So far it has been known that there are 4 epigenetic modifications of Cytosines. They are
1) Methylation (5mC)
2) Hydroxy methylation(5hmC)
4) carboxymethylation (5caC)
5mC modification has been well characterized but the rest of the modifications are not so well understood. Generally it has been seen that 6 modifications alter the structure of DNA making it F- DNA. All possible states that is both methylated and non- methylated are taken into consideration when working on the multiple epigenetic changes. Krawczyk K. et. al.(2017) have recently used Natural Move Monte Carlo method to in-silico assess the structure of DNA with epigenetic marks. Their technique also accurately works on finding the more energetically favourable state dependimg on the epigenetic signatures of the DNA.
The code can be found at the following URL: http://www.cs.ox.ac.uk/mosaics
Krawczyk K. et. al. (2017) In-Silico structural modelling of multiple epigenetic marks on DNA. Bioinformatics 34(1) 41-48.