BAF subunit switching regulates chromatin accessibility to control cell cycle exit in the developing mammalian cortex [RNA-seq]

mSWI/SNF or BAF chromatin regulatory complexes are dosage-sensitive regulators of human neural development frequently mutated in autism and intellectual disability. Cell cycle exit and differentiation of neural stem/progenitor cells is accompanied by BAF subunit switching to generate neuron-specific nBAF complexes. We manipulated the timing of BAF subunit exchange in vivo and found that early loss of the npBAF subunit BAF53a stalls cell cycle exit to disrupt neurogenesis. Loss of BAF53a results in decreased chromatin accessibility at specific neural transcription factor binding sites, including the pioneer factors Sox2 and Ascl1, due to Polycomb accumulation. This results in repression of cell cycle genes, thereby blocking cell cycle progression and differentiation. Cell cycle block upon Baf53a deletion could be rescued by premature expression of the nBAF subunit BAF53b but not by other major drivers of proliferation or differentiation. Wnt, EGF, FGF, Sox2, myc or Pax6 all fail to maintain proliferation in the absence of BAF53a, highlighting a novel mechanism underlying neural progenitor cell cycle exit in the continued presence of extrinsic proliferative cues. We conducted RNAseq on Baf53aHet and Baf53aKO mouse forebrains from embryonic day E15.5mSWI/SNF或BAF染色质调控复合物是人类神经发育的剂量敏感性调控因子，常于自闭症与智力障碍中发生突变。神经干细胞/祖细胞的细胞周期退出与分化过程伴随BAF亚基重排，以生成神经元特异性nBAF复合物（neuron-specific nBAF complexes）。我们在体内操控了BAF亚基替换的时序，发现神经前体细胞特异性BAF（neural progenitor cell-specific BAF，简称npBAF）亚基BAF53a的早期缺失会阻滞细胞周期退出，进而破坏神经发生。BAF53a的缺失会导致特定神经转录因子结合位点（包括先锋转录因子Sox2与Ascl1）的染色质可及性降低，这源于多梳蛋白（Polycomb）的富集。该现象会引发细胞周期相关基因的表达抑制，进而阻滞细胞周期进程与分化。Baf53a缺失引发的细胞周期阻滞可通过提前表达nBAF亚基BAF53b得以挽救，但无法通过其他主要的增殖或分化调控因子实现。Wnt、EGF、FGF、Sox2、myc及Pax6均无法在BAF53a缺失的情况下维持细胞增殖，这揭示了一种新的机制：即使存在外源性增殖信号，神经祖细胞仍可实现细胞周期退出。我们对胚胎发育第15.5天（E15.5）的Baf53a杂合缺失（Baf53aHet）与纯合敲除（Baf53aKO）小鼠前脑组织开展了RNA测序（RNAseq）。