Epigenetics. The code of life is more than a sequence of A’s, C’s, T’s, and G’s. Heart cells in the human body contain the same DNA as skin cells in the foot, yet these two cell types behave in radically different ways. Both contain the DNA for every one of over 20,000 human genes but express only the ones needed for their own form and function. These differences are due to epigenetic controls. Epigenetics refers to any regulation of gene expression and phenotype that is not based on the sequence of bases in DNA. In addition to governing cellular differentiation, epigenetic mechanisms facilitate the proper functioning of a cell. When these mechanisms go awry, neurodevelopmental disorders, immunodeficiency, and cancer can result. Epigenetic phenomena are amongst the primary ways gene expression is regulated; yet, our current understanding of them is limited, especially due to the challenge of studying them in noisy mammalian systems. By virtue of its emphasis on the isolation and testing of biological networks in engineered systems with reduced complexity, synthetic biology offers the promise of fostering understanding of phenomena difficult to study in their native environments. It is thus an ideal forum for epigenetic studies. At its core, synthetic biology also involves the engineering of non-native networks for useful purposes. Well-tuned gene expression is essential to the proper functioning of synthetic biological circuitry, yet epigenetics has not yet been fully explored as a tool for this application.

DNA Methylation. DNA methylation is one of the most prominent and powerful mechanisms of epigenetic control. In mammals, enzymes called methyltransferases catalyze the addition of methyl groups to cytosines in CpG sites (a cytosine next to a guanine); these sites are abundant throughout the human genome (Venter 2001). Methylated cytosines in CpG sites can block transcription factors from binding to DNA and repress gene expression (Jones 1998 and Nan 1998). Although epigenetic factors do not affect genotype, they do affect phenotype. Specific methylation patterns are necessary for healthy development and disruption of methylation patterns has been shown to lead to many diseases (Cooper 1988, Rideout III 1990, Baylin 1998, Jones 1999, and Amir 1999).