Prokaryotic vs prokaryotic genomes

List 3 differences between eukaryotic and prokaryotic genomes. Describe how one of these differences might impact laboratory applications. What are two issues that might arise when genetically engineering a prokaryotic cell to express a eukaryotic protein.

I know three differences are that prokaryotic cells do not have a nucleus or histones, and that their DNA is methylated. I don’t quite understand how that affects laboratory applications or the issues it would cause.