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Yeast Signaling01:28

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Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes (cells with a nucleus). Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule released from a yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases to activate or inactivate transcription factors that further regulate gene expression. Many of the yeast intracellular signaling cascades have similar...
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Delineating yeast cleavage and polyadenylation signals using deep learning.

Emily Kunce Stroup, Zhe Ji

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    Deep learning models reveal how yeast polyadenylation signals form. These models uncover distinct cis-regulatory elements governing polyA site selection and cleavage in Saccharomyces cerevisiae and Schizosaccharomyces pombe.

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    Area of Science:

    • Molecular Biology
    • Genomics
    • Bioinformatics

    Background:

    • 3'-end cleavage and polyadenylation is crucial for eukaryotic mRNA maturation.
    • Yeast polyadenylation signals are degenerate and poorly understood compared to mammalian systems.
    • Deep sequencing revealed cleavage heterogeneity and inter-species motif differences in yeast.

    Approach:

    • Developed deep learning models to analyze degenerate cis-regulatory elements.
    • Quantified the positional importance of elements in polyA site formation, cleavage heterogeneity, and strength.
    • Modeled distinct polyA site motifs in Saccharomyces cerevisiae and Schizosaccharomyces pombe.

    Key Points:

    • In S. cerevisiae, U-rich element depletion and upstream UA-rich elements drive cleavage heterogeneity.
    • High cleavage heterogeneity correlates with lower polyA site strength.
    • Alternative polyadenylation (APA) is modulated by site strength and tandem site distances under stress.
    • Distinct motif configurations explain more precise cleavage in S. pombe compared to S. cerevisiae.

    Conclusions:

    • Deep learning models provide novel insights into yeast polyadenylation signal formation.
    • The study elucidates mechanisms of cleavage heterogeneity and site strength regulation in yeast.
    • Identified species-specific differences in polyA site motif configurations between S. cerevisiae and S. pombe.