Different levels of alternative splicing among eukaryotes

Abstract

Alternative splicing increases transcriptome and proteome diversification. Previous analyses aiming at comparing the rate of alternative splicing between different organisms provided contradicting results. These contradicting results were attributed to the fact that both analyses were dependent on the expressed sequence tag (EST) coverage, which varies greatly between the tested organisms. In this study we compare the level of alternative splicing among eight different organisms. By employing an EST independent approach we reveal that the percentage of genes and exons undergoing alternative splicing is higher in vertebrates compared with invertebrates. We also find that alternative exons of the skipping type are flanked by longer introns compared to constitutive ones, whereas alternative 5′ and 3′ splice sites events are generally not. In addition, although the regulation of alternative splicing and sizes of introns and exons have changed during metazoan evolution, intron retention remained the rarest type of alternative splicing, whereas exon skipping is more prevalent and exhibits a slight increase, from invertebrates to vertebrates. The difference in the level of alternative splicing suggests that alternative splicing may contribute greatly to the mammal higher level of phenotypic complexity, and that accumulation of introns confers an evolutionary advantage as it allows increasing the number of alternative splicing forms.

Structural basis for synaptic adhesion mediated by neuroligin-neurexin interactions

“…This fundamental difference is based on different natures of splicing: the splicing of Dscam generates mutually exclusive, but inter-replaceable regions that are essential parts of the structure, whereas the splicing of neuroligins and neurexins generates inserts or deletions that are not essential to structural integrity. It was estimated that 60% of the human genes have two or more splicing variants 33 , in which the insertion/deletion-type splicing represented by neuroligins and neurexins is predominant 33 . Since the minimal transcript is functional in most splicing cases, most of the extra inserts/deletions should be not essential to the structural integrity of and should extend from the core scaffold, as observed in neuroligins and neurexins.…”

Alternative Splicing Studies of the Reactive Oxygen Species Gene Network inPopulusReveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase

“…It has recently been established that AS is a further frequent, important regulatory mechanism of gene expression in Caenorhabditis elegans, human, mouse, and Drosophila, and analyses of the developmental stage-and/or tissue-specific expression patterns of AS variants are likely to become important components of biological research (Lareau et al, 2004;Pajares et al, 2007). In humans, it is estimated that about 60% of genes undergo AS (Modrek and Lee, 2002), exon skipping being the most common form and intron retention (IntronR) the least common (Kim et al, 2007). Most of the AS genes in humans are involved in signaling and regulation (Valdivia, 2007).…”

One Gene, Many Proteins: Mapping Cell-Specific Alternative Splicing in Plants

“…Whilst exon skipping is widespread in metazoan systems (Kim et al 2007), this appears relatively rare in Arabidopsis (<5%).…”