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  • Data for Impact of Acute Endurance Exercise on Alternative Splicing in Skeletal Muscle

    work
    Creator:
    Ludlow, Andrew and Ahn, Alexander
    Description:
    Publicly accessible short-read RNA sequencing (SRS) of clinical exercise studies were extracted from the Gene Expression Omnibus. Oxford Nanopore long-read RNA sequencing (LRS) was performed on mouse gastrocnemius before and following treadmill exercise. Differential gene expression (DGE), differential alternative splicing (DAS), and differential isoform expression (DIE) were analyzed. Gel-based/droplet digital RT-PCR and western blots were performed to validate expression changes of select genes. Both SRS and LRS illustrated significant DGE in skeletal muscle post-exercise, whereby 89 RBPs were significantly up-/down-regulated. rMATS analysis of SRS data revealed that exon-skipping and intron-retaining splicing events were the most common. Swan analysis of LRS data revealed 61 RBPs with significant isoform switching: one of these RBPs, mHnrnpa3, underwent a significant non-coding to protein-coding switch. HnRNP-A3 protein levels validated nearly two-fold increases at 1 hour and 24 hours post-exercise.
    Keyword:
    Alternative splicing and Exercise
    Citation to related publication:
    Impact of Acute Endurance Exercise on Alternative Splicing in Skeletal Muscle. Alexander Ahn, Jeongjin J. Kim, Aaron L. Slusher, Jeffrey Y. Ying, Eric Y. Zhang, Andrew T. Ludlow bioRxiv 2024.11.21.624690; doi:  https://doi.org/10.1101/2024.11.21.624690
    Discipline:
    Health Sciences

  • Data for Discovery and characterization of a novel telomerase alternative splicing isoform that protects lung cancer cells from chemotherapy induced cell death.

    work
    Creator:
    Ludlow, Andrew
    Description:
    Single molecule long read RNA/cDNA sequencing of TERT revealed 45 TERT mRNA variants including 13 known and 32 novel variants. Among the variants, TERT Delta 2-4, which lacks exons 2-4 but retains the original open reading frame, was selected for further study. Induced pluripotent stem cells and cancer cells express higher levels of TERT Delta 2-4 compared to primary human bronchial epithelial cells. Overexpression of TERT Delta 2-4 enhanced clonogenicity and resistance to cisplatin-induced apoptosis. Knockdown of endogenous TERT Delta 2-4 in Calu-6 cells reduced clonogenicity and resistance to cisplatin. Our results suggest that TERT Delta 2-4 enhances cancer cells’ resistance to intrinsic apoptosis. RNA sequencing following knockdown of Delta 2-4 TERT indicates that translation is downregulated and that mitochondrial related proteins are upregulated compared to controls.
    Keyword:
    TERT, Alternative splicing, Telomere, and Telomerase
    Citation to related publication:
    Kim, J.J., Ahn, A., Ying, J.Y. et al. Discovery and characterization of a novel telomerase alternative splicing isoform that protects lung cancer cells from chemotherapy induced cell death. Sci Rep 15, 6787 (2025).  https://doi.org/10.1038/s41598-025-90639-3
    Discipline:
    Science