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Plant Cell Advance Online Publication
Published on March 4, 2008; 10.1105/tpc.107.057190

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Received November 27, 2007
Returned for revision February 1, 2008
Accepted February 16, 2008

Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression

Alan B. Rose 1*, Tali Elfersi 2, Genis Parra 2, and Ian Korf 3

1 Molecular and Cellular Biology, University of California, Davis, California 95616
2 Genome Center, University of California, Davis, California 95616
3 Molecular and Cellular Biology, University of California, Davis, California 95616; Genome Center, University of California, Davis, California 95616

* To whom correspondence should be addressed. E-mail: abrose{at}ucdavis.edu.

Introns that elevate mRNA accumulation have been found in a wide range of eukaryotes. However, not all introns affect gene expression, and direct testing is currently the only way to identify stimulatory introns. Our genome-wide analysis in Arabidopsis thaliana revealed that promoter-proximal introns as a group are compositionally distinct from distal introns and that the degree to which an individual intron matches the promoter-proximal intron profile is a strong predictor of its ability to increase expression. We found that the sequences responsible for elevating expression are dispersed throughout an enhancing intron, as is a candidate motif that is overrepresented in first introns and whose occurrence in tested introns is proportional to its effect on expression. The signals responsible for intron-mediated enhancement are apparently conserved between Arabidopsis and rice (Oryza sativa) despite the large evolutionary distance separating these plants.




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