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U2-2 snRNA Mutations Alter the Transcriptome

Zhongxuan Chi, Varun Gupta, Charles Query

    Biorxiv : the Preprint Server for Biology
    |March 31, 2025
    PubMed

    Insights

    Mutations in U2-2 small nuclear RNA (snRNA) impact gene expression and splicing. Reduced U2-2 levels, like in knockout cells, significantly alter the transcriptome, influencing RNA processing pathways.

    Area of Science:

    • Molecular Biology
    • Genetics
    • RNA Biology

    Background:

    • The spliceosome, crucial for intron removal from pre-mRNA, is composed of snRNPs containing snRNAs.
    • U2 snRNA plays a vital role in splicing through RNA-RNA and RNA-protein interactions.
    • Mutations in U2 snRNA, especially at C28, are associated with cancer development.

    Purpose of the Study:

    • To investigate gene expression alterations caused by U2-2 snRNA mutations.
    • To compare the effects of U2-2 mutations versus U2-2 levels on splicing and gene expression.

    Main Methods:

    • Construction of U2-2 C28 mutant, knockout (KO), and overexpression (OE) cell lines.
    • RNA sequencing to analyze global gene expression changes.
    • Analysis of splicing patterns and differentially expressed genes.

    Main Results:

    • Knocking out U2-2 snRNA led to significant splicing changes and altered expression of over 4,000 genes.
    • Gene expression pathways related to RNA processing and non-coding RNAs were notably enriched.
    • Splicing patterns were more sensitive to U2-2 dosage than to mutations alone.

    Conclusions:

    • U2-2 snRNA mutations and altered levels significantly impact splicing and the transcriptome.
    • U2-2 knockout largely mimics the splicing alterations observed in U2-2 mutants.
    • Both U2-2 levels and specific mutations contribute to altered splicing, with many events potentially leading to nonsense-mediated decay (NMD).

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