2718.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. M. Kater, L. Dreni, and L. Colombo
Functional conservation of MADS-box factors controlling floral organ identity in rice and Arabidopsis
J. Exp. Bot.,
October 1, 2006;
57(13):
3433 - 3444.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. M. Brady, T. A. Long, and P. N. Benfey
Unraveling the dynamic transcriptome.
PLANT CELL,
September 1, 2006;
18(9):
2101 - 2111.
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Wang, X. Tang, Z. Cheng, L. Mueller, J. Giovannoni, and S. D. Tanksley
Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome
Genetics,
April 1, 2006;
172(4):
2529 - 2540.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Jiao, L. Ma, E. Strickland, and X. W. Deng
Conservation and Divergence of Light-Regulated Genome Expression Patterns during Seedling Development in Rice and Arabidopsis
PLANT CELL,
December 1, 2005;
17(12):
3239 - 3256.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. E. Bowers, M. A. Arias, R. Asher, J. A. Avise, R. T. Ball, G. A. Brewer, R. W. Buss, A. H. Chen, T. M. Edwards, J. C. Estill, et al.
Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses
PNAS,
September 13, 2005;
102(37):
13206 - 13211.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
