DNA oxidative demethylase

DNA oxidative demethylases belong under the broader category of Fe(II)/α-ketoglutarate-dependent dioxygenase enzyme family. This is a class of enzymes catalyze oxidative reactions that remove methyl groups from DNA bases, thereby reversing DNA methylation modifications. These enzymes are share characteristics such as the iron-binding motif His1-X-Asp/Glu-Xn-His2, which is the catalytic site for oxygen activation. Additionally, the active site of all Fe(II)/α-ketoglutarate-dependent dioxygenase enzymes contains a double-stranded β-helix (DSBH) fold. AlkB was discovered in 1977 by Samson and Cairns in E. coli cells. The TET (ten-eleven translocation) proteins play an important role in epigenetic regulation of the cell by catalyzing iterative oxidative demethylation steps of the epigenetic mark 5-methylcytosine (5mC). == Structure and mechanism ==

DNA oxidative demethylases operate through several mechanisms that oxidize the methyl group to achieve DNA demethylation. The methyl group is both chemically and genetically stable as it is connected to the cystine in a carbon-carbon bond. This creates a barrier for the removal of the methyl group and a need for enzymes like DNA oxidative demethylase. • Additional processing (as needed): For 5-methylcytosine iterative oxidations are needed instead of one-step removal. This is facilitated by TET that converts 5mC -> 5hmC -> 5fC -> 5caC. == Function ==

DNA methylation can modify but also damage DNA when dysregulated leading to various human diseases including cancer. DNA oxidative demethylation serves a major role in DNA repair and epigenetic regulation by protecting from mutations and genomic instability. Additionally, fumarate and succinate, which are other metabolic intermediates, are also similar in structure to αKG. They are competitive inhibitors of Fe(II)/αKG-dependent dioxygenases. == Clinical relevance ==

TET proteins have been shown to play a role in hematological cancer. TET2 mutations are often early events in cancer evolution and increase a patient's risk of developing blood cancers. For example, TET2 mutations are observed in 20%-58% of patients with Chronic Myelomonocytic Leukemia (CMML), 20%-83% with T-cell lymphomas, and are associated with many more blood cancers. TET2 mutations are not unique to a disease subtype but instead involved in many disease processes in ways still not fully understood. Studying diseases associated with DNA oxidative demethylation knockouts can give further insight on the function of the enzymes. In knockouts, the enzymes are absent or impaired. Studies using mouse embryonic stem cells (ESCs) have provided insight into the functional roles of DNA oxidative demethylases, particularly the TET family proteins. Loss of TET1 in ESCs skews differentiation toward specific lineages. Similarly, loss of TET2 delays enhancer activation and slows transcriptional changes during differentiation. TET1/2/3 triple knockouts severely impairs the normal differentiation process, leading to widespread dysregulation of gene expression, although some pluripotency markers remain intact. == References ==