SETDB1 promotes tubulin deacetylation and Golgi fragmentation by HDAC6

Microtubules (MTs) are dynamic cytoskeletal structures essential for intracellular transport, cell division, and organelle positioning. Their functions are regulated by post-translational modifications, including α-tubulin acetylation at Lys40, which enhances MT stability and resilience. Histone deacetylase 6 (HDAC6) is the primary enzyme that reverses this modification, but its access to the luminal Lys40 residue is restricted. Previously, we identified SETDB1, a histone methyltransferase and known oncogene, as a cytoplasmic regulator of MT dynamics, attenuating MT polymerization and destabilizing MTs. Here, we uncover the molecular mechanism by which SETDB1 destabilizes MTs. SETDB1 interacts with HDAC6 and promotes its tubulin deacetylation activity. Mechanistically, SETDB1 enhances HDAC6 recruitment to polymerized MTs and induces repairable damage along MT shafts, generating entry points for HDAC6 into the MT lumen. Functionally, this axis regulates Golgi organization: SETDB1 overexpression disperses the Golgi in an HDAC6-dependent manner, while SETDB1 knockdown or HDAC6 inhibition compacts it. Notably, SETDB1’s role in Golgi regulation is independent of its methyltransferase activity. These findings reveal crosstalk among the histone methylation machinery, MT dynamics, and Golgi organization. Since Golgi dispersal is thought to promote tumorigenesis, our results suggest that the SETDB1-HDAC6 axis is a potential therapeutic target.