Heterozygous mutations in SMARCA2 reprogram the enhancer landscape by 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.哺乳动物SWI/SNF复合物是一类多亚基染色质重塑复合物，其关联的ATP酶为SMARCA4或SMARCA2。SMARCA2 ATP酶的杂合突变会导致Nicolaides-Baraitser综合征（NCBRS），这是一类以言语发育迟缓为特征的智力障碍综合征。我们构建了携带NCBRS相关杂合SMARCA2 K755R或R1159Q突变的人类胚胎干细胞（hESCs）。尽管携带SMARCA2突变的hESCs表型正常，但其向神经前体细胞（NPCs）的分化过程却受到严重损害。我们发现，SMARCA2突变会引发增强子重组：SOX3依赖型神经增强子丢失，同时星形胶质细胞特异性的从头（de novo）增强子显著出现。增强子区域染色质可及性的变化，与SMARCA2结合水平的升高以及SMARCA4的重靶向结合密切相关。我们证实，AP-1家族成员FRA2在SMARCA2突变的NPCs中异常高表达，并在从头增强子区域发挥先锋因子（pioneer factor）的功能。综上，本研究结果表明，SMARCA2突变通过异常靶向SMARCA4引发增强子重编程，进而导致分化过程受损。