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Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences

Author

Listed:
  • Volker Boehm

    (Institute for Genetics, University of Cologne)

  • Jennifer V. Gerbracht

    (Institute for Genetics, University of Cologne)

  • Marie-Charlotte Marx

    (Institute for Genetics, University of Cologne)

  • Niels H. Gehring

    (Institute for Genetics, University of Cologne)

Abstract

The turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5′–3′ mRNA decay. In tethering assays, monitoring xrFrag accumulation allows to distinguish decapping and endocleavage activities from deadenylation. Moreover, xrFrag analysis of mRNA degradation induced by miRNAs, AU-rich elements (AREs) as well as the 3′ UTRs of cytokine mRNAs reveals the contribution of 5′–3′ decay and endonucleolytic cleavage. Our work uncovers formerly unrecognized modes of mRNA turnover and establishes xrFrag as a powerful tool for RNA decay analyses.

Suggested Citation

  • Volker Boehm & Jennifer V. Gerbracht & Marie-Charlotte Marx & Niels H. Gehring, 2016. "Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences," Nature Communications, Nature, vol. 7(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13691
    DOI: 10.1038/ncomms13691
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    Cited by:

    1. Xiaolin Niu & Ruirui Sun & Zhifeng Chen & Yirong Yao & Xiaobing Zuo & Chunlai Chen & Xianyang Fang, 2021. "Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs," Nature Communications, Nature, vol. 12(1), pages 1-14, December.

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