ArticleFrontiers in genetics2020
GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 24 citations in OpenAlex.
- A long first intron of PROS1 modulates protein S expression across tissues in mice and humans.Blood advances · 2026Article
- Metamorphosis and lncRNAs: A Close Relationship.Genesis (New York, N.Y. : 2000) · 2026Review
- The "cutting edge" of non-canonical RNA splicing.Frontiers in molecular biosciences · 2026Review
- Alternative splicing of the Snap23 microexon is regulated by MBNL, QKI, and RBFOX2 in a tissue-specific manner and is altered in striated muscle diseases.RNA biology · 2025Article
- A novel PADI6 splice-site variant induces non-canonical GC-AG splicing and embryonic arrest in humans.Functional & integrative genomics · 2025Article
- Long non-coding RNAs (lncRNAs) in cancer development: new insight from STAT3 signaling pathway to immune evasion.Clinical and experimental medicine · 2025Review
- CaTCH: Calculating transcript complexity of human genes.MethodsX · 2024Article
- Exitron splicing of odor receptor genes inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- The roles of lncRNAs in Th17-associated diseases, with special focus on JAK/STAT signaling pathway.Clinical and experimental medicine · 2023Review
- Distinct regulatory functions and biological roles of lncRNA splice variants.Molecular therapy. Nucleic acids · 2023Review
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
- Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse.RNA biology · 2023Article
- Introns: the "dark matter" of the eukaryotic genome.Frontiers in genetics · 2023Review
- Article
- DDX39B contributes to the proliferation of colorectal cancer through direct binding to CDK6/CCND1.Cell death discovery · 2022Article
- Analysis on the interactions between the first introns and other introns in mitochondrial ribosomal protein genes.Frontiers in microbiology · 2022Article
- Comparative genomics in the search for conserved long noncoding RNAs.Essays in biochemistry · 2021Article
- High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs.Epigenetics & chromatin · 2021Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long non-coding RNAs (lncRNAs) are recognized as an important class of regulatory molecules involved in a variety of biological functions. However, the regulatory mechanisms of long non-coding genes expression are still poorly understood. The characterization of the genomic features of lncRNAs is crucial to get insight into their function. In this study, we exploited recent annotations by GENCODE to characterize the genomic and splicing features of long non-coding genes in comparison with protein-coding ones, both in human and mouse. Our analysis highlighted differences between the two classes of genes in terms of their gene architecture. Significant differences in the splice sites usage were observed between long non-coding and protein-coding genes (PCG). While the frequency of non-canonical GC-AG splice junctions represents about 0.8% of total splice sites in PCGs, we identified a significant enrichment of the GC-AG splice sites in long non-coding genes, both in human (3.0%) and mouse (1.9%). In addition, we found a positional bias of GC-AG splice sites being enriched in the first intron in both classes of genes. Moreover, a significant shorter length and weaker donor and acceptor sites were found comparing GC-AG introns to GT-AG introns. Genes containing at least one GC-AG intron were found conserved in many species, more prone to alternative splicing and a functional analysis pointed toward their enrichment in specific biological processes such as DNA repair. Our study shows for the first time that GC-AG introns are mainly associated with lncRNAs and are preferentially located in the first intron. Additionally, we discovered their regulatory potential indicating the existence of a new mechanism of non-coding and PCGs expression regulation.
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