Is there any intron sliding in mammals?
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RESEARCH ARTICLE
Is there any intron sliding in mammals? Irina V. Poverennaya1,2*† , Nadezhda A. Potapova3,4† and Sergey A. Spirin5,6,7
Abstract Background: Eukaryotic protein-coding genes consist of exons and introns. Exon–intron borders are conserved between species and thus their changes might be observed only on quite long evolutionary distances. One of the rarest types of change, in which intron relocates over a short distance, is called "intron sliding", but the reality of this event has been debated for a long time. The main idea of a search for intron sliding is to use the most accurate genome annotation and genome sequence, as well as high-quality transcriptome data. We applied them in a search for sliding introns in mammals in order to widen knowledge about the presence or absence of such phenomena in this group. Results: We didn’t find any significant evidence of intron sliding in the primate group (human, chimpanzee, rhesus macaque, crab-eating macaque, green monkey, marmoset). Only one possible intron sliding event supported by a set of high quality transcriptomes was observed between EIF1AX human and sheep gene orthologs. Also, we checked a list of previously observed intron sliding events in mammals and showed that most likely they are artifacts of genome annotations and are not shown in subsequent annotation versions as well as are not supported by transcriptomic data. Conclusions: We assume that intron sliding is indeed a very rare evolutionary event if it exists at all. Every case of intron sliding needs a lot of supportive data for detection and confirmation. Keywords: Intron sliding, Introns, Gene annotation, Transcriptome, Intron evolution Background Eukaryotic genes consist of exons and introns whose borders, i.e. genomic coordinates, are evolutionarily conservative which means they are under the pressure of negative selection [1–4]. The changes of exon–intron boundaries might affect coding protein, therefore they are rare events and can be seen only on the long evolutionary distances [5]. Such changes differ from the alternative splicing, which is widespread in eukaryotes and does not affect exon–intron coordinates. Various reasons for exon–intron boundaries alterations were observed. All of them happen as a result of *Correspondence: [email protected] † Irina V. Poverennaya and Nadezhda A. Potapova contributed equally to this work as first authors 1 Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia Full list of author information is available at the end of the article
mutations in splice sites or nearby, such as a birth or death of new splice sites resulted in a loss or acquisition of exons or their part [6–9]. But the rarest type of such alterations is called “intron sliding” (also known as “intron shifting”, “intron drift”, “intron slippage” or “intron migration”). Intron sliding is a movement of intron from one position to another within a gene [10]. In other words, during sliding the start and end of the certain intron move in the
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