A General Molecular Affinity Strategy for Global Detection and Proteomic Analysis of Lysine Methylation

• Published in: Molecular cell 2013-05, Vol.50 (3), p.444-456
• Main Authors: Moore, Kaitlyn E., Carlson, Scott M., Camp, Nathan D., Cheung, Peggie, James, Richard G., Chua, Katrin F., Wolf-Yadlin, Alejandro, Gozani, Or
• Format: Article
• Language: English
• Subjects: Animals; Cell Line; chromatin; HEK293 Cells; histones; Humans; Insecta; lysine; Lysine - genetics; Lysine - metabolism; Methylation; methyltransferases; Protein Structure, Tertiary; Proteome - genetics; Proteome - metabolism; proteomics; Proteomics - methods; quantitative analysis; Sf9 Cells; Sirtuin 1 - genetics; Sirtuin 1 - metabolism
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2013.03.005

Lysine methylation of histone proteins regulates chromatin dynamics and plays important roles in diverse physiological and pathological processes. However, beyond histone proteins, the proteome-wide extent of lysine methylation remains largely unknown. We have engineered the naturally occurring MBT domain repeats of L3MBTL1 to serve as a universal affinity reagent for detecting, enriching, and identifying proteins carrying a mono- or dimethylated lysine. The domain is broadly specific for methylated lysine (“pan-specific”) and can be applied to any biological system. We have used our approach to demonstrate that SIRT1 is a substrate of the methyltransferase G9a both in vitro and in cells, to perform proteome-wide detection and enrichment of methylated proteins, and to identify candidate in-cell substrates of G9a and the related methyltransferase GLP. Together, our results demonstrate a powerful new approach for global and quantitative analysis of methylated lysine, and they represent the first systems biology understanding of lysine methylation. ► 3xMBT domain is a “pan-specific” tool for detecting mono- and dimethylated lysine ► 3xMBT allows for rapid analysis of methylated proteins in vitro and in vivo ► Proteomic analysis shows that lysine methylation occurs widely across the proteome ► A cell-based proteomic assay allows global analysis of dynamic lysine methylation