Klf5相邻的超级增强器作为3D基因组结构依赖的转录驱动器,以保护ESC身份
Guangsong Su1,2, Bohan Chen1,2, Yingjie Song2
1Department of Laboratory Medicine and Institute of Precise Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China.
Nature communications
|July 1, 2025
概括
超级增强剂 (SE) 和主转录因子 (TF) 调节胚胎干细胞 (ESC) 的身份. 这项研究揭示了一个3D基因组机制,其中SE通过TF相互作用和多基因调节来控制ESC命运.
科学领域:
- 表观遗传学和基因调控
- 干细胞生物学 干细胞生物学
- 基因组学就是基因组学.
背景情况:
- 超级增强剂 (SE) 和主转录因子 (TF) 对于胚胎干细胞 (ESC) 命运的动态重塑至关重要.
- 在控制ESC身份方面,SE和TF之间的准确监管相互作用仍然不完全理解.
研究的目的:
- 阐明SE通过TF相互作用和3D基因组组织来管理ESC身份的监管机制.
- 确定特定的SE及其参与维持ESC多能性和差异化的目标基因.
主要方法:
- 整合多omics数据,包括H3K27ac,Hi-C和单细胞RNA测序 (scRNA-seq) 在不同的ESC状态.
- 通过CRISPR介导的SE删除和激活 (CRISPRa) 来评估基因功能.
- 高通量3D基因组查和CTCF枯竭实验,以调查染色质循环和拓相关域 (TAD).
主要成果:
- 确定与主TF相互作用的Klf5相邻超增强器 (K5aSE),这对ESC的扩散和差异化至关重要.
- 删除K5aSE导致ESC功能受损,与Klf5淘汰赛ESC相比,具有明显的差异化轨迹,表明K5aSE调节额外的目标.
- 通过染色体循环,K5aSE被证明可以激活四个远端基因,它们的激活挽救了K5aSE删除表型.
- 通过调节Klf5和基因表达,CTCF介导的TAD被发现对维持K5aSE活性至关重要.
结论:
- 一个3D基因组依赖机制决定了SE如何通过协调TF相互作用和调节多个基因来控制ESC身份.
- SE在维持ESC多能性和通过涉及染色体架构的复杂监管网络指导差异化途径方面发挥着关键作用.
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