DNA methylation changes in Dnmt3L-deficient mouse embryonic stem cells (mESCs)

We used RRBS to analyze DNA methylation in mESC lines deficient for maternal Dnmt3L (Dnmt3L mKO), zygotic Dnmt3L (Dnmt3L KO), and both maternal and zygotic Dnmt3L (Dnmt3L mzKO). Compared to wild-type (WT) mESCs, Dnmt3L mKO mESCs exhibit severe loss of methylation at imprinted loci but no changes in global DNA methylation, Dnmt3L KO mESCs exhibit moderate loss of methylation at many Dnmt3a target regions but do not affect methylation at imprinted loci, and Dnmt3L mzKO mESCs exhibit combined changes of mKO and KO cells, with severe loss of methylation at imprinted loci and moderate loss of methylation at Dnmt3a target regions. Dnmt3L mKO, KO and mzKO mESC lines, as well as control WT mESC lines, were derived from blastocyst-stage embryos from intercrosses between Dnmt3L-/- or Dnmt3L+/- female mice and Dnmt3L+/- male mice. 2-3 male (XY) lines per genotype were analyzed by RRBS.