ArticleRNA (New York, N.Y.)2009
Splicing of designer exons reveals unexpected complexity in pre-mRNA splicing.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Article
- Deciphering RNA splicing logic with interpretable machine learning.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects.Nature reviews. Genetics · 2023Review
- Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer.RNA biology · 2023Review
- Article
- Processed pseudogene insertion in GLB1 causes Morquio B disease by altering intronic splicing regulatory landscape.NPJ genomic medicine · 2022Article
- Identification of splice defects due to noncanonical splice site or deep-intronic variants in ABCA4.Human mutation · 2019Article
- Ranking noncanonical 5' splice site usage by genome-wide RNA-seq analysis and splicing reporter assays.Genome research · 2018Article
- A small, portable RNA device for the control of exon skipping in mammalian cells.Nucleic acids research · 2018Article
- Activation of a cryptic 5' splice site reverses the impact of pathogenic splice site mutations in the spinal muscular atrophy gene.Nucleic acids research · 2017Article
- Analysis of Competing HIV-1 Splice Donor Sites Uncovers a Tight Cluster of Splicing Regulatory Elements within Exon 2/2b.Journal of virology · 2017Article
- Succession of splicing regulatory elements determines cryptic 5΄ss functionality.Nucleic acids research · 2017Article
- A purine-rich element in foamy virus pol regulates env splicing and gag/pol expression.Retrovirology · 2017Article
- Splicing of designer exons informs a biophysical model for exon definition.RNA (New York, N.Y.) · 2015Article
- Introns and gene expression: cellular constraints, transcriptional regulation, and evolutionary consequences.BioEssays : news and reviews in molecular, cellular and developmental biology · 2015Article
- Genomic HEXploring allows landscaping of novel potential splicing regulatory elements.Nucleic acids research · 2014Article
- Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans.RNA (New York, N.Y.) · 2011Article
- Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders.Nucleic acids research · 2011Article
- Nonsense mutation-associated Becker muscular dystrophy: interplay between exon definition and splicing regulatory elements within the DMD gene.Human mutation · 2011Article
- Stoichiometry of a regulatory splicing complex revealed by single-molecule analyses.The EMBO journal · 2010Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Pre-messengerRNA (mRNA) splicing requires the accurate recognition of splice sites by the cellular RNA processing machinery. In addition to sequences that comprise the branchpoint and the 3' and 5' splice sites, the cellular splicing machinery relies on additional information in the form of exonic and intronic splicing enhancer and silencer sequences. The high abundance of these motifs makes it difficult to investigate their effects using standard genetic perturbations, since their disruption often leads to the formation of yet new elements. To lessen this problem, we have designed synthetic exons comprised of multiple copies of a single prototypical exonic enhancer and a single prototypical exonic silencer sequence separated by neutral spacer sequences. The spacer sequences buffer the exon against the formation of new elements as the number and order of the original elements are varied. Over 100 such designer exons were constructed by random ligation of enhancer, silencer, and neutral elements. Each exon was positioned as the central exon in a 3-exon minigene and tested for exon inclusion after transient transfection. The level of inclusion of the test exons was seen to be dependent on the provision of enhancers and could be decreased by the provision of silencers. In general, there was a good quantitative correlation between the proportion of enhancers and splicing. However, widely varying inclusion levels could be produced by different permutations of the enhancer and silencer elements, indicating that even in this simplified system splicing decisions rest on complex interplays of yet to be determined parameters.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.