The BAF chromatin remodeling complex regulates gene expression programs essential for mammalian neural crest development

Neural crest cells (NCCs) are a multipotent cell population that contributes to the development of many tissues including craniofacial, pharyngeal arch arteries, and cardiac outflow tract (OFT). The BAF complex plays an important role in the development of a wide range of tissues by modulating gene expression programs at the chromatin level. However, its role in neural crest development has remained unclear. To determine the role BAF complex, we deleted BAF155 and BAF170, the core subunits required for the assembly, stability, and functions of the BAF complex in NCCs. Mouse embryos lacking BAF155/170 in NCCs displayed early lethality due to a wide range of developmental defects including craniofacial defects, pharyngeal arch artery defects, and OFT defects. We observed reduced proliferation, increased cell death, and impaired migration of cardiac NCCs to the OFT in BAF155/170 mutants. RNAseq analysis on sorted NCCs revealed that the BAF complex regulates the expression of numerous genes essential for neural crest development. We observed downregulation of Hippo and Notch signaling pathways, both essential for the migration, proliferation, and differentiation of the NCCs. The BAF complex interacts with transcription factors to modulate the transcriptional program. Therefore, we performed transcription factor enrichment analysis on the RNAseq data set and identified several transcription factors including Hey1, Hey2, and Hes5 that may directly or indirectly interact with the BAF complex in NCCs. We also found that Brg1 interact with Tead transcription factors and the interaction was impaired in BAF155/170 knockdown cells. Together, our results demonstrate an important role of the BAF complex in modulating the gene regulatory network essential for neural crest development. 6 samples are analyzed comprises of control (n = 3) and mutant (n = 3)神经嵴细胞（Neural crest cells, NCCs）是一类多能细胞群，可参与颅面部组织、咽弓动脉及心脏流出道（cardiac outflow tract, OFT）等多种组织的发育过程。BAF复合体（BAF complex）通过在染色质层面调控基因表达程序，在多种组织的发育中发挥关键作用。然而，其在神经嵴发育中的功能仍未明确。为探究BAF复合体的作用，我们在神经嵴细胞中敲除了其组装、稳定性及功能所必需的核心亚基BAF155与BAF170。在神经嵴细胞中缺失BAF155/170的小鼠胚胎，会因颅面部缺陷、咽弓动脉缺陷、心脏流出道缺陷等多种发育异常而早期致死。我们观察到，BAF155/170突变体的心脏神经嵴细胞增殖能力降低、细胞死亡增多，且向心脏流出道的迁移功能受损。对分选后的神经嵴细胞进行RNA测序（RNAseq）分析显示，BAF复合体可调控众多神经嵴发育必需基因的表达。我们发现Hippo信号通路与Notch信号通路均出现下调，而这两条通路对神经嵴细胞的迁移、增殖与分化均至关重要。BAF复合体可通过与转录因子相互作用来调控转录程序。为此，我们对该RNA测序数据集开展了转录因子富集分析，鉴定出Hey1、Hey2及Hes5等若干可在神经嵴细胞中与BAF复合体直接或间接相互作用的转录因子。此外我们还发现，Brg1可与Tead转录因子结合，且该相互作用在BAF155/170敲低细胞中受到显著削弱。综上，本研究结果证实，BAF复合体在调控神经嵴发育必需的基因调控网络中发挥着重要作用。本研究共分析6个样本，其中对照组（n=3）与突变组（n=3）各3例。