DNA METHYLATION IN MOUSE A-REPEATS IN DNA METHYLTRANSFERASE-KNOCKOUT ES CELLS AND IN NORMAL-CELLS DETERMINED BY BISULFITE GENOMIC SEQUENCING

Mouse ES cells with a null mutation of the known DNA methyltransferase retain some residual DNA methylation and can methylate foreign sequen ces de novo. We have used bisulfite genomic sequencing to examine the sequence specificity and distributions of methylation of a hypermethyl ated CG island sequence, mouse A-repeats. There were 13 CG dinucleotid es in the region examined, 12 of which were methylated to variable ext ents in all DNAs. We found that: (1) there is considerable residual DN A methylation in ES cells lacking the known DNA methyltransferase (29% of normal methylation in the complete knockout ES DNA); (2) this othe r activity methylates at exactly the same CG sites as the major methyl transferase; and (3) differences in the distribution of methylated sit es between A-repeats in these DNAs are consistent with this other acti vity methylating in a random de novo fashion. Also, the lack of any me thylation in non-CG sites argues that, in other studies where non-CG m ethylation sites have been found by bisulfite sequencing, detection of such sites of non-CG methylation is not an inherent artifact in this methodology. (C) 1997 Elsevier Science B.V.