Decoding protein methylation function with thermal stability analysis

Cristina Sayago, Jana Sánchez-Wandelmer, Fernando García, Begoña Hurtado, Vanesa Lafarga, Patricia Prieto, Eduardo Zarzuela, Pilar Ximénez-Embún, Sagrario Ortega, Diego Megías, Oscar Fernández-Capetillo, Marcos Malumbres and Javier Munoz ()
Additional contact information
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)
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)
Javier Munoz: Proteomics Unit, Spanish National Cancer Research Centre (CNIO)

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-38863-1

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