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CAPRI enables comparison of evolutionarily conserved RNA interacting regions

Author

Listed:
  • Amol Panhale

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Florian M. Richter

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Fidel Ramírez

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Maria Shvedunova

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Thomas Manke

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Gerhard Mittler

    (Max Planck Institute of Immunobiology and Epigenetics)

  • Asifa Akhtar

    (Max Planck Institute of Immunobiology and Epigenetics)

Abstract

RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence.

Suggested Citation

  • Amol Panhale & Florian M. Richter & Fidel Ramírez & Maria Shvedunova & Thomas Manke & Gerhard Mittler & Asifa Akhtar, 2019. "CAPRI enables comparison of evolutionarily conserved RNA interacting regions," Nature Communications, Nature, vol. 10(1), pages 1-22, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10585-3
    DOI: 10.1038/s41467-019-10585-3
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    Cited by:

    1. Aditya Kshirsagar & Svetlana Maslov Doroshev & Anna Gorelik & Tsviya Olender & Tamar Sapir & Daisuke Tsuboi & Irit Rosenhek-Goldian & Sergey Malitsky & Maxim Itkin & Amir Argoetti & Yael Mandel-Gutfre, 2023. "LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    2. Anna Knörlein & Chris P. Sarnowski & Tebbe Vries & Moritz Stoltz & Michael Götze & Ruedi Aebersold & Frédéric H.-T. Allain & Alexander Leitner & Jonathan Hall, 2022. "Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Huijuan Feng & Xiang-Jun Lu & Suvrajit Maji & Linxi Liu & Dmytro Ustianenko & Noam D. Rudnick & Chaolin Zhang, 2024. "Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    4. Jong Woo Bae & Sangtae Kim & V. Narry Kim & Jong-Seo Kim, 2021. "Photoactivatable ribonucleosides mark base-specific RNA-binding sites," Nature Communications, Nature, vol. 12(1), pages 1-10, December.

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