Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ChIP-seq Histone-Modifications]. Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ChIP-seq Histone-Modifications]

Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors. Overall design: Histone modifications analysis in ES, mesendoderm and endoderm cells; Foxa2 over expressing cells ES cells

先锋转录因子（Pioneer transcription factors, PTF）能够识别核小体DNA上的结合位点，并触发染色质开放，以招募其他非先锋转录因子。然而，先锋转录因子的关键特性仍未得到充分阐释，例如这类转录因子如何选择性识别细胞类型特异性结合位点，以及它们可在何种条件下启动染色质重塑。本研究显示，经典先锋转录因子Foxa2的早期内胚层结合位点，在胚胎干细胞（ESC）中因低水平的活性染色质修饰而被表观遗传预致敏。当在胚胎干细胞中异位表达Foxa2时，相较于谱系非适配结合位点，Foxa2更倾向于招募至内胚层结合位点，这一现象支持了上述结合位点的预致敏机制。我们进一步证实，Foxa2的结合是内胚层分化过程中染色质开放的必要条件。但仅在与其他内胚层转录因子协同结合的结合位点上，才能检测到染色质可及性的提升。因此，我们的数据表明，先锋转录因子的结合位点选择由染色质环境主导，且染色质开放需要先锋转录因子与其他转录因子协同作用。实验设计概述：对胚胎干细胞、中内胚层及内胚层细胞进行组蛋白修饰分析；对过表达Foxa2的胚胎干细胞进行分析。