Embryonic stem cells (ESCs) generally rely on repressive histone modifications to silence retrotransposons, rather than DNA methylation as in differentiated cells. In this issue of Cell Stem Cell, He et al. (2015) show that Daxx/Atrx repress transposons in ESCs devoid of 5mC, demonstrating dynamic reorganization of epigenetic networks and crosstalk between distinct repressive mechanisms to maintain transposon silencing.