  The understanding of mechanisms that control epigenetic changes is an
important research area in modern functional biology. Epigenetic modifications
such as DNA methylation are in general very stable over many cell divisions.
DNA methylation can however be subject to specific and fast changes over a
short time scale even in non-dividing (i.e. not-replicating) cells. Such
dynamic DNA methylation changes are caused by a combination of active
demethylation and de novo methylation processes which have not been
investigated in integrated models. Here we present a hybrid (hidden) Markov
model to describe the cycle of methylation and demethylation over (short) time
scales. Our hybrid model decribes several molecular events either happening at
deterministic points (i.e. describing mechanisms that occur only during cell
division) and other events occurring at random time points. We test our model
on mouse embryonic stem cells using time-resolved data. We predict methylation
changes and estimate the efficiencies of the different modification steps
related to DNA methylation and demethylation.
