Liquid-Liquid Phase Separation of Sp100-HMG: Driving Biogenesis and Functional Diversity of PML Nuclear Bodies

Promyelocytic leukemia nuclear bodies (PML NBs) are membraneless organelles (0.1-1 m) integral to numerous fundamental cellular processes. Recent advances in cryo-EM and liquid-liquid phase separation (LLPS) research substantially advanced our understanding of PML NBs biophysical features and structural organization. Here, we identify Sp100-HMG, an Sp100 isoform, as a driver of PML NBs formation via LLPS, recruiting PML and accessory proteins (DAXX, ATRX). Dissection of this assembly process uncovered a hierarchical mechanism orchestrated by three distinct yet cooperative processes: I. Multimerization domain- and intrinsically disordered region (IDR)-mediated LLPS of Sp100-HMG, nucleating the initial core; II. C-terminal-dependent protein-protein interactions that enrich client components; and III. SUMOylation-directed PML recruitment, facilitating the formation of a stabilizing peripheral shell. Notably, this assembly paradigm extends beyond Sp100-HMG, as evidenced by ZBTB16--a PML NB-associated oncoprotein implicated in acute promyelocytic leukemia--adopting an analogous mechanism to organize PML-positive condensates. Functional validation further revealed that Sp100-HMG positive PML NBs exert dual regulatory control over transcriptional programs and cell cycle progression, highlighting their pleiotropic roles. Critically, this work redefines the canonical PML NB assembly model by demonstrating that Sp100-HMG, rather than PML, acts as a primary scaffold, with PML polymerization relegated to a secondary, shell-forming stabilizer. By correlating the unique spatial architecture of Sp100-HMG positive PML NBs with their functional outputs, our findings establish a mechanistic framework for understanding how PML condensate biogenesis dictates transcriptional and cell cycle regulation, offering new avenues for exploring PML NB function in physical and disease contexts. Key findingsLLPS of Sp100-HMG directs de novo formation of PML NBs Polymerization, IDR and SUMOylation collectively contribute to PML NBs formation Sp100-HMG organized PML NBs in proximity to promoters strengthens local transcriptional regulation Sp100-HMG regulates cell cycle progression by regulating DAXX levels in the nucleoplasm SignificanceThis study fundamentally redefines our understanding of PML NBs assembly by identifying Sp100-HMG -driven phase separation as a primary scaffold mechanism, challenging/complementing the canonical PML-centric model. We demonstrate that Sp100-HMG undergoes LLPS via its multimerization domain and IDR, forming an initial condensate core that recruits PML as a peripheral shell. Notably, this mechanism extends to ZBTB16, an oncoprotein linked to APL, suggesting broad biological relevance. Functionally, Sp100-HMG - PML NBs regulate transcription and cell cycle progression, acting as dynamic "protein sponges" that modulate nucleoplasmic or regional protein concentrations through their LLPS-driven breathing effect--expansion and contraction constrained by the PML shell. This work unveils a novel architectural paradigm for PML NBs and provides a mechanistic framework for future investigations.