The Sixth Base: 5-hydroxymethylcytosine enriched in mammalian brains

ECO · 04-16-2009, 09:06 PM

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 · 04-22-2009, 05:24 PM

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 · 08-30-2009, 09:06 AM

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

cgb · 08-31-2009, 01:58 AM

nanopores !

polivares · 09-16-2009, 02:18 AM

? nanopores?

04-16-2009, 09:06 PM	#1
ECO --Site Admin-- Join Date: Oct 2007 Location: SF Bay Area, CA, USA Posts: 660	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.

04-22-2009, 05:24 PM	#2
Michael.James.Clark Member Join Date: Apr 2009 Location: Los Angeles Posts: 55	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. __________________ Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog] Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post] *Projects*: U87MG whole genome sequence [Website] [Paper]

08-30-2009, 09:06 AM	#3
polivares Member Join Date: Jan 2009 Location: Manchester, UK Posts: 29	What is the difference with methylated DNA? is it the same thing?

08-31-2009, 01:58 AM	#4
cgb Member Join Date: May 2008 Location: Cambridge Posts: 50	nanopores !

09-16-2009, 02:18 AM	#5
polivares Member Join Date: Jan 2009 Location: Manchester, UK Posts: 29	? nanopores?