The molecular origins of diversity
According to the central dogma of biology, DNA gets transcribed into messenger RNA (mRNA), which in turn is translated into protein. Regulation of gene expression occurs at various levels during the whole process. The coding potential and functional versatility of genes is dramatically increased by AS, a process whereby the mRNA is changed by retaining or leaving out exons to generate different protein isoforms. Scientists on the EU-funded EVOALTSPLICE project have investigated the evolution of the mechanisms of AS in vertebrates. The idea was to identify biologically informative conserved and condition-specific splicing patterns. EVOALTSPLICE team members compared the transcriptomes of multiple organs from 10 vertebrate species spanning some 350 million years of evolution. They found that the AS profile of genes in those organs correlates more to the identity of a species rather than to the type of organ, even when comparing species that diverged only around 6 million years ago. Using a computational method, they successfully identified combinations of cis-regulatory elements that could act as predictive markers for tissue-dependent splicing patterns in vertebrate species. Data from the mouse showed that AS patterns are generally controlled by significantly conserved cis-regulatory features. However, only a subset of AS events that cause alterations in protein-protein interactions was probably responsible for the diversification of splicing and the phenotypic differences of vertebrates. The researchers found that intron retention, responsible for AS in plants and single-celled eukaryotes, is surprisingly common in mammals and affects some 75 % of multi-exonic genes. The researchers also investigated an alternative exon in the PTBP1 gene using human cell lines. Exon skipping results in a less potent PTBP1 protein and indicates that its evolution has contributed to change of its splicing targets in mammals. Using intron labelling and spinning disc confocal microscopy, the scientists also looked into how different splicing signals affect splicing in live human cells. The results provide evidence that splice site strength has an impact on splicing kinetics. Work by the EVOALTSPLICE group culminated in publications in the highly prestigious peer-reviewed journals Science, Molecular Cell, Nature, Genome Research and Molecular Microbiology. Research into splicing and gene transcription has wide significance in molecular biology and underpins development and disease.
Keywords
Vertebrates, alternative splicing, evolutionary variation, protein isoforms