In-Depth Functional Analysis of BRD9 in Fetal Hematopoiesis Reveals Context-Dependent Roles [scRNA-seq]

The hierarchical organization of hematopoietic stem cells (HSCs) governing adult hematopoiesis has been extensively investigated. However, the dynamic epigenomic transition from fetal to adult hematopoiesis remains incompletely understood, particularly regarding the involvement of epigenetic factors. In this study, we investigate the roles of BRD9, an essential component of the non-canonical BAF (ncBAF) complex known to govern the fate of adult HSCs, in fetal hematopoiesis. Consistent with observations in adult hematopoiesis, BRD9 loss impairs fetal HSC stemness and disturbs erythroid maturation. Intriguingly, the impact on myeloid lineage was discrepant: BRD9 loss inhibited and promoted myeloid differentiation in fetal and adult models, respectively. Through comprehensive transcriptomic and epigenomic analyses, we elucidate the differential roles of BRD9 in a context- and lineage-dependent manner. Our data uncover how BRD9/ncBAF complex modulates transcription in a stage-specific manner, providing deeper insights into the epigenetic regulation underlying the transition from fetal to adult hematopoiesis. To obtain fetal livers (FL), mating pairs were setup between Brd9fl/fl male mice and Vav1-iCre; Brd9fl/fl female mice. The day when mouse pregnancy was confirmed was counted as E0.5. On E14.5, the mice were sacrificed for sample preparation.调控成体造血的造血干细胞（hematopoietic stem cells, HSCs）层级组织已被广泛研究。然而，从胎儿到成体造血过程中的动态表观基因组转变仍未完全阐明，尤其是在表观遗传因子的参与机制方面。本研究探讨了BRD9——作为已知调控成体HSCs命运的非经典BAF（ncBAF）复合体（non-canonical BAF complex）的核心组分——在胎儿造血中的作用。与成体造血中的观察结果一致，BRD9缺失会损害胎儿HSCs的干细胞干性并扰乱红细胞成熟过程。有趣的是，其对髓系谱系的影响存在差异：BRD9缺失分别抑制胎儿模型的髓系分化、促进成体模型的髓系分化。通过全面的转录组和表观基因组分析，我们阐明了BRD9以环境和谱系依赖的方式发挥差异化作用。我们的数据揭示了BRD9/ncBAF复合体如何以阶段特异性方式调控转录，为理解胎儿到成体造血转变背后的表观遗传调控机制提供了更深入的见解。为获取胎肝（FL），我们将Brd9fl/fl雄性小鼠与Vav1-iCre; Brd9fl/fl雌性小鼠进行配繁。确认小鼠怀孕的当日记为E0.5。在E14.5时处死小鼠以进行样本制备。