Genome-wide Transcription Analyses in Rice Using Tiling Microarrays

Nat Genet. 2006 Jan;38(1):124-9. doi: 10.1038/ng1704. Epub 2005 Dec 20.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

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


  • DNA, Intergenic

Associated data

  • GEO/GSE3452