Histone methyltransferase SETDB1 safeguards mouse fetal hematopoiesis by suppressing activation of cryptic enhancers [ATAC-seq]

The H3K9me3-specific histone methyltransferase SETDB1 is critical for proper regulation of developmental processes, but the underlying mechanisms are only partially understood. Here, we show that deletion of Setdb1 in mouse fetal liver hematopoietic stem and progenitor cells (HSPCs) results in compromised stem cell function, enhanced myeloerythroid differentiation, and impaired lymphoid development. Notably, Setdb1-deficient HSPCs exhibit reduced quiescence and increased proliferation, accompanied by the acquisition of a lineage-biased transcriptional program. In Setdb1-deficient HSPCs, we identify genomic regions that are characterized by loss of H3K9me3 and increased chromatin accessibility, suggesting enhanced transcription factor (TF) activity. Interestingly, hematopoietic TFs like PU.1 bind these cryptic enhancers in wild-type HSPCs, despite the H3K9me3 status. Thus, our data indicate that SETDB1 restricts activation of nonphysiological TF binding sites which helps to ensure proper maintenance and differentiation of fetal liver HSPCs. Overall design: ATAC-seq of Setdb1 mutant vs Setdb1 control fetal liver LSK cells at E13.5

针对组蛋白H3赖氨酸9三甲基化（H3K9me3）的组蛋白甲基转移酶SETDB1，对发育过程的正常调控至关重要，但其背后的分子机制仍仅部分明晰。本研究显示，在小鼠胎肝造血干细胞和祖细胞（HSPCs）中敲除Setdb1，会导致干细胞功能受损、髓系红细胞分化增强以及淋巴发育受损。值得注意的是，Setdb1缺陷型HSPCs表现出静息状态减弱、增殖活性升高，并伴随谱系偏向性转录程序的获得。在Setdb1缺陷型HSPCs中，我们鉴定出一类基因组区域，其特征为H3K9me3信号丢失以及染色质可及性升高，这提示转录因子（TF）活性增强。有趣的是，尽管存在H3K9me3修饰，造血系统转录因子（如PU.1）仍可结合野生型HSPCs中的这些隐蔽增强子。综上，我们的数据表明SETDB1可通过限制非生理性转录因子结合位点的激活，从而保障胎肝HSPCs的正常维持与分化。实验整体设计：于胚胎发育第13.5天（E13.5），对Setdb1突变型与野生型对照胎肝LSK细胞开展转座酶可及性测序（ATAC-seq）。