MORC2 Mediates Transcriptional Regulation Through Liquid-Liquid Phase Separation and DNA Binding

MORC2 is a chromatin-associated ATPase implicated in transcriptional silencing and human neuropathies such as Charcot–Marie–Tooth disease and spinal muscular atrophy. However, the molecular mechanisms governing its transcriptional regulatory activity remain elusive. Here, we demonstrate that full-length MORC2 undergoes liquid-liquid phase separation (LLPS) to form nuclear condensates, a process essential for transcriptional repression. Endogenous MORC2 forms dynamic condensates in neurons from EGFP-MORC2 knock-in mice, supporting the physiological relevance of LLPS in vivo . The 3.1 Å crystal structure of coiled-coil 3 (CC3) reveals a dimeric scaffold that drives phase separation, while multivalent interactions between the intrinsically disordered region (IDR) and a newly defined IDR-binding domain (IBD) further promote condensate formation. Moreover, LLPS enhances MORC2’s ATPase activity in a DNA-dependent manner, indicating a functional coupling between phase separation, DNA binding, and enzymatic regulation. RNA-seq analysis shows that only wild-type, but not LLPS-deficient MORC2, represses core target genes in knockout cells, directly linking condensate formation to transcriptional control. Furthermore, disease-associated MORC2 variants alter condensate dynamics, ATPase activity, and DNA binding, offering mechanistic insights into their pathogenic effects. Together, these findings identify LLPS as a key regulatory mechanism for MORC2 function and provide a molecular framework for understanding its role in transcriptional regulation and human disease.