Abstract

Homorepeat sequences are abundant in proteomes, and their expansion or deletion is linked to neurodegenerative and developmental diseases. Runx2, a master regulator of osteogenesis, contains a unique polyglutamine (polyQ) and polyalanine (polyA) tandem domain (QA). Here, we show that the deletion of polyQ, but not polyA, induces Runx2 aggregation in the cytoplasm. KPNA3/importin α4 specifically governs Runx2 nuclear import and condensation, and its depletion inhibits osteoblast differentiation. We find that an intrinsically disordered region (IDR) adjacent to the nuclear localization sequence (NLS) drives Runx2 condensation. Structural modeling indicates that polyQ deletion causes folding of the remaining N terminus, including the polyA region, thereby blocking KPNA3 access to the NLS. Low bone mineral density-associated deletion mutations in polyQ impair the Runx2-KPNA3 interaction, leading to aberrant cytoplasmic aggregation. These results unveil a unique role for the polyQ repeat in sustaining KPNA3 interaction, which is essential for Runx2 nuclear import and maintaining its liquid-like condensate state.