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First published online March 4, 2008; 10.1105/tpc.108.200310

The Plant Cell 20:498

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IN BRIEF

The IMEter Predicts an Intron's Ability to Boost Gene Expression

Kathleen L. Farquharson

Science Editor

kfarquharson{at}aspb.org

Most eukaryotic genes are interrupted by one or more introns that are transcribed and then removed by splicing before the mRNA exits the nucleus. Some intron-containing genes have much higher expression levels than intronless versions of the same gene (reviewed in Le Hir et al., 2003Go). The first intron of the shrunken-1 gene from maize produced a 91-fold increase in expression of a reporter gene construct (Vasil et al., 1989Go). Enhancing introns must fall within 1 kb of the transcription start site to have a positive effect on mRNA accumulation (Rose, 2004Go). However, the mechanism underlying intron-mediated enhancement (IME) in plants is largely unknown.

Rose et al.Go (pages 543–551) adopted a bioinformatics approach to identify introns that stimulate gene expression in Arabidopsis and rice. The authors reason that introns near the start of transcription would be enriched in IME signals and that distal introns, which do not seem to affect gene expression, would be depleted in IME signals. They designed a word-based discriminator, the IMEter (http://korflab.ucdavis.edu/cgi-bin/web-imeter.pl), that assigns a positive score to input sequences that are similar to proximal introns and a negative score to sequences that resemble distal introns. After training the IMEter on more than 40,000 introns from Arabidopsis, they found that the calculated IMEter scores strongly correlate with the enhancing ability of experimentally tested introns. Thus, the degree to which an individual intron matches the proximal intron profile strongly predicts its ability to augment gene expression. Analysis of the top-scoring introns revealed a motif (see figure) that is dispersed throughout enhancing introns but is scarce in nonenhancing introns. By inserting a series of hybrid introns into a reporter gene construct, the authors further demonstrate that the sequences responsible for elevating gene expression are distributed throughout the enhancing intron.


Figure 1
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  		Sequence motifs that may be responsible for IME in Arabidopsis and rice.

 
To determine if IME signals are conserved across plant species, the researchers trained the IMEter on more than 30,000 introns from rice and again tested its ability to detect expression-enhancing introns in Arabidopsis. Once more, the calculated IMEter scores were in good agreement with the observed expression-enhancing abilities of the introns. This suggests that the signals responsible for IME are conserved between Arabidopsis and rice. The rice-trained IMEter also predicted enhancing introns from maize and rice, and further analysis identified an IME signal in rice that is similar to the enhancing motif of Arabidiopsis (see figure). Because addition of an intron from the host species can often enhance transgene expression, the authors suggest that the IMEter may be a useful tool for optimizing expression in transgenic plants.

Footnotes

www.plantcell.org/cgi/doi/10.1105/tpc.108.200310

REFERENCES

Le Hir, H., Nott, A., and Moore, M.J. (2003). How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci. 28: 215–220.[CrossRef][ISI][Medline]

Rose, A.B. (2004). The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis. Plant J. 40: 744–751.[CrossRef][ISI][Medline]

Rose, A.B., Elfersi, T., Parra, G., and Korf, I. (2008). Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. Plant Cell 20: 543–551.[Abstract/Free Full Text]

Vasil, V., Clancy, M., Ferl, R.J., Vasil, I.K., and Hannah, L.C. (1989). Increased gene expression by the first intron of maize shrunken-1 locus in grass species. Plant Physiol. 91: 1575–1579.[Abstract/Free Full Text]


Related articles in Plant Cell:

Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression
Alan B. Rose, Tali Elfersi, Genis Parra, and Ian Korf
Plant Cell 2008 20: 543-551. [Abstract] [Full Text]  




This Article
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