Spliceosomal Introns: Features, Functions, and Evolution

Poverennaya, Irina; Roytberg, Mikhail A.

doi:10.1134/s0006297920070019

Cited by 22 publications

(12 citation statements)

References 92 publications

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“…However, host neutral evolutionary rates based on known mammal rates might be not accurate for cetaceans. Instead, in this study, we directly compared the genetic distance of LTRs with that of cetacean neutrally evolving regions (introns used in this study) [39,40]. We first estimated the genetic distance of orthologous introns between Balaenoptera acutorostrata and H. amphibious (reflecting the divergence between cetaceans and hippopotamuses) as well as the genetic distance of orthologous introns between B. acutorostrata and Orcinus orca (reflecting the divergence between mysticetes and odontocetes).…”

Section: Temporal Dynamics Of Cetacean Erv Amplificationmentioning

confidence: 99%

Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

et al. 2021

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The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history.

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Section: Temporal Dynamics Of Cetacean Erv Amplificationmentioning

confidence: 99%

Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

et al. 2021

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“…genomic coordinates, are evolutionarily conservative which means they are under the pressure of negative selection [1][2][3][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.…”

Section: Introductionmentioning

confidence: 99%

Is there any intron sliding in mammals?

2020

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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.

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“…It is now clear that eukaryotic protein coding genes are generally organized as a succession of exons that code for the sequence of amino acids, and are spaced by introns that do not code for amino acids. Nevertheless, long-standing debates remain on the origin of the eukaryotic gene structure [ 9 , 10 ]. Overall, the splicing reaction is a crucial maturation step by which non-coding sequences are spliced out from the pre-mRNA to yield a functional mRNA [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

Principles and correction of 5’-splice site selection

2022

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In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing , and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.

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Spliceosomal Introns: Features, Functions, and Evolution

Cited by 22 publications

References 92 publications

Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

Is there any intron sliding in mammals?

Principles and correction of 5’-splice site selection

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