Abstract
BackgroundThe costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating such splicing-mediated expression enhancement has not been defined. Previous studies have shown that intron splicing is a time-consuming process, indicating that splicing may not reduce the time required for transcription and processing of spliced pre-mRNA molecules; rather, it might facilitate the later rounds of transcription. Because the densities of active RNA polymerase II on most genes are less than one molecule per gene, direct interactions between the splicing apparatus and transcriptional complexes (from the later rounds of transcription) are infrequent, and thus unlikely to account for splicing-mediated gene expression enhancement.Presentation of the hypothesisThe serine/arginine-rich protein SF2/ASF can inhibit the DNA topoisomerase I activity that removes negative supercoiling of DNA generated by transcription. Consequently, splicing could make genes more receptive to RNA polymerase II during the later rounds of transcription, and thus affect the frequency of gene transcription. Compared with the transcriptional enhancement mediated by strong promoters, intron-containing genes experience a lower frequency of cut-and-paste processes. The cleavage and religation activity of DNA strands by DNA topoisomerase I was recently shown to account for transcription-associated mutagenesis. Therefore, intron-mediated enhancement of gene expression could reduce transcription-associated genome instability.Testing the hypothesisExperimentally test whether transcription-associated mutagenesis is lower in intron-containing genes than in intronless genes. Use bioinformatic analysis to check whether exons flanking lost introns have higher frequencies of short deletions.Implications of the hypothesisThe mechanism of intron-mediated enhancement proposed here may also explain the positive correlation observed between intron size and gene expression levels in unicellular organisms, and the greater number of intron containing genes in higher organisms.ReviewersThis article was reviewed by Dr Arcady Mushegian, Dr Igor B Rogozin (nominated by Dr I King Jordan) and Dr Alexey S Kondrashov. For the full reviews, please go to the Reviewer's Reports section.
Highlights
The costs and benefits of spliceosomal introns in eukaryotes have not been established
Splicing could enhance later rounds of transcription Spliceosomal introns are a landmark feature of eukaryotic nuclear genes
Comparison of the densities of active RNA polymerase II molecules present on genes between intron-containing genes and intronless genes in S. cerevisiae showed that introns could enhance transcription (Table 1)
Summary
Splicing could enhance later rounds of transcription Spliceosomal introns are a landmark feature of eukaryotic nuclear genes. Referring to the 18.6 kb median size of mouse genes (data from Ensembl Release 60), the 2.37 × 10-3 molecules/kb can be converted into 0.044 molecules/gene, a value which is lower than the 0.096 molecules/gene in yeast From this we can estimate that genes that have recruited multiple active RNA polymerase II molecules are probably infrequent in mice. In both yeast and mice, direct interactions between splicing factors and the later rounds of transcription are probably infrequent events. If future studies show that multiple active RNA polymerase II molecules on a single gene are common and direct interactions between splicing factors and later rounds of transcription are not infrequent, indirect enhancement of the later rounds of transcription by splicing would contribute less than we envision here. The binding of proteins to less twisted DNA is thermodynamically favored, and the separation of two strands is facilitated [49,50,64,65]
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