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Old 04-16-2009, 10:06 PM   #1
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Default The Sixth Base: 5-hydroxymethylcytosine enriched in mammalian brains

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.
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Old 04-22-2009, 06:24 PM   #2
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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.
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Old 08-30-2009, 10:06 AM   #3
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What is the difference with methylated DNA? is it the same thing?
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Old 08-31-2009, 02:58 AM   #4
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nanopores !
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Old 09-16-2009, 03:18 AM   #5
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? nanopores?
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