Sin3a is a central component of a class of histone deacetylase containing transcriptional co-regulatory complexes. In this issue of The EMBO Journal, Streubel et al. purify Sin3a and identify a variant Sin3a complex containing Fam60a in undifferentiated embryonic stem cells (ESCs). Fam60a is a critical component of the ESC Sin3a complex since Fam60a knock-down leads to an extended G1 cell cycle phase and reduced ESC self-renewal. These exciting results open up new questions about how biochemical differences between variant Sin3a complexes may facilitate alterations in cell-specific function.