Paraspeckle Protein NONO Regulates Active Chromatin by Allosterically Stimulating NSD1

NSD1 is a key histone methyltransferase that catalyzes di-methylation of lysine 36 of histone H3 (H3K36me2), essential for active chromatin domains. While the loss of NSD1 activity halts embryonic development and its aberrant gain drives oncogenesis in leukemia and glioma, the regulatory mechanisms remain poorly understood. Here, we uncover that NSD1 requires allosteric activation through the aromatic pocket of its PWWP2 domain. Surprisingly, NSD1-PWWP2 binds to a non-canonical target, nuclear paraspeckle protein NONO, and this protein-protein interaction allosterically stimulates NSD1. Mouse embryonic stem cells (mESC) engineered with mutations in the aromatic pocket of NSD1-PWWP2 cannot differentiate into neural progenitor cells (NPC), and genetic depletion of NONO partially phenocopied this defect, potentially explaining the neurodevelopmental disorder phenotypes in NSD1- and NONO-deficient diseases. Our work uncovered a mechanism driving active chromatin domain formation, an implication in the interplay between nuclear paraspeckles and active chromatin, and a vulnerability of NSD1 for therapeutic interventions. Overall design: The study seeks to interrogate 1) the gene expression profiles affected by NSD1 or NONO in mESC undergoing neural differentiation, and 2) How NSD1 and NONO affect each other's chromatin occupancy and H3K36me2 global levels on chromatin in HEK293T and mESC. For 1), WT, NSD1-KO, and NONO-KO mESC were differentiated by retinoic acid (RA) for 0, 3, or 6 days. Total RNAs were extracted and polyA selected for pair-end (PE) sequencing for 40M reads each. For 2), ChIP using H3K36me2, NSD1, or NONO antibody were conducted in WT, NSD1-KO, and NONO-KO HEK293T and mESC.