Friday, April 27, 2012

Just what we've been waiting for: Quantitative Sequencing of 5-Methyl-cytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

In this paper published yesterday in Science Express by Wolf Reik and Shankar Balasubramanian and friends, a novel method to quantitate hydroxymethylcytosine is described -- as anyone who has tried to quantitate this "new" base knows, it is not so easy -- but this technique takes advantage of the specific oxidation of 5hmC to 5fC, using a readily available chemical, potassium perruthenate. This is followed by bisulfite conversion, which differentially converts 5hmC, leaving 5mC unconverted (typically both 5hmC and 5mC are protected during bisulfite conversion).  The sequence resulting from this oxBS is compared to a regularBS (bisulfite conversion),  allowing quantification of 5hmC content.  Why do we care?  Well it has already been shown that 5hmC regulates cell lineage determination in mouse stem cells -- we work on cancer, but it doesn't take a rocket scientist to figure out that there are similarities between cancer cells and stem cells -- now we have an "easy" tool to look at this within particular genes -- Note to my Lab: I have just ordered potassium perruthenate....please read this paper!  Here's the link to the manuscript -- you may need to have access to Science magazine --click here--

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