Almost every cell in an organism contains the identical DNA sequence; yet different tissues transcribe unique sets of genes. Differences in transcription are mediated in part through epigenetic marks including DNA methylation and histone modifications. Epigenetic regulation is also important for heritable silencing of transcription at transposons, repeated sequences and the inactive X chromosome. Altered epigenetic profiles lead to abnormal development and are almost always detected in cancer genomes. We are interested in understanding the mechanisms of epigenetic regulation and their roles in vertebrate development with a primary focus on the DNA modification, 5-methylcytosine.