WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [Nanog_WT_R153A_RNAseq]

Stem cell pluripotency relies on a finely tuned interplay between transcription factors and epigenetic regulators. Here, we identify a direct interaction between NANOG, a master pluripotency transcription factor, and WDR5, a core component of the SET1/MLL complex that is essential for maintaining stem cell identity. Mechanistically, WDR5 reshapes the prion-like structures of NANOG into dynamic, liquid-liquid phase-separated (LLPS) condensates, facilitating its recruitment to pluripotency-associated promoters and activating target gene expression. X-ray crystallography and NMR spectroscopy reveal that the NANOG homeodomain engages WDR5 through an extensive structural interface distinct from previously characterized short linear motifs. The NANOGR153A mutation disrupts its interaction with WDR5, leading to impaired LLPS formation, reduced chromatin co-occupancy, and diminished levels of active histone marks (H3K4me3 and H4K16ac), ultimately compromising the pluripotency of embryonic stem cells. Furthermore, pharmacological inhibition of the WDR5-NANOG interaction using a WIN motif inhibitor robustly suppresses leukemia stem cell expansion in vivo, highlighting its therapeutic potential. Collectively, this study uncovers an LLPS-mediated regulatory mechanism whereby WDR5 modulates NANOG condensate dynamics to sustain stem cell identity in both physiological and pathological contexts.