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Genome-wide transcription analyses in rice using tiling microarrays


Sequencing and computational annotation revealed several features, including high gene numbers1,2,3,4,5,6, unusual composition of the predicted genes1,7 and a large number of genes lacking homology to known genes8,9, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species. We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions that share similar compositional properties with the annotated exons and have significant homology to other plant proteins. Elucidating and mapping of all transcribed regions revealed an association between global transcription and cytological chromosome features, and an overall similarity of transcriptional activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome.

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Figure 1: Tiling microarray analysis of indica rice gene models and intergenic regions.
Figure 2: Tiling array detection of annotated indica gene models.
Figure 3: Identification and characterization of TARs.
Figure 4: Tiling microarray analysis of chromosome-wide transcriptional activities.
Figure 5: Transcription analysis of duplicated segments in the indica genome.

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The collaborative indica rice tiling microarray project in China was supported by the 863 rice functional genomics program from the Ministry of Science and Technology of China and by the National Institute of Biological Sciences at Beijing. The rice tiling microarray project at Yale University was supported by a grant from the US National Science Foundation Plant Genome Program.

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Corresponding author

Correspondence to Xing Wang Deng.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Hybridization rate (HR) distribution in exons and introns of full-length cDNA supported (CG) gene models. (PDF 708 kb)

Supplementary Fig. 2

Transcription analysis of the 12 indica chromosomes. (PDF 353 kb)

Supplementary Fig. 3

Structural properties of different indica gene models. (PDF 245 kb)

Supplementary Fig. 4

Compositional property of the six groups if indica gene models. (PDF 466 kb)

Supplementary Fig. 5

Distribution of signal probes along the 12 indica chromosomes. (PDF 975 kb)

Supplementary Fig. 6

Cytological image of the 12 indica chromosomes. (PDF 1043 kb)

Supplementary Table 1

Transcriptional analysis of duplicated segments in the indica genome. (PDF 45 kb)

Supplementary Note (PDF 126 kb)

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Li, L., Wang, X., Stolc, V. et al. Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38, 124–129 (2006).

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