Proximal proteomics analysis reveals DNA polymerase δ subunit 3 is a new MCM2 binding partner and promotes parental histones inheritance in mammalian cells

In mammalian cells, MCM2 and POLE3/4 safeguard the symmetrical segregation of parental histones to the leading and lagging strands of newly synthesized DNA. However, the identity of additional proteins involved in parental histone distribution remains elusive. We used TurboID proximity labeling to identify interaction partners of MCM2 and POLE3/4 in mouse cells. This approach provided a candidate protein library potentially involved in the MCM2 and POLE3/POLE4-mediated process of parental histone segregation. DNA polymerase δ subunit 3 (POLD3) was a protein whose intensity differed between the interactomes of wild-type MCM2 and its histone-binding mutant. We showed POLD3 bound to both MCM2 and the histone (H3-H4)₂ tetramers. Moreover, MCM2’s histone binding affected interactions between POLD3 and histone H3. More importantly, POLD3 was required for the symmetrical transfer of parental histones H3-H4 to the leading and lagging strands of newly synthesized DNA in mouse cells. In short, our findings establish that POLD3 forms a protein complex with MCM2 and histone (H3-H4)₂ tetramers, functioning as a novel histone chaperone to regulate parental histone segregation in mammalian cells. © The Author(s) 2025.