EZ DNA Methylation kit - (May/07/2009 )
Is there any possibility that the bisulfite treatment would "bypass" methylation, and convert even methylated cytosines to uracil? I've used the Zymo EZ DNA Methylation-Gold kit, and followed their specifications exactly. I get nice sequences, with every single C changed to T. I was just wondering if that was a possibility. I have no reason to think anything went wrong though.
Even 5-methylcytosine undergoes the bisulfite reaction but much more slower than cytosine. Therefore conversion of 5mC to thymidine is possible. In most cases you won't detect these converted positions if the DNA input amount is high enough.
If you observe a lower methylation level it is caused in most cases by an incomplete enzymatic methylation of your control DNA.