The Sixth Base: 5-hydroxymethylcytosine enriched in mammalian brains

[ECO]

This is undoubtedly a big finding that will cause all sorts of controversy and reevaluation of theories of epigenetics. Not to mention that it's probably of interest to the sequencing community that there is a sixth base to worry about!

Skirmantas Kriaucionis of the Heintz lab at the Rockefeller University has just published a paper in Science which describes the discovery of yet another modified cytosine nucleotide, 5-hydroxymethylcytosine, which seems particularly enriched in neuronal cells. A partner paper suggests one mechanism for the conversion from 5mC.

The structure of 5-hydroxymethylcytosine at PubChem.

[Michael.James.Clark]

Oh, but I'm afraid this isn't the sixth base! That title probably belongs to base J (β-d-glucopyranosyloxymethyluracil), which to my knowledge is still impossible to sequence directly!

I don't want to show my hand, but I've been mentally challenging myself to come up with a strategy for sequencing it. Throw 5-Hydroxymethylcytosine on the "to-do" list.

[polivares]

What is the difference with methylated DNA? is it the same thing?

[cgb]

nanopores !

[polivares]

? nanopores?