after bisulfite treatment, unmethylated cytosine is changed to uracil. How is the uracil converted to thymine??
After bissulfide treatment, usually you make a PCR and then you sequence the DNA.
In this PCR the uracil will pair with adenine at first round, this is caused by the DNA polymerase recognition, that does not recognize Uracil. Then this adenine will pair with thymine in the next. With this you have your non methylated cytosine turned into thymine in the sequenced DNA. Then you compare your sequence with the known sequence of the gene and have the "map" of the methylated cythosines.
So DNA is bisulfite treated, converting C to U. The amplification in PCR of the modified DNA produced DNA with the original C replaced by T. From here, cloning then followed by sequencing give DNA sequences with all original C being changed to T. That said, the met-C in the original DNA will remained unchanged and descendant DNA have them. This way we can find out the site of met-C in DNA in the "bisulfite sequencing" process.
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