ArticleGenome research2008
Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
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Who cites it
102 citing papers in PubMed, 185 citations in OpenAlex.
- The shortest animal introns: insights from parasitic cnidarians.Molecular biology and evolution · 2026Article
- Integration of epigenetics into ecotoxicology: insights and fundamental research needs.Biological reviews of the Cambridge Philosophical Society · 2026Review
- Omics-based dissection of alternative splicing and the regulatory architecture in fungal genomes.Current research in microbial sciences · 2026Review
- Article
- Heterozygous pathogenic variants in the splicing factor SF1 lead to a large spectrum of neurodevelopmental disorders.American journal of human genetics · 2025Article
- Utargetome: A targetome prediction tool for modified U1-snRNAs to identify distal-target positions with improved selectivity.PLoS computational biology · 2025Article
- LUC7 proteins define two major classes of 5' splice sites in animals and plants.Nature communications · 2025Article
- Splicing accuracy varies across human introns, tissues, age and disease.Nature communications · 2025Article
- Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron-Exon Gene Structures Across Eukaryotic Lineages.Molecular biology and evolution · 2024Article
- RNA-Binding Protein-Mediated Alternative Splicing Regulates Abiotic Stress Responses in Plants.International journal of molecular sciences · 2024Review
- Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using thePlants (Basel, Switzerland) · 2024Article
- Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species.Nucleic acids research · 2023Article
- Article
- Interplays betweenInternational journal of molecular sciences · 2023Article
- Article
- Conserved and divergent signals in 5' splice site sequences across fungi, metazoa and plants.PLoS computational biology · 2023Article
- Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species.Open biology · 2023Article
- MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome.Briefings in bioinformatics · 2023Article
- Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.Journal of evolutionary biology · 2023Article
- Alternative splicing as a source of phenotypic diversity.Nature reviews. Genetics · 2022Review
42 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Introns are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5' splice site (5'ss), the branch site (BS), and the polypyrimdine tract/3'splice site (PPT-3'ss). To study the evolution of these splicing signals, we have conducted a systematic comparative analysis of these signals in over 1.2 million introns from 22 eukaryotes. Our analyses suggest that all these signals have dramatically evolved: The PPT is weak among most fungi, intermediate in plants and protozoans, and strongest in metazoans. Within metazoans it shows a gradual strengthening from Caenorhabditis elegans to human. The 5'ss and the BS were found to be degenerate among most organisms, but highly conserved among some fungi. A maximum parsimony-based algorithm for reconstructing ancestral position-specific scoring matrices suggested that the ancestral 5'ss and BS were degenerate, as in metazoans. To shed light on the evolutionary variation in splicing signals, we have analyzed the evolutionary changes in the factors that bind these signals. Our analysis reveals coevolution of splicing signals and their corresponding splicing factors: The strength of the PPT is correlated to changes in key residues in its corresponding splicing factor U2AF2; limited correlation was found between changes in the 5'ss and U1 snRNA that binds it; but not between the BS and U2 snRNA. Thus, although the basic ability of eukaryotes to splice introns has remained conserved throughout evolution, the splicing signals and their corresponding splicing factors have considerably evolved, uniquely shaping the splicing mechanisms of different organisms.
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Registered trials
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