We acknowledge that early embryo culture systems do not allow for the evaluation tissue- or cell type-specific change in methylation levels; rather, the results represent an average across embryo cell types and tissues. In this regard, the current analysis does not address methylation changes in genes that may be hypomethylated in one cell type and hypermethylated in another in the same probe regions.64 While the whole-embryo approach is likely to be less sensitive for identifying methylation changes in a very small number of cells, our results clearly demonstrate that it is sufficiently sensitive for identifying small methylation changes in a large number of cells types (discussed above for different genes). To address these and other important issues, our future investigations will include tissue-specific studies of DNA methylation profiling and histone modification. Furthermore, the current approach concentrates on interrogating potential changes in DNA methylation around promoter regions, while distal regulatory elements (enhancer, insulator, intergene and non-code sequence regions) are not included. However, in our future investigations, we will extend the analysis to distal regulatory elements using next-generation, massive parallel-sequencing approaches and
