CRISPR screen identifies BAP1 as a deubiquitinase regulating SPIN4 stability

Protein homeostasis is tightly controlled by the coordinated actions of E3 ubiquitin ligases and deubiquitinases (DUBs). We identify Spindlin-4 (SPIN4), a histone H3K4me3 reader, as a substrate regulated by opposing pathways: degradation mediated by the Cullin-RING E3 ligase DCAF16 and stabilization by the DUB BAP1. Through CRISPR-Cas9 knockout screens and biochemical analyses, we demonstrate that DCAF16 promotes SPIN4 degradation, while BAP1 interacts with and stabilizes SPIN4 through its catalytic activity. Inhibition or loss of BAP1 reduces SPIN4 levels, highlighting its critical role in maintaining SPIN4 homeostasis. Proteomics and interactome analyses further support this regulatory axis. These findings reveal a dynamic balance controlling SPIN4 stability, with potential implications for epigenetic regulation and disease processes.