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A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription

^a Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8014
^b National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
^c National Institute of Biological Sciences, Beijing 102206, China, and Center of Bioinformatics, College of Life Sciences, Peking University, Beijing 100871, China
^d Peking–Yale Joint Research Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
^e Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
^f Division of Biostatistics, Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520

² To whom correspondence should be addressed. E-mail bhan{at}ncgr.ac.cn or xingwang.deng{at}yale.edu; fax 86-21-64825775 or fax 203-432-3854.

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.

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