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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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    Area of Science:

    • Molecular Biology
    • Genetics
    • Bioinformatics

    Background:

    • MicroRNAs (miRNAs) are key regulators of gene expression.
    • The mechanism determining which miRNA strand (5p or 3p) is preferentially used during biogenesis is not fully understood.
    • Understanding miRNA strand selection is crucial for deciphering gene regulation.

    Purpose of the Study:

    • To develop a comprehensive framework for understanding miRNA strand selection.
    • To identify the molecular rules governing the choice between miRNA 5p and 3p strands.
    • To create a predictive model for miRNA strand usage across different species.

    Main Methods:

    • Developed a high-throughput quantitative PCR (qPCR) platform for precise miRNA strand quantification in *Caenorhabditis elegans*.
    • Constructed a machine learning model trained on experimentally validated strand usage data.
    • Integrated 77 biologically informed features into the AI model for prediction.

    Main Results:

    • The developed framework accurately predicts miRNA strand preference in *C. elegans* and vertebrates, including humans.
    • Identified conserved compositional and structural biases influencing strand selection across species.
    • Demonstrated that miRNA strand selection is a regulated, context-dependent process, not random.

    Conclusions:

    • This study presents the first unified, generalizable model for miRNA strand selection.
    • The findings reveal a conserved, programmable layer of gene regulation governed by specific rules.
    • Open-access resources, including a database and predictive tools, are provided to the research community.