Abstract
BackgroundThe U12-type spliceosome is responsible for the removal of a subset of introns from eukaryotic mRNAs. U12-type introns are spliced less efficiently than normal U2-type introns, which suggests a rate-limiting role in gene expression. The Drosophila genome contains about 20 U12-type introns, many of them in essential genes, and the U12-type spliceosome has previously been shown to be essential in the fly.Methodology/Principal FindingsWe have used a Drosophila line with a P-element insertion in U6atac snRNA, an essential component of the U12-type spliceosome, to investigate the impact of U12-type introns on gene expression at the organismal level during fly development. This line exhibits progressive accumulation of unspliced U12-type introns during larval development and the death of larvae at the third instar stage. Surprisingly, microarray and RT-PCR analyses revealed that most genes containing U12-type introns showed only mild perturbations in the splicing of U12-type introns. In contrast, we detected widespread downstream effects on genes that do not contain U12-type introns, with genes related to various metabolic pathways constituting the largest group.Conclusions/SignificanceU12-type intron-containing genes exhibited variable gene-specific responses to the splicing defect, with some genes showing up- or downregulation, while most did not change significantly. The observed residual U12-type splicing activity could be explained with the mutant U6atac allele having a low level of catalytic activity. Detailed analysis of all genes suggested that a defect in the splicing of the U12-type intron of the mitochondrial prohibitin gene may be the primary cause of the various downstream effects detected in the microarray analysis.
Highlights
The removal of noncoding introns by the spliceosome is an essential step in the posttranscriptional processing of mRNAs in eukaryotic organisms
In addition to the ubiquitous U2-type ‘‘major’’ spliceosome that removes the majority of all introns, the U12-type ‘‘minor’’ spliceosome excises a subset of introns containing highly conserved 59 splice site (59ss) and branch point sequences (BPS) [1,2,3,4]
Both spliceosomes use a similar mechanism for intron removal and consist of five small nuclear RNAs assembled into ribonucleoprotein particles containing more than 150 different protein species
Summary
The removal of noncoding introns by the spliceosome is an essential step in the posttranscriptional processing of mRNAs in eukaryotic organisms. In addition to the ubiquitous U2-type ‘‘major’’ spliceosome that removes the majority of all introns, the U12-type ‘‘minor’’ spliceosome excises a subset of introns containing highly conserved 59 splice site (59ss) and branch point sequences (BPS) [1,2,3,4]. Both spliceosomes use a similar mechanism for intron removal and consist of five small nuclear RNAs (snRNA) assembled into ribonucleoprotein (snRNP) particles containing more than 150 different protein species (for reviews, see [5,6]). The Drosophila genome contains about 20 U12-type introns, many of them in essential genes, and the U12-type spliceosome has previously been shown to be essential in the fly
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