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Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells

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  • Andreas R. Gruber

    (Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics)

  • Georges Martin

    (Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics)

  • Philipp Müller

    (University of Basel and University Hospital Basel, Hebelstrasse 20
    Infection Biology, Biozentrum, University of Basel)

  • Alexander Schmidt

    (Proteomics Core Facility, Biozentrum, University of Basel)

  • Andreas J. Gruber

    (Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics)

  • Rafal Gumienny

    (Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics)

  • Nitish Mittal

    (Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics)

  • Rajesh Jayachandran

    (Infection Biology, Biozentrum, University of Basel)

  • Jean Pieters

    (Infection Biology, Biozentrum, University of Basel)

  • Walter Keller

    (Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics)

  • Erik van Nimwegen

    (Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics)

  • Mihaela Zavolan

    (Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics)

Abstract

Alternative polyadenylation is a cellular mechanism that generates mRNA isoforms differing in their 3′ untranslated regions (3′ UTRs). Changes in polyadenylation site usage have been described upon induction of proliferation in resting cells, but the underlying mechanism and functional significance of this phenomenon remain largely unknown. To understand the functional consequences of shortened 3′ UTR isoforms in a physiological setting, we used 3′ end sequencing and quantitative mass spectrometry to determine polyadenylation site usage, mRNA and protein levels in murine and human naive and activated T cells. Although 3′ UTR shortening in proliferating cells is conserved between human and mouse, orthologous genes do not exhibit similar expression of alternative 3′ UTR isoforms. We generally find that 3′ UTR shortening is not accompanied by a corresponding change in mRNA and protein levels. This suggests that although 3′ UTR shortening may lead to changes in the RNA-binding protein interactome, it has limited effects on protein output.

Suggested Citation

  • Andreas R. Gruber & Georges Martin & Philipp Müller & Alexander Schmidt & Andreas J. Gruber & Rafal Gumienny & Nitish Mittal & Rajesh Jayachandran & Jean Pieters & Walter Keller & Erik van Nimwegen & , 2014. "Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells," Nature Communications, Nature, vol. 5(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6465
    DOI: 10.1038/ncomms6465
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    Cited by:

    1. Timofey A. Karginov & Antoine Ménoret & Anthony T. Vella, 2022. "Optimal CD8+ T cell effector function requires costimulation-induced RNA-binding proteins that reprogram the transcript isoform landscape," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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