A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (ATAC-Seq)

During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into distinct cell fates are not fully understood. Here, we identify chromatin-regulating and cell-fate-determining transcription factors (TF) governing dendritic cell (DC) development by annotating the enhancer and promoter landscapes of the DC lineage. Combining these analyses with detailed over-expression, knockdown and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, differential activity of TF can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes.

在造血作用（hematopoiesis）过程中，源自同一干细胞库的细胞会分化为不同的细胞类型。介导普通祖细胞向不同细胞命运分化的机制尚未完全阐明。本研究通过注释树突状细胞（dendritic cell, DC）谱系的增强子（enhancer）与启动子（promoter）图谱，鉴定出了调控DC发育的染色质调控型与细胞命运决定型转录因子（transcription factors, TF）。结合上述分析与详细的过表达（over-expression）、敲低（knockdown）及染色质免疫沉淀测序（ChIP-Seq）实验，我们证实干扰素调节因子8（Irf8）可作为浆细胞样树突状细胞（plasmacytoid DC, pDC）的表观遗传与命运决定型转录因子，调控数千个pDC增强子中大量的细胞特异性染色质改变。值得注意的是，Irf8与Cebpb——一种单核细胞来源DC的表观遗传命运决定型转录因子——形成负反馈环路。我们证实，依托这一环路逻辑，转录因子的差异活性可稳定界定表观遗传与转录状态，且不受微环境影响。从更广泛的视角来看，本研究提出了一种通用范式：拥有相似信号依赖因子的紧密相关细胞，可通过该范式生成差异化且持久的增强子图谱。