ArticlePLoS computational biology2009
Alu exonization events reveal features required for precise recognition of exons by the splicing machinery.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- 30 Years Since the Proposal of Exon Skipping Therapy for Duchenne Muscular Dystrophy and the Future of Pseudoexon Skipping.International journal of molecular sciences · 2025Review
- PredictingbioRxiv : the preprint server for biology · 2024Article
- Alu RNA fold links splicing with signal recognition particle proteins.Nucleic acids research · 2023Article
- Transcriptome innovations in primates revealed by single-molecule long-read sequencing.Genome research · 2022Article
- Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing.Molecular cell · 2021Article
- Deep Intronic Mutation in SERPING1 Caused Hereditary Angioedema Through Pseudoexon Activation.Journal of clinical immunology · 2020Article
- Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts.RNA biology · 2019Article
- HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo.Genome research · 2018Article
- Genome-wide analysis of a recently active retrotransposon, Au SINE, in wheat: content, distribution within subgenomes and chromosomes, and gene associations.Plant cell reports · 2018Article
- Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.Biology · 2016Review
- The contribution of Alu exons to the human proteome.Genome biology · 2016Article
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- The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat.RNA biology · 2015Article
- Alport syndrome caused by a COL4A5 deletion and exonization of an adjacent AluY.Molecular genetics & genomic medicine · 2014Article
- Reverse transcriptase and intron number evolution.Stem cell investigation · 2014Article
- Inferring the expression variability of human transposable element-derived exons by linear model analysis of deep RNA sequencing data.BMC genomics · 2013Article
- The intertwining of transposable elements and non-coding RNAs.International journal of molecular sciences · 2013Review
- A simple model to explain evolutionary trends of eukaryotic gene architecture and expression: how competition between splicing and cleavage/polyadenylation factors may affect gene expression and splice-site recognition in eukaryotes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2013Review
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Authors and funding
6 authors.
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Abstract
Despite decades of research, the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure. In this study, we analyzed Alu exonization events, aiming to understand the requirements for correct selection of exons. Comparison of exonizing Alus to their non-exonizing counterparts is informative because Alus in these two groups have retained high sequence similarity but are perceived differently by the splicing machinery. We identified and characterized numerous features used by the splicing machinery to discriminate between Alu exons and their non-exonizing counterparts. Of these, the most novel is secondary structure: Alu exons in general and their 5' splice sites (5'ss) in particular are characterized by decreased stability of local secondary structures with respect to their non-exonizing counterparts. We detected numerous further differences between Alu exons and their non-exonizing counterparts, among others in terms of exon-intron architecture and strength of splicing signals, enhancers, and silencers. Support vector machine analysis revealed that these features allow a high level of discrimination (AUC = 0.91) between exonizing and non-exonizing Alus. Moreover, the computationally derived probabilities of exonization significantly correlated with the biological inclusion level of the Alu exons, and the model could also be extended to general datasets of constitutive and alternative exons. This indicates that the features detected and explored in this study provide the basis not only for precise exon selection but also for the fine-tuned regulation thereof, manifested in cases of alternative splicing.
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