ArticleProceedings of the National Academy of Sciences of the United States of America2007
Coevolutionary networks of splicing cis-regulatory elements.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Review
- Exonic splicing code and coordination of divalent metals in proteins.Nucleic acids research · 2024Article
- Bioinformatics detection of modulators controlling splicing factor-dependent intron retention in the human brain.Human mutation · 2022Article
- Exon size and sequence conservation improves identification of splice-altering nucleotides.RNA (New York, N.Y.) · 2019Article
- Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5' splice-site sequences due to weak interactions with SR proteins.Nucleic acids research · 2019Article
- A synonymous RET substitution enhances the oncogenic effect of an in-cis missense mutation by increasing constitutive splicing efficiency.PLoS genetics · 2018Article
- Review
- Normal and altered pre-mRNA processing in the DMD gene.Human genetics · 2017Review
- Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells.Journal of visualized experiments : JoVE · 2017Article
- RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure.The Journal of clinical investigation · 2016Article
- Analysis of the preferences for splice codes across tissues.Protein & cell · 2015Article
- Regulation of a strong F9 cryptic 5'ss by intrinsic elements and by combination of tailored U1snRNAs with antisense oligonucleotides.Human molecular genetics · 2015Article
- Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing.Molecular systems biology · 2015Article
- Splicing of designer exons informs a biophysical model for exon definition.RNA (New York, N.Y.) · 2015Article
- Efficient backsplicing produces translatable circular mRNAs.RNA (New York, N.Y.) · 2015Article
- Context-dependent control of alternative splicing by RNA-binding proteins.Nature reviews. Genetics · 2014Review
- Exonic splicing signals impose constraints upon the evolution of enzymatic activity.Nucleic acids research · 2014Article
- Systematical identification of splicing regulatory cis-elements and cognate trans-factors.Methods (San Diego, Calif.) · 2014Article
- A day in the life of the spliceosome.Nature reviews. Molecular cell biology · 2014Review
- Testing for natural selection in human exonic splicing regulators associated with evolutionary rate shifts.Journal of molecular evolution · 2013Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Accurate and efficient splicing of eukaryotic pre-mRNAs requires recognition by trans-acting factors of a complex array of cis-acting RNA elements. Here, we developed a generalized Bayesian network to model the coevolution of splicing cis elements in diverse eukaryotic taxa. Cross-exon but not cross-intron compensatory interactions between the 5' splice site (5'ss) and 3' splice site (3'ss) were observed in human/mouse, indicating that the exon is the primary evolutionary unit in mammals. Studied plants, fungi, and invertebrates exhibited exclusively cross-intron interactions, suggesting that intron definition drives evolution in these organisms. In mammals, 5'ss strength and the strength of several classes of exonic splicing silencers (ESSs) evolved in a correlated way, whereas specific exonic splicing enhancers (ESEs), including motifs associated with hTra2, SRp55, and SRp20, evolved in a compensatory manner relative to the 5'ss and 3'ss. Interactions between specific ESS or ESE motifs were not observed, suggesting that elements bound by different factors are not commonly interchangeable. Thus, the splicing elements defining exons coevolve in a way that preserves overall exon strength, allowing specific elements to substitute for loss or weakening of others.
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