A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

Viktor Stolc, Lei Li, Xiangfeng Wang, Xueyong Li, Ning Su, Waraporn Tongprasit, Bin Han, Yongbiao Xue, Jiayang Li, Michael Snyder, Mark Gerstein, Jun Wang, Xing Wang Deng

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcription units that will facilitate rice genome annotation.
Udgivelsesdato: 2005-Sep
Original languageEnglish
JournalPlant Molecular Biology
Volume59
Issue number1
Pages (from-to)137-49
Number of pages12
ISSN0167-4412
DOIs
Publication statusPublished - 1. Sept 2005

Keywords

  • Carbocyanines
  • Chromosomes, Plant
  • DNA, Complementary
  • Genome, Plant
  • Oligonucleotide Array Sequence Analysis
  • Oryza sativa
  • Pilot Projects
  • RNA, Plant
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Transcription, Genetic

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