  DNA methylation is an epigenetic mechanism whose important role in
development has been widely recognized. This epigenetic modification results in
heritable changes in gene expression not encoded by the DNA sequence. The
underlying mechanisms controlling DNA methylation are only partly understood
and recently different mechanistic models of enzyme activities responsible for
DNA methylation have been proposed. Here we extend existing Hidden Markov
Models (HMMs) for DNA methylation by describing the occurrence of spatial
methylation patterns over time and propose several models with different
neighborhood dependencies. We perform numerical analysis of the HMMs applied to
bisulfite sequencing measurements and accurately predict wild-type data. In
addition, we find evidence that the enzymes' activities depend on the left 5'
neighborhood but not on the right 3' neighborhood.
