I assume that the key biological meaning of cytosine de-methylation during germline development in germline progenitor cells is to reset imprinted genes and then set methylation pattern on these genes according to the gender of the embryo. (this is simply my best guess, so if there is an alternative interpretation, please mention it in the answer)

This de-methylation procedure is dangerous, because DNA-demethylation affects a lot of different regions and some transpons get de-repressed. So there is a risk of novel transposon insertions. However, since it is important to set imprinting in your own gamets properly, the embryo takes this risk.

But I don't understand why does de-methylation in mammalian development happen twice. Well, the first round it is not as deep and, I am guessing, that the transposons are probably not affected very much during the first round, so the risk of novel transposon insertions is not as high. However, since the resetting of imprinting marks is happening in the second round anyway, why does the embryo bother the first time around at all?



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