Abstract
BackgroundThe 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.ResultsA 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 EF1α-A3 gene affects the gene expression and the size of the 5'UTR intron influences the level of gene expression.ConclusionIntrons within the 5'UTR show specific features that distinguish them from introns that reside within the coding sequence and the 3'UTR. In the EF1α-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.
Highlights
The majority of introns in gene transcripts are found within the coding sequences (CDSs)
Our findings indicate that 5'UTR introns may be subject to different selective forces from the introns in CDSs and 3'UTRs, possibly due to a specific regulatory role in gene expression
While it is known that the presence of a 5'UTR intron can enhance gene expression [36], not much is known about the underlying mechanism for this phenomenon
Summary
The majority of introns in gene transcripts are found within the coding sequences (CDSs). First discovered in 1977 [1], are genomic sequences that are removed from the corresponding RNA transcripts of genes. The most abundant class are spliceosomal introns, which are found in the nuclear genomes of all characterized eukaryotes, and rely on spliceosomes – a complex that comprises five RNAs and hundreds of proteins – for successful splicing from RNA transcripts [2,3]. Inclusion of an intron in the 5' region of a gene, either in the 5'UTR or fused to the 5' portion of the coding sequence, leads to enhanced RNA levels [11,12,13,14,15].
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