ArticleBMC genomics2011
GC content around splice sites affects splicing through pre-mRNA secondary structures.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
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- Improving spliced alignment by modeling splice sites with deep learning.Algorithms for molecular biology : AMB · 2026Article
- BlendSplice: A Frequency-Blended Generative Framework forComputational and structural biotechnology journal · 2026Article
- Omics-based dissection of alternative splicing and the regulatory architecture in fungal genomes.Current research in microbial sciences · 2026Review
- INTS1 is required for maintaining accurate transcriptional integrity and behavior in zebrafish.NAR genomics and bioinformatics · 2025Article
- ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering.bioRxiv : the preprint server for biology · 2025Article
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- Molecular evolution of TRPC4 regulatory sequences supports a role in mammalian thermoregulatory adaptation.PeerJ · 2025Article
- Transcriptome-wide prediction of heat-sensitive RNA structures inFrontiers in plant science · 2025Article
- Alternative splicing drives a dynamic transcriptomic response duringMicrobial cell (Graz, Austria) · 2025Article
- Intronic RNA secondary structural information captured for the humanNAR genomics and bioinformatics · 2024Article
- Progerin mRNA expression in non-HGPS patients is correlated with widespread shifts in transcript isoforms.NAR genomics and bioinformatics · 2024Article
- RNA structure in alternative splicing regulation: from mechanism to therapy.Acta biochimica et biophysica Sinica · 2024Review
- RNA structure: implications in viral infections and neurodegenerative diseases.Advanced biotechnology · 2024Review
- PredictingbioRxiv : the preprint server for biology · 2024Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundAlternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (Homo sapiens), mice (Mus musculus), fruit flies (Drosophila melanogaster), and nematodes (Caenorhabditis elegans) to further investigate this phenomenon.
resultsWe observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures.
conclusionAll of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.
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