Proteome-wide Prediction of Lysine Methylation Leads to Identification of H2BK43 Methylation and Outlines the Potential Methyllysine Proteome
Kyle K. Biggar,
Francois Charih,
Huadong Liu,
Yasser B. Ruiz-Blanco,
Leanne Stalker,
Anand Chopra,
Justin Connolly,
Hemanta Adhikary,
Kristin Frensemier,
Matthew Hoekstra,
Marek Galka,
Qi Fang,
Christopher Wynder,
William L. Stanford,
James R. Green,
Shawn S.-C. Li
Affiliations
Kyle K. Biggar
Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
Francois Charih
Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; Systems and Computer Engineering, Carleton University, Ottawa, ON K1S 5BS, Canada
Huadong Liu
Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
Yasser B. Ruiz-Blanco
Systems and Computer Engineering, Carleton University, Ottawa, ON K1S 5BS, Canada; Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg, Essen, Germany
Leanne Stalker
Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
Anand Chopra
Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
Justin Connolly
Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
Hemanta Adhikary
Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
Kristin Frensemier
Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
Matthew Hoekstra
Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
Marek Galka
Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
Qi Fang
Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
Christopher Wynder
Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
William L. Stanford
Ottawa Hospital Research Institute, Sprott Center for Stem Cell Research, Ottawa, ON K1H 8L6, Canada
James R. Green
Systems and Computer Engineering, Carleton University, Ottawa, ON K1S 5BS, Canada
Shawn S.-C. Li
Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada; Corresponding author
Summary: Protein Lys methylation plays a critical role in numerous cellular processes, but it is challenging to identify Lys methylation in a systematic manner. Here we present an approach combining in silico prediction with targeted mass spectrometry (MS) to identify Lys methylation (Kme) sites at the proteome level. We develop MethylSight, a program that predicts Kme events solely on the physicochemical properties of residues surrounding the putative methylation sites, which then requires validation by targeted MS. Using this approach, we identify 70 new histone Kme marks with a 90% validation rate. H2BK43me2, which undergoes dynamic changes during stem cell differentiation, is found to be a substrate of KDM5b. Furthermore, MethylSight predicts that Lys methylation is a prevalent post-translational modification in the human proteome. Our work provides a useful resource for guiding systematic exploration of the role of Lys methylation in human health and disease.
