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Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture

Author

Listed:
  • Joel I. Perez-Perri

    (European Molecular Biology Laboratory (EMBL))

  • Birgit Rogell

    (European Molecular Biology Laboratory (EMBL))

  • Thomas Schwarzl

    (European Molecular Biology Laboratory (EMBL))

  • Frank Stein

    (European Molecular Biology Laboratory (EMBL))

  • Yang Zhou

    (European Molecular Biology Laboratory (EMBL)
    Molecular Medicine Partnership Unit (MMPU)
    Heidelberg University)

  • Mandy Rettel

    (European Molecular Biology Laboratory (EMBL))

  • Annika Brosig

    (European Molecular Biology Laboratory (EMBL)
    Molecular Medicine Partnership Unit (MMPU)
    Heidelberg University
    Heidelberg University)

  • Matthias W. Hentze

    (European Molecular Biology Laboratory (EMBL)
    Molecular Medicine Partnership Unit (MMPU))

Abstract

Following the realization that eukaryotic RNA-binding proteomes are substantially larger than anticipated, we must now understand their detailed composition and dynamics. Methods such as RNA interactome capture (RIC) have begun to address this need. However, limitations of RIC have been reported. Here we describe enhanced RNA interactome capture (eRIC), a method based on the use of an LNA-modified capture probe, which yields numerous advantages including greater specificity and increased signal-to-noise ratios compared to existing methods. In Jurkat cells, eRIC reduces the rRNA and DNA contamination by >10-fold compared to RIC and increases the detection of RNA-binding proteins. Due to its low background, eRIC also empowers comparative analyses of changes of RNA-bound proteomes missed by RIC. For example, in cells treated with dimethyloxalylglycine, which inhibits RNA demethylases, eRIC identifies m6A-responsive RNA-binding proteins that escape RIC. eRIC will facilitate the unbiased characterization of RBP dynamics in response to biological and pharmacological cues.

Suggested Citation

  • Joel I. Perez-Perri & Birgit Rogell & Thomas Schwarzl & Frank Stein & Yang Zhou & Mandy Rettel & Annika Brosig & Matthias W. Hentze, 2018. "Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06557-8
    DOI: 10.1038/s41467-018-06557-8
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    Cited by:

    1. Yang Zhou & Partho Sarothi Ray & Jianguo Zhu & Frank Stein & Mandy Rettel & Thileepan Sekaran & Sudeep Sahadevan & Joel I. Perez-Perri & Eva K. Roth & Ola Myklebost & Leonardo A. Meza-Zepeda & Andreas, 2024. "Systematic analysis of RNA-binding proteins identifies targetable therapeutic vulnerabilities in osteosarcoma," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    2. Andrew J. Heindel & Jeffrey W. Brulet & Xiantao Wang & Michael W. Founds & Adam H. Libby & Dina L. Bai & Michael C. Lemke & David M. Leace & Thurl E. Harris & Markus Hafner & Ku-Lung Hsu, 2023. "Chemoproteomic capture of RNA binding activity in living cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Johanna Luige & Alexandros Armaos & Gian Gaetano Tartaglia & Ulf Andersson Vang Ørom, 2024. "Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. JohnCarlo Kristofich & Christopher V. Nicchitta, 2023. "Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics," Nature Communications, Nature, vol. 14(1), pages 1-20, December.

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