Genome-wide transcription analyses in rice using tiling microarrays.

Lei Li, Xiangfeng Wang, Viktor Stolc, Xueyong Li, Dongfen Zhang, Ning Su, Waraporn Tongprasit, Songgang Li, Zhukuan Cheng, Jun Wang, Xing Wang Deng

Research output: Contribution to journalJournal articleResearchpeer-review


Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, 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.
Udgivelsesdato: 2006-Jan
Original languageEnglish
JournalNature Genetics
Issue number1
Pages (from-to)124-9
Number of pages5
Publication statusPublished - 1. Jan 2006


  • Chromosomes
  • DNA, Intergenic
  • Expressed Sequence Tags
  • Gene Expression Regulation, Plant
  • Genome, Plant
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Oryza sativa
  • Tandem Repeat Sequences
  • Transcription, Genetic

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