ArticleMolecular and cellular biology2008
Multifactorial interplay controls the splicing profile of Alu-derived exons.
Article in Molecular and cellular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Alu RNA fold links splicing with signal recognition particle proteins.Nucleic acids research · 2023Article
- A deep intronic TCTN2 variant activating a cryptic exon predicted by SpliceRover in a patient with Joubert syndrome.Journal of human genetics · 2023Article
- Detection ofFrontiers in molecular biosciences · 2021Article
- Identification of a deep intronic POLR3A variant causing inclusion of a pseudoexon derived from an Alu element in Pol III-related leukodystrophy.Journal of human genetics · 2020Article
- The role of Alu elements in the cis-regulation of RNA processing.Cellular and molecular life sciences : CMLS · 2015Review
- Article
- The extent of Ds1 transposon to enrich transcriptomes and proteomes by exonization.Botanical studies · 2013Article
- Alu elements: an intrinsic source of human genome instability.Current opinion in virology · 2013Review
- The intertwining of transposable elements and non-coding RNAs.International journal of molecular sciences · 2013Review
- Analysis of new functional profiles of protein isoforms yielded by ds exonization in rice.Evolutionary bioinformatics online · 2013Article
- Genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants.Evolutionary bioinformatics online · 2012Article
- The origins, evolution, and functional potential of alternative splicing in vertebrates.Molecular biology and evolution · 2011Article
- Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome.Nucleic acids research · 2010Article
- Article
- Overlapping splicing regulatory motifs--combinatorial effects on splicing.Nucleic acids research · 2010Article
- Alternative splicing and evolution: diversification, exon definition and function.Nature reviews. Genetics · 2010Review
- Genomic gems: SINE RNAs regulate mRNA production.Current opinion in genetics & development · 2010Review
- Transposable elements in disease-associated cryptic exons.Human genetics · 2010Article
- The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution.PLoS genetics · 2009Article
- An Alu-derived intronic splicing enhancer facilitates intronic processing and modulates aberrant splicing in ATM.Nucleic acids research · 2009Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exonization of Alu elements creates primate-specific genomic diversity. Here we combine bioinformatic and experimental methodologies to reconstruct the molecular changes leading to exon selection. Our analyses revealed an intricate network involved in Alu exonization. A typical Alu element contains multiple sites with the potential to serve as 5' splice sites (5'ss). First, we demonstrated the role of 5'ss strength in controlling exonization events. Second, we found that a cryptic 5'ss enhances the selection of a more upstream site and demonstrate that this is mediated by binding of U1 snRNA to the cryptic splice site, challenging the traditional role attributed to U1 snRNA of binding the 5'ss only. Third, we used a simple algorithm to identify specific sequences that determine splice site selection within specific Alu exons. Finally, by inserting identical exons within different sequences, we demonstrated the importance of flanking genomic sequences in determining whether an Alu exon will undergo exonization. Overall, our results demonstrate the complex interplay between at least four interacting layers that affect Alu exonization. These results shed light on the mechanism through which Alu elements enrich the primate transcriptome and allow a better understanding of the exonization process in general.
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