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Decoding protein methylation function with thermal stability analysis

Author

Listed:
  • Cristina Sayago

    (Proteomics Unit, Spanish National Cancer Research Centre (CNIO))

  • Jana Sánchez-Wandelmer

    (Proteomics Unit, Spanish National Cancer Research Centre (CNIO))

  • Fernando García

    (Proteomics Unit, Spanish National Cancer Research Centre (CNIO))

  • Begoña Hurtado

    (Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO)
    Cancer Cell Cycle group, Vall d’Hebron Institute of Oncology (VHIO))

  • Vanesa Lafarga

    (Genomic Instability Group, Spanish National Cancer Research Centre (CNIO))

  • Patricia Prieto

    (Mouse Genome Editing Unit, Spanish National Cancer Research Centre (CNIO))

  • Eduardo Zarzuela

    (Proteomics Unit, Spanish National Cancer Research Centre (CNIO))

  • Pilar Ximénez-Embún

    (Proteomics Unit, Spanish National Cancer Research Centre (CNIO))

  • Sagrario Ortega

    (Mouse Genome Editing Unit, Spanish National Cancer Research Centre (CNIO))

  • Diego Megías

    (Confocal Microscopy Unit, Spanish National Cancer Research Centre (CNIO))

  • Oscar Fernández-Capetillo

    (Genomic Instability Group, Spanish National Cancer Research Centre (CNIO))

  • Marcos Malumbres

    (Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO)
    Cancer Cell Cycle group, Vall d’Hebron Institute of Oncology (VHIO)
    Catalan Institution for Research and Advanced Studies (ICREA))

  • Javier Munoz

    (Proteomics Unit, Spanish National Cancer Research Centre (CNIO)
    Cell Signaling and Clinical Proteomics Group, Biocruces Bizkaia Health Research Institute
    Ikerbasque, Basque foundation for science)

Abstract

Protein methylation is an important modification beyond epigenetics. However, systems analyses of protein methylation lag behind compared to other modifications. Recently, thermal stability analyses have been developed which provide a proxy of a protein functional status. Here, we show that molecular and functional events closely linked to protein methylation can be revealed by the analysis of thermal stability. Using mouse embryonic stem cells as a model, we show that Prmt5 regulates mRNA binding proteins that are enriched in intrinsically disordered regions and involved in liquid-liquid phase separation mechanisms, including the formation of stress granules. Moreover, we reveal a non-canonical function of Ezh2 in mitotic chromosomes and the perichromosomal layer, and identify Mki67 as a putative Ezh2 substrate. Our approach provides an opportunity to systematically explore protein methylation function and represents a rich resource for understanding its role in pluripotency.

Suggested Citation

  • Cristina Sayago & Jana Sánchez-Wandelmer & Fernando García & Begoña Hurtado & Vanesa Lafarga & Patricia Prieto & Eduardo Zarzuela & Pilar Ximénez-Embún & Sagrario Ortega & Diego Megías & Oscar Fernánd, 2023. "Decoding protein methylation function with thermal stability analysis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38863-1
    DOI: 10.1038/s41467-023-38863-1
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    References listed on IDEAS

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    1. Dounia Djeghloul & Bhavik Patel & Holger Kramer & Andrew Dimond & Chad Whilding & Karen Brown & Anne-Céline Kohler & Amelie Feytout & Nicolas Veland & James Elliott & Tanmay A. M. Bharat & Abul K. Tar, 2020. "Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    2. André Mateus & Johannes Hevler & Jacob Bobonis & Nils Kurzawa & Malay Shah & Karin Mitosch & Camille V. Goemans & Dominic Helm & Frank Stein & Athanasios Typas & Mikhail M. Savitski, 2020. "The functional proteome landscape of Escherichia coli," Nature, Nature, vol. 588(7838), pages 473-478, December.
    3. Sindhuja Sridharan & Nils Kurzawa & Thilo Werner & Ina Günthner & Dominic Helm & Wolfgang Huber & Marcus Bantscheff & Mikhail M. Savitski, 2019. "Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
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