Postembryonic development in plants relies on stem cells located within the shoot apical meristem. Male and female gametes are descendants of those stem cells and maintenance of genome stability in this pool of cells is thus fundamental. In-depth molecular analysis has so far been hindered by the tedious isolation of shoot apical meristem stem cells. Gutzat et al. generated a development stage series of transcriptomes from stem cells isolated using fluorescence nuclear sorting. Together with stem-cell specific genes, the authors report the increased expression of transposons in stem cells. This is correlated with changes in DNA methylation at transposons occurring prior the commitment of the stem cells to the reproductive lineage. This suggests an early event of epigenetic reprogramming, and opens new perspectives for the study of epigenetic heritability. (Summary by Matthias Benoit).