A fine kinetic balance of interactions directs transcription factor hubs to genes [RNA-Seq]

Eukaryotic gene regulation relies on the binding of sequence-specific transcription factors (TFs). TFs bind chromatin transiently yet occupy their target sites by forming high-local concentration microenvironments (hubs and condensates) that increase the frequency of binding events. Despite their ubiquity, such microenvironments have been difficult to study in endogenous contexts due to technical limitations. Here, we overcome these limitations and investigate how hubs drive TF occupancy at their targets. Using a DNA binding perturbation to a hub-forming TF, Zelda, in Drosophila embryos, we find that hub properties, including the stability and frequencies of associations to targets, are key determinants of TF occupancy. Our data suggest that hub targeting is driven not just by specific DNA motif recognition, but also by a fine-tuned kinetic balance of interactions between TFs and their co-binding partners. WT embryos were compared to embryos with the 5th Zinc Finger of Zelda deleted

真核基因调控依赖于序列特异性转录因子（transcription factors，TFs）的结合。转录因子会瞬时结合染色质，但通过形成高局部浓度微环境（hubs与condensates）以占据靶位点，进而提升结合事件的发生频率。尽管这类微环境广泛存在，但受限于技术瓶颈，在内源性生理环境中对其开展研究始终颇具挑战。本研究突破了上述技术局限，探究了枢纽如何驱动转录因子在靶位点的占据情况。本研究以果蝇胚胎中的枢纽形成型转录因子Zelda为对象，通过干扰其DNA结合能力，发现枢纽的相关特性——包括与靶位点结合的稳定性及结合频率——是决定转录因子占据情况的关键因素。我们的研究数据表明，枢纽的靶向定位不仅依赖于特异性DNA基序识别，还得益于转录因子与其协同结合伴侣之间相互作用的精细动态平衡。本研究将野生型胚胎与缺失Zelda第5个锌指结构的胚胎进行了对照分析。