The Curious Chemical Biology of Cytosine: Deamination, Methylation and Oxidation as Modulators of Genomic Potential

In poker, the rules of the game can occasionally change. Adding a “wild card” to the mix introduces a new degree of variety and presents opportunities for a skilled player to steal the pot. Given that evolution is governed by the same principles of risk and reward that are common to a poker game, it is perhaps not surprising that a genomic “wild card” has an integral role in biology. In the conventional view, the genome is a long polymer of A, C, G and T, which together define and differentiate organisms. However, it is increasingly clear that diversity within an organism is often governed by dynamic changes that take place within this scaffold (1). Here, we make the case that cytosine is the key residue that has taken on the role of genomic “wild card” in DNA. In particular, enzymes that chemically modify cytosine introduce a physiologically important layer of complexity to the genome, beyond that seen in the primary sequence. Remarkably, modifications of every single position in the nucleobase of purines or pyrimidines in RNA have been described (2). Cytosine, for example, can be deaminated or methylated in many different non-coding RNAs to regulate various aspects of protein translation (3, 4). The mechanisms and physiologic significance of RNA cytosine modification have been discussed elsewhere and their scope continues to expand (5, 6, 7). It is striking that relative to RNA, modifications of nucleobases within genomic DNA have been comparatively underappreciated. In this review, we examine the curious chemistry of cytosine and the DNA modifying enzymes that change its identity (Figure 1). We begin by examining the non-canonical ways in which genomic DNA fosters adaptability and variety. To understand how cytosine is the key to generating this genomic flexibility, we describe nature’s toolbox of enzymes for modifying the nucleobase and its analogs. Numerous modifications beyond cytosine methylation are now coming to the fore, including cytosine deamination, oxidation and demethylation. We examine the common thread that runs through these modifications: by influencing the identity of cytosine, a new degree of variety can be produced. Figure 1 Cytosine as the Genomic “Wild Card”