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A Mammalian Genomic Signature Shaped by Single Nucleotide Variants Controlling Transcriptome Integrity and Diversity.

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    A newly identified genomic signature, G-tract-AG motifs, is linked to genetic variants affecting gene splicing. Disruption of these motifs by single-nucleotide variants (SNVs) alters transcript isoforms and can lead to genetic diseases.

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Genetics

    Background:

    • Mammalian genomic sequences possess many poorly understood functional features.
    • Genomic signatures play crucial roles in maintaining transcriptome integrity and diversity.

    Purpose of the Study:

    • To identify and characterize a novel genomic signature associated with genetic variants.
    • To elucidate the functional mechanism of this signature in gene splicing and its link to genetic diseases.

    Main Methods:

    • Identification of G-tract-AG motifs across mammalian genomes.
    • Analysis of associations between G-tract-AG motifs and single-nucleotide variants (SNVs) from genome-wide association studies (GWAS).
    • Functional assays to determine the role of G-tracts in splicing regulation using data from the Genotype-Tissue Expression (GTEx) project.

    Main Results:

    • A widely evolved genomic signature, G-tract-AG motifs (guanine tracts upstream of AG dinucleotides), was identified.
    • These motifs are significantly associated with SNVs, especially in non-coding regions (NCRs).
    • G-tracts repress splicing at the adjacent 3'AG by stalling the second transesterification step; SNVs disrupting G-tracts relieve this repression, generating novel transcript isoforms.
    • Thousands of human G-tracts are disrupted by splicing quantitative trait loci (sQTLs), with G-tract-disrupting SNVs found in cis across most protein-coding genes and linked to genetic diseases.

    Conclusions:

    • G-tract-AG motifs represent a mammalian-evolved genomic signature crucial for maintaining transcriptome integrity.
    • Disruption of these motifs by SNVs provides mechanistic insights into transcript diversity and the etiology of genetic diseases.
    • This study offers a new framework for the functional annotation of non-coding region SNVs associated with various traits.