ArticleNucleic acids research2009
Modulation of alternative splicing by long-range RNA structures in Drosophila.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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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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Who cites it
38 citing papers in PubMed, 72 citations in OpenAlex.
- An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal.Nucleic acids research · 2026Article
- MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS) regulates long-range alternative splicing in Drosophila.Nucleic acids research · 2026Article
- Article
- Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states.Cell chemical biology · 2024Review
- Impact on splicing inRNA (New York, N.Y.) · 2023Article
- The Cynosure of CtBP: Evolution of a Bilaterian Transcriptional Corepressor.Molecular biology and evolution · 2023Article
- LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods.Bioinformatics advances · 2022Article
- Improved recognition of splice sites in3 Biotech · 2021Article
- Conserved long-range base pairings are associated with pre-mRNA processing of human genes.Nature communications · 2021Article
- Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing.Molecular cell · 2021Article
- Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control.International journal of molecular sciences · 2020Review
- MicroRNA miR-1002 Enhances NMNAT-Mediated Stress Response by Modulating Alternative Splicing.iScience · 2019Article
- Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay.Nucleic acids research · 2019Article
- Article
- Review
- Introns provide a platform for intergenic regulatory feedback of RPL22 paralogs in yeast.PloS one · 2018Article
- The identification and functional annotation of RNA structures conserved in vertebrates.Genome research · 2017Article
- RNA structure in splicing: An evolutionary perspective.RNA biology · 2016Review
- The Conservation and Function of RNA Secondary Structure in Plants.Annual review of plant biology · 2016Review
- Staufen1 Regulates Multiple Alternative Splicing Events either Positively or Negatively in DM1 Indicating Its Role as a Disease Modifier.PLoS genetics · 2016Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Accurate and efficient recognition of splice sites during pre-mRNA splicing is essential for proper transcriptome expression. Splice site usage can be modulated by secondary structures, but it is unclear if this type of modulation is commonly used or occurs to a significant degree with secondary structures forming over long distances. Using phlyogenetic comparisons of intronic sequences among 12 Drosophila genomes, we elucidated a group of 202 highly conserved pairs of sequences, each at least nine nucleotides long, capable of forming stable stem structures. This set was highly enriched in alternatively spliced introns and introns with weak acceptor sites and long introns, and most occurred over long distances (>150 nucleotides). Experimentally, we analyzed the splicing of several of these introns using mini-genes in Drosophila S2 cells. Wild-type splicing patterns were changed by mutations that opened the stem structure, and restored by compensatory mutations that re-established the base-pairing potential, demonstrating that these secondary structures were indeed implicated in the splice site choice. Mechanistically, the RNA structures masked splice sites, brought together distant splice sites and/or looped out introns. Thus, base-pairing interactions within introns, even those occurring over long distances, are more frequent modulators of alternative splicing than is currently assumed.
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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.