Recent advances reveal emerging unique functions of poly(ADP-ribose) polymerase-1 (Parp-1) and Parp-2 in heterochromatin integrity and cell differentiation. However, the chromatin-mediated molecular and cellular events involved remain elusive. Here we describe specific physical and functional interactions of Parp-1 and Parp-2 with the transcriptional intermediary factor (TIF1beta) and the heterochromatin proteins (HP1) that affect endodermal differentiation. We show that Parp-2 binds to TIF1beta with high affinity both directly and through HP1alpha. Both partners colocalize at pericentric heterochromatin in primitive endoderm-like cells. Parp-2 also binds to HP1beta but not to HP1gamma. In contrast Parp-1 binds weakly to TIF1beta and HP1beta only. Both Parps selectively poly(ADP-ribosyl)ate HP1alpha. Using shRNA approaches, we provide evidence for distinct participation of both Parps in endodermal differentiation. Whereas Parp-2 and its activity are required for the relocation of TIF1beta to heterochromatic foci during primitive endodermal differentiation, Parp-1 and its activity modulate TIF1beta-HP1alpha association with consequences on parietal endodermal differentiation. Both Parps control TIF1beta transcriptional activity. In addition, this work identifies both Parps as new modulators of the HP1-mediated subcode histone.-Quénet, D., Gasser, V., Fouillen, L., Cammas, F., Sanglier-Cianferani, S., Losson, R., Dantzer, F. The histone subcode: poly(ADP-ribose) polymerase-1 (Parp-1) and Parp-2 control cell differentiation by regulating the transcriptional intermediary factor TIF1beta and the heterochromatin protein HP1alpha.