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Proteome-wide quantitative RNA-interactome capture identifies phosphorylation sites with regulatory potential in RBM20.

Author information

Affiliations

  • 1. Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Humboldt-Universität zu Berlin, Faculty of Life Sciences, Unter den Linden 6, 10099 Berlin, Germany.
      Authors
    • Vieira-Vieira CH 1
    (1 author)
  • 2. Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany.
      Authors
    • Dauksaite V 2
    • Sporbert A 2
    (2 authors)
  • 3. Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.
      Authors
    • Gotthardt M 3
    (1 author)
  • 4. Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.
      Authors
    • Selbach M 4
    (1 author)

ORCIDs linked to this article

Molecular Cell, 14 Apr 2022, 82(11):2069-2083.e8
https://doi.org/10.1016/j.molcel.2022.03.024 PMID: 35427468 

This article is based on a previously available preprint.

Abstract 

Cellular mRNA-binding proteins (mRBPs) are major posttranscriptional regulators of gene expression. Although many posttranslational modification sites in mRBPs have been identified, little is known about how these modifications regulate mRBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of mRBPs pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and nonphosphorylated forms of mRBPs. Almost 200 phosphorylation events affected pull-down efficiency compared with the unmodified mRBPs and thus have regulatory potential. Our data capture known regulatory phosphorylation sites in ELAVL1, SF3B1, and UPF1 and identify potential regulatory sites. Follow-up experiments on the splicing regulator RBM20 revealed multiple phosphorylation sites in the C-terminal disordered region affecting nucleocytoplasmic localization, association with cytoplasmic ribonucleoprotein granules, and alternative splicing. Together, we show that qRIC in conjunction with phosphoproteomics is a scalable method to identify functional posttranslational modification sites in mRBPs.

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Read article at publisher's site: https://doi.org/10.1016/j.molcel.2022.03.024

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Funding 

Funders who supported this work.

Deutsche Forschungsgemeinschaft

    Fondation Leducq (1)