Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle [OCT4OFF SOX2OFF ChIP-seq]

The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state. Overall design: ZHBTc4 and 2TS22C mouse embryonic stem cell lines were grown in the presence or absence of doxycycline and subjected to ChIP-seq

转录因子（transcription factors）的先驱活性（pioneer activity）可使难以接近的调控元件得以开放，这一过程已在细胞分化与重编程领域得到广泛研究。与之形成鲜明对比的是，人们对先驱活性在自我更新细胞分裂及全细胞周期中的功能尚知之甚少。
本研究针对OCT4与SOX2在调控小鼠胚胎干细胞染色质开放性中的相互作用展开了评估。我们发现，即便在共同结合的位点上，OCT4与SOX2仍主要以独立模式运作，二者的协同结合大多通过调控染色质开放性间接介导。
通过可控蛋白质降解实验策略的分析，我们证实：维持OCT4的持续存在，是实现有丝分裂后染色质开放性重建以及间期染色质开放性维持的必要条件；且高度结合OCT4的增强子对OCT4表达的短暂缺失尤为敏感。
本研究揭示了维持动态多能性调控景观处于开放状态所需的持续性先驱活性。
整体实验设计：将ZHBTc4与2TS22C小鼠胚胎干细胞系分别在含有或不含强力霉素（doxycycline）的条件下培养，并进行染色质免疫共沉淀测序（ChIP-seq）。