IMEter

Introns in a wide range of organisms including plants, animals and fungi are able
to increase the expression of the gene that they are contained in. This process
of intron-mediated enhancement (IME) is most thoroughly studied in Arabidopsis
thaliana, where it has been shown that enhancing introns are typically located
near the promoter and are compositionally distinct from downstream introns. In
this study, we perform a comprehensive comparative analysis of several sequenced
plant genomes. We find that enhancing sequences are conserved in the
multi-cellular plants but are either absent or unrecognizable in algae. IME
signals are preferentially located towards the 5'-end of first introns but also
appear to be enriched in 5'-UTRs and coding regions near the transcription start
site. Enhancing introns are found most prominently in genes that are highly
expressed in a wide range of tissues. Through site-directed mutagenesis in A.
thaliana, we show that IME signals can be inserted or removed from introns to
increase or decrease gene expression. Although we do not yet know the specific
mechanism of IME, the predicted signals appear to be both functional and highly
conserved.

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants.

IMEter is a web-based tool for evaluating whether an intron enhances gene expression. Currently works for Arabidopsis thaliana (thale cress) and Oryza sativa (rice).

IMEter

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