Gene Expression, Intron Density, and Splice Site Strength in Drosophila and Caenorhabditis

Abstract

In this paper we investigate the relationships among intron density (number of introns per kilobase of coding sequence), gene expression level, and strength of splicing signals in two species: Drosophila melanogaster and Caenorhabditis elegans. We report a negative correlation between intron density and gene expression levels, opposite to the effect previously observed in human. An increase in splice site strength has been observed in long introns in D. melanogaster. We show this is also true of C. elegans. We also examine the relationship between intron density and splice site strength. There is an increase in splice site strength as the intron structure becomes less dense. This could suggest that introns are not recognized in isolation but could function in a cooperative manner to ensure proper splicing. This effect remains if we control for the effects of alternative splicing on splice site strength.

Unique genome of dicyemid mesozoan: Highly shortened spliceosomal introns in conservative exon/intron structure

“…In contrast to metazoans, high-expression genes in plants and unicellular eukaryotes have longer intron sequence than low-expression genes (Vinogradov 2001;Ren et al, 2006). On the other hand, positive correlation between intron density and gene expression level has been proposed in metazoans, plants, and unicellular eukaryotes (Comeron 2004;Fahey and Higgins, 2007;Lanier et al, 2008). So, highexpression genes in metazoans have a tendency to have shorter intron sequence and higher intron density.…”

Molecular basis of Cyperus difformis cross-resistance to ALS-inhibiting herbicides

“…According to Yenerall and Zhou [27], introns might be a result of transposon insertion in the AG|GT (| denotes the splice junction) sequence, which results in the duplication of this sequence on each side of the transposon without altering the coding sequence of the intronised gene. AG|GT, also known as protosplice, is the preferred site for intron gain [27,28] and has been found in many organisms such as fungi, Caenorhabditis, Drosophila and other plants [10,28,29,30,31,32,33]. The effect of an intron on gene expression is affected by the intron identity, exon sequence context, intron position within the gene, and in some cases, its influence at one step of the gene expression multiple steps [8,9].…”

Prediction of alternatively spliced exons using Support Vector Machines

“…In other words, the structure can affect the selection of the splice sites. Other studies (Wang and Marin, 2006; Fahey and Higgins, 2007) have shown that the strength of the general splice sites constitutes another important sequence feature with respect to the splicing process, as strong splice sites allow the spliceosomes to recognise pairs of splice sites between long introns. When the splice 4 J. Xia et al sites degenerate and weaken, other splicing regulatory elements, such as exon or intron splicing enhancers and silencers, are needed (Pertea et al, 2007).…”