A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by SETMAR [DNA and Chromosomes]

March 20th, 2015 by Carlson, S. M., Moore, K. E., Sankaran, S. M., Elias, J. E., Gozani, O.

The lysine methyltransferase (KMT) SETMAR is implicated in response to and repair of DNA damage but its molecular function is not clear. More broadly, enzyme/substrate relationships are largely unknown for the dozens of predicted KMTs and hundreds or thousands of proteins modified by lysine methylation. SETMAR has been associated with di-methylation of histone H3 lysine 36 (H3K36) at sites of DNA damage. However, SETMAR does not methylate H3K36 in vitro. This and the observation that SETMAR is not active on nucleosomes suggest that H3K36 methylation is not a physiologically relevant activity. To identify potential non-histone substrates we utilized a strategy based on quantitative proteomic analysis of methylated lysine. Our approach identified lysine 130 (K130) of mRNA splicing factor snRNP70 as a SETMAR substrate in vitro, and we show that the enzyme primarily generates mono-methylation at this position. Further, we show that SETMAR methylates snRNP70 K130 in cells. As snRNP70 is a key early regulator of 5' splice site selection, our results suggest a model in which methylation of snRNP70 by SETMAR regulates constitutive and/or alternative splicing. In addition, the proteomic strategy described here is broadly applicable and is a promising route for large-scale mapping of KMT substrates.