Just how many DNA bases can there possibly be? It was a pretty big deal when the 6th base, 5-hydroxymethylcytosine (5-hmC) was found in 2009, and now the same University of North Carolina team has discovered two more cytosine analogs to bring the total to eight…for now.
In the uproar over 5-hmC, researchers were sent scrambling harder than a Washington politician in a debt-ceiling negotiation to figure out its cellular role, and it was during that work that Yi Zhang, co-discoverer of 5-hmC, and his group unearthed the 7th and 8th bases.
From the start, researchers thought that 5-hmC, which is converted from 5-mC by Tet proteins, might be a way station on the road to DNA demethylation. But they couldn’t detect any other intermediates in this pathway. By manipulating restriction enzyme and thin-layer chromatography conditions, the UNC crew revealed two new flavors of cytosine that Tet proteins can produce from 5-mC: 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). They also showed that Tet proteins can perform these reactions in cells and even detected low levels of 5fC and 5caC in the genomic DNA of mouse embryonic stem cells.
Much like another known enzymatic pathway converts thymine to uracil, the researchers think that Tet proteins convert 5-mC to 5-hmC to 5fC to 5caC. Despite figuring out most of this demethylation mechanism, the scientists are still hunting for a missing enzyme that converts 5caC to unmethylated cytosine, which Tet proteins don’t seem capable of doing themselves.
See more about how the 7th and 8th bases were found at Science, July 2011.