增强子如何在 3D 染色质组织背景下调节其靶基因已被广泛研究，并且最近出现了不需要直接增强子-启动子接触的模型。在这里，我们利用乳腺癌细胞系中雌激素受体依赖性增强子的激活来研究两个位点的增强子-启动子通讯。这允许对从激素刺激到有效基因激活的分子事件进行高时间分辨率跟踪。我们研究了通过 DNA 荧光原位杂交测定的增强子-启动子空间邻近性以及染色质原位断裂和邻近连接产生的接触频率在增强子驱动的基因激活过程中如何动态变化。这些正交方法产生看似矛盾的结果：增强子激活后，增强子-启动子接触频率增加，而空间接近度降低。我们使用不同的雌激素受体配体和转录抑制剂探索这种明显的差异。我们的数据表明增强子-启动子接触频率是转录无关的，而改变的增强子-启动子接近度取决于转录。我们的结果强调，接触频率和细胞核中的物理距离之间的关系，尤其是在短基因组距离上，并不总是一个简单的关系。版权所有：© 2024 Gómez Acuña 等人。这是一篇根据知识共享署名许可条款分发的开放获取文章，允许在任何媒体上不受限制地使用、分发和复制，前提是注明原始作者和来源。

How enhancers regulate their target genes in the context of 3D chromatin organization is extensively studied and models which do not require direct enhancer-promoter contact have recently emerged. Here, we use the activation of estrogen receptor-dependent enhancers in a breast cancer cell line to study enhancer-promoter communication at two loci. This allows high temporal resolution tracking of molecular events from hormone stimulation to efficient gene activation. We examine how both enhancer-promoter spatial proximity assayed by DNA fluorescence in situ hybridization, and contact frequencies resulting from chromatin in situ fragmentation and proximity ligation, change dynamically during enhancer-driven gene activation. These orthogonal methods produce seemingly paradoxical results: upon enhancer activation enhancer-promoter contact frequencies increase while spatial proximity decreases. We explore this apparent discrepancy using different estrogen receptor ligands and transcription inhibitors. Our data demonstrate that enhancer-promoter contact frequencies are transcription independent whereas altered enhancer-promoter proximity depends on transcription. Our results emphasize that the relationship between contact frequencies and physical distance in the nucleus, especially over short genomic distances, is not always a simple one.Copyright: © 2024 Gómez Acuña et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.