Expression, purification and characterization of the GpC methyltransferase M.CviPI v1

Methylation footprinting can be used to map protein-DNA contacts at the resolution of individual DNA molecules1. Enzymes with various nucleotide specificities have been successfully used to footprint genomes including GpC, CpG and A methyl-transfereases2–7. Among these M.CviPI methylate DNA in GpC context, that is distinct from CpGs that are endogenously methylated in mammals. This feature has been leveraged to profile nucleosome occupancy8,9; the binding of General Transcription Factors and RNA Pol II6; the co-occupancy of Transcription Factors (TFs)10 and the relation between TF binding and endogenous DNA methylation11. Here, we present a protocol for the production and purification of M.CviPI in E. coli. Our protocol routinely yields milligrams of protein at a quality and a concentration compatible with DNA footprinting applications. We characterize the purity and the activity of the purified enzyme, providing a benchmark for future production.