GSE169654
Impaired attenuation of pluripotency enhancers at the onset of neural crest formation in ARID1B haploinsufficient Coffin-Siris patients
De-novo ARID1B haploinsufficient mutations cause many developmental disorders characterized by neurological and craniofacial phenotypes, including Coffin-Siris Syndrome.  ARID1B and its paralog ARID1A encode for mutually exclusive subunits of the BAF chromatin remodeler, yet their role in cell-fate determination is poorly understood.   We discovered a novel neural crest configuration of the BAF complex (ARID1B-BAF), which includes ARID1B, SMARCA4, and eight additional subunits. The ARID1B-BAF regulates lineage commitment upon differentiation cues through attenuation of pluripotency enhancers of the SOX2 network.  Consistently, the ARID1B-BAF interacts with SALL4, which is known to have repressing abilities during lineage commitment.  In iPSCs, pluripotency enhancers are maintained in active state by cooperation between the pioneer activity of SOX2 and the ARID1A-containing BAF.  At the onset of differentiation, ARID1B-BAF replaces ARID1A-BAF at these enhancers, eliciting chromatin repression and coordinating the exit from pluripotency. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at the pluripotency enhancers throughout CNCC differentiation.  This correlates with aberrant SOX2 binding at the pluripotency enhancers, and failure to reposition SOX2 at the developmental enhancers. SOX2 dysregulation promotes upregulation of the NANOG regulatory network, impairing CNCC differentiation.  Intriguingly, the patient with the most extreme molecular phenotype is also affected by a more severe version of the syndrome.  These findings have significant biomedical implications, since they suggest a direct connection between ARID1B mutations and developmental disorders. Overall design: Using patient-derived iPSCs to study ARID1B's function in craniofacial development