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DNA Research Advance Access originally published online on September 16, 2006
DNA Research 2006 13(3):111-121; doi:10.1093/dnares/dsl003
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Whole-Genome Microarray in Arabidopsis Facilitates Global Analysis of Retained Introns

Hadas Ner-Gaon and Robert Fluhr*

Department of Plant Sciences, Weizmann Institute of Science Rehovot 76100, Israel

Alternative splicing (AS) is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Different types of AS have been observed; these include exon skipping, alternative donor or acceptor site and intron retention. In humans, exon skipping is the most common type while intron retention is rare. In contrast, in Arabidopsis, intron retention is the most prevalent AS type (~40%). Here we show that direct transcript expression analysis using high-density oligonucleotide-based whole-genome microarrays (WGAs) is particularly amenable for assessing global intron retention in Arabidopsis. By applying a novel algorithm retained introns are detected in 8% of the transcripts examined. A sampling of 14 transcripts showed that 86% can be confirmed by RT–PCR. This rate of detection predicts an overall total AS rate of 20% for Arabidopsis compared with 10–22% based on EST/cDNA-based analysis. These findings will facilitate monitoring constitutive and dynamic whole-genome splicing on the next generation WGA slides.

Key words: microarray; TILING; alternative splicing; Arabidopsis; intron retention; NPR-1; GIGANTEA

*To whom correspondence should be addressed. Tel. +972-8-9342175. Fax. +972-8-9344181, E-mail: robert.fluhr{at}weizmann.ac.il

Communicated by Kazuo Shinozaki


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