Biological systems respond to extracellular and intracellular signals in myriad ways by activating diverse signaling pathways. Reversible covalent post-translational modifications (PTMs) such as phosphorylation, acetylation and methylation are critical modulators of these signaling pathways. While phosphorylation is the most extensively studied PTM, lysine methylation is emerging as a key player in regulating intracellular signaling pathways. The methylation of lysine residues is performed by protein lysine (K) methyltransferases (PKMTs). It is estimated that in the human proteome there are ~50 PKMT and greater than 25 demethylases (PKDMs) which can reverse the process and remove the methyl mark away. A lysine residue can be mono, di or tri methylated.

The degree of methylation is enzyme specific and can define a distinct biological outcome by recruiting specialized regulatory factor, named “readers” that specifically recognize distinct modification in a state (degree of methylation) and in a sequence dependent manner.

In recent years, lysine methylation has been studied in depth in the context of histones. However, there is a growing appreciation that non-histone proteins are also subjected to lysine methylation with a clear role in the regulation of oncogenic and cell differentiation processes. Most studies aiming to identify lysine methylation events have focused on only a few target proteins via a candidate-based approach. We have developed a unique proteomic methodology to identify new substrates for different PKMTs.

Using a ProtoArray-based proteomic platform, we demonstrated that more than 9500 unique substrates can be screened in a single experiment in a reproducible and efficient manner (Levy et al, Epigenetics & Chromatin, 2011). Employing this system, we identified 118 new targets for SETD6 and 321 substrates for the related PKMT SETD7. As part of our research program, we will continue to harness and develop protein and peptide array proteomic tools towards the goal of understanding how novel methylation signaling networks impact cancer pathways and cell differentiation programs.