Effect of 5′UTR introns on gene expression in Arabidopsis thaliana

Background: The majority of introns in gene transcripts are found within the coding sequences (CDSs). A small but significant fraction of introns are also found to reside within the untranslated regions (5 ' UTRs and 3 ' UTRs) of expressed sequences. Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome. Results: A bioinformatic analysis revealed some interesting observations: (1) the density of introns in 5 ' UTRs is similar to that in CDSs but much higher than that in 3 ' UTRs; (2) the 5 ' UTR introns are preferentially located close to the initiating ATG codon; (3) introns in the 5 ' UTRs are, on average, longer than introns in the CDSs and 3 ' UTRs; and (4) 5 ' UTR introns have a different nucleotide composition to that of CDS and 3 ' UTR introns. Furthermore, we show that the 5 ' UTR intron of the A. thaliana EF1 alpha-A3 gene affects the gene expression and the size of the 5 ' UTR intron influences the level of gene expression. Conclusion: Introns within the 5 ' UTR show specific features that distinguish them from introns that reside within the coding sequence and the 3 ' UTR. In the EF1 alpha-A3 gene, the presence of a long intron in the 5 ' UTR is sufficient to enhance gene expression in plants in a size dependent manner.