Heterozygous mutations in SMARCA2 lead to impaired neurogenesis due to global retargeting of SMARCA4

Mammalian SWI/SNF complexes are multi-subunit chromatin remodeling complexes associated with an ATPase, either SMARCA4 or SMARCA2. Heterozygous mutations in the SMARCA2 ATPase cause Nicolaides-Baraitser Syndrome (NCBRS), an intellectual disability syndrome associated with delayed speech onset. We engineered human embryonic stem cells (hESCs) to carry NCBRS-associated heterozygous SMARCA2 K755R or R1159Q mutations. While SMARCA2 mutant hESCs were phenotypically normal, differentiation to neural progenitors cells (NPCs) was severely impaired. We find that SMARCA2 mutations cause enhancer reorganization with loss of SOX3-dependent neural enhancers and prominent emergence of astrocyte-specific de novo enhancers. Changes in chromatin accessibility at enhancers were associated with an increase in SMARCA2 binding and retargeting of SMARCA4. We show that AP-1 family member FRA2 is aberrantly overexpressed in SMARCA2 mutant NPCs, where it functions as a pioneer factor at de novo enhancers. Together, our results demonstrate SMARCA2 mutations cause impaired differentiation through enhancer reprogramming via inappropriate targeting of SMARCA4. Overall design: RNA-seq of human Neural Progenitor Cell(hNPC) derived from WT, K755R/+, R1159Q/+ H9 human embryonic stem cell(hESC). ChIP-seq of H3K4me, H3K4me3, H3K27me, H3K27ac, SMARCA2, SMARCA4, FRA2, SOX2, SOX3 in WT, K755R/+, R1159Q/+ hNPCs. ChIP-seq of AM in R1159Q/+ hNPCs with lenti-viral expression of SMARCA2-WT-AM or SMARCA2-R1159Q-AM. ChIP-seq of SMARCA4 in WT hNPCs with siCT or siSOX2/SOX3. ChIP-seq of SMARCA2 and SMARCA4 in K755R/+ hNPCs with siCT or siFOSL1/siFOSL2/siJUNB. ATAC-seq of WT, K755R/+, R1159Q/+ hNPCs. ATAC-seq of K755R/+ hNPCs with siCT or siFOSL1/siFOSL2/siJUNB.