| Recently, new DNA modifications have been discovered in the mammalian genome, namely 5-hydroxymethylcytosine (5hmC), 5-formylcysotine (5fC) and 5-carboxylcytosine (5caC), which are supposedly related to epigenetic functions. We have been working on developing effective sequencing technologies to dissect the exact functional roles of these newly discovered DNA modifications by using selective chemical labeling and high-throughput DNA sequencing technologies. We have developed 5hmC selective chemical labeling (hMe-Seal) for genome-wide profiling of 5hmC; single-molecule real-time (SMRT)-Seal and Tet-assisted bisulfite sequencing (TAB-Seq) for base-resolution sequencing of 5hmC; 5fC selective chemical labeling (fC-Seal) for genome-wide profiling of 5fC; and 5fC chemically assisted bisulfite sequencing (fCAB-Seq) for base-resolution sequencing of 5fC. By applying these methods, we have studied the functions of these new mammalian DNA modifications as DNA demethylation intermediates as well as bona fide epigenetic marks with unique regulatory functions. Together our studies add to a more complete picture of the dynamic epigenetic regulatory network that plays critical roles in human development and disease. |
