Highlights • Depletion of ZFC3H1 in mouse ESCs results in differentiation defects • PRC2 target genes are deregulated in Zfc3h1−/− cells • Chromatin binding of PRC2 and H3K27me3 is reduced in Zfc3h1−/− cells • Increased binding of RNA impairs PRC2 complex stability Summary Pluripotent embryonic stem cells (ESCs) constitute an essential cellular niche sustained by epigenomic and transcriptional regulation. Any role of post-transcriptional processes remains less explored.