Identification with SILAC Proteomics of Novel Short Linear Motifs in Demethylase Enzymes Regulated During Myoblast Differentiation

Abstract

Methylation and demethylation of Lysine and Arginine on proteins is quantitatively an extensive and functionally a significant post-translational modification yet there is a dearth of information at a functional systems level. Using SILAC proteomics and high resolution mass spectrometry we have identified eight demethylase and two methylase proteins whose levels are regulated during myogenic differentiation in a mouse myoblast-to-myocyte model. Using the general methylation inhibitor adenosine dialdehyde (AdOX) we established that methylation is required for differentiation. Whole proteome analysis revealed that 1134 out of 4600 proteins identified were differentially expressed, of which 488 were up-regulated and 646 down-regulated. Of these, two were methylases and eight were demethylases. Notably, five of the eight enzymes demethylate Lysine 9 on histone 3 (H3K9) whereas two also demethylate H3K4. Lastly, we have identified short linear motifs (SliMs) in the demethylase enzymes that are enriched in differentiation. We briefly discuss the significance of our findings within a developmental/epigenomics framework.