DNA methylation occurs predominantly as covalent modification of cytosines within a CpG sequence context. It represents the most stable epigenetic mark and has an impact on different biological processes in both healthy and diseased cells, including e.g. neural cell differentiation 
. Large-scale DNA methylation profiling has demonstrated that tissue-specific differentially methylated regions (tDMRs) are highly correlated with cellular phenotypes 
Much effort has been made to understand the dynamics of DNA methylation during neural cell differentiation and the identification of epigenetic biomarkers that capture different aspects of cellular differentiation processes. ESCs are of particular interest in this context as they have previously been shown to acquire characteristic epigenetic marks during their differentiation from ESCs to NSCs and, subsequently, to tissues 
. Probably the best-known marker of neural cell differentiation is Pou5f1
(usually referred as Oct4
), encoding a homeobox protein essential in the maintenance of pluripotency 
. A tDMR at this gene is hypomethylated in ESCs and hypermethylated in NSCs and terminally differentiated tissues 
. In a recent targeted study, we reported a tDMR in the body of the Ddah2
gene to be an epigenetic biomarker for neural stem cell differentiation 
. Here, we conducted a genome-wide study to generate and analyze DNA methylation profiles of E.14 embryonic stem cells (ESCs) and in vitro
induced neural stem cells (NSCs), as well as 4 embryonic and 4 adult murine tissues using a custom mouse DMH array.
Numerous methods have been developed for genome-wide DNA methylation profiling 
. Among them, Differential Methylation Hybridization (DMH) allows the detection of tDMRs by digesting genomic DNA into a defined fragment library using first methylation-insensitive restriction enzymes, adaptor ligation, digestion of unmethylated template fragments using methylation-sensitive restriction enzymes, adaptor-mediated amplification and subsequent hybridization to microarrays 
. By coupling this technology to custom-designed arrays, genome-wide coverage of DNA methylation profiles can be achieved 
. Recently, we developed a mouse-specific DMH array that contains 51,243 features covering 17,384 genes and 16,656 promoter regions distributed across all chromosomes. Our results highlight the relevance of differential DNA methylation in neural cell differentiation and identify novel candidate markers for neural cell differentiation. Furthermore, as our data are compatible with a human-specific DMH array these results potentially enable an extrapolation to orthologous human genes.