PAPI interacts with PIWI proteins, especially AGO3. (A) PAPI is a strong PIWI-interacting protein in a Y2H screen. Three baits were used in the Y2H screen: PIWI-FL, residues 1-843; PIWI-NT, residues 1-491; and PIWI-CT, residues 492-843. PAPI interacts strongly with the PIWI-FL and the PIWI-NT baits, but not with the PIWI-CT bait. (B) Y2H assay showing that PAPI interacts with PIWI proteins, especially AGO3, but not with AGO proteins or the LexA DNA-binding moiety of the bait plasmid pEG202. (C,D) AGO3 interacts with PAPI in vivo. Endogenous PAPI (C) and AGO3 (D) were immunoprecipitated from ovarian extract treated with or without RNase A using anti-PAPI (C) and anti-AGO3 (D) antibodies, respectively. Extract plus beads (−Ab) and antibody plus beads (−Extract) were used as negative controls for IP. Both immunoblots were probed for PAPI and AGO3. IgG bands were probed as a loading control. The interaction between PAPI and AGO3 is RNA independent.