Fallacaro Samantha, Mukherjee Apratim, Turner Meghan A, Garcia Hernan G, Mir Mustafa
Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA.
Developmental, Stem Cell, and Regenerative Biology Graduate Group, Perelman School of Medicine; Philadelphia, PA 19104, USA.
bioRxiv. 2025 Apr 8:2025.04.07.647578. doi: 10.1101/2025.04.07.647578.
The spatial and temporal control of gene expression relies on transcription factors binding to and occupying their target sites. Transcription factor hubs-localized, high-concentration microenvironments-promote transcription by facilitating binding and recruitment of transcriptional machinery and co-factors. Hubs are often thought to have emergent nucleus-wide properties depending on transcription factor nuclear concentrations and intrinsic, protein sequence-dependent properties. This global model does not account for gene-specific hub regulation. Using high-resolution lattice light-sheet microscopy in embryos, we examined hubs formed by the morphogen transcription factor, Dorsal, at reporter genes with distinct enhancer compositions. We found that recruits long-lived, high-intensity hubs; exhibits shorter-lived, lower-intensity hubs; and , lacking Dorsal binding sites, shows only transient hub interactions. Hub intensity and interaction duration correlate with burst amplitude, RNAPII loading rate, and transcriptional output. These findings challenge the global view of hub formation and support a model where hub properties are locally tuned in a gene-specific manner to regulate transcriptional kinetics.
基因表达的时空控制依赖于转录因子与它们的靶位点结合并占据这些位点。转录因子枢纽——局部化的高浓度微环境——通过促进转录机器和辅助因子的结合与募集来促进转录。枢纽通常被认为具有全细胞核范围的特性，这取决于转录因子的核浓度以及内在的、蛋白质序列依赖性的特性。这种全局模型无法解释基因特异性的枢纽调控。我们在胚胎中使用高分辨率晶格光片显微镜，研究了形态发生素转录因子背侧（Dorsal）在具有不同增强子组成的报告基因处形成的枢纽。我们发现，[具体基因1]募集寿命长、强度高的枢纽；[具体基因2]表现出寿命较短、强度较低的枢纽；而[具体基因3]缺乏背侧结合位点，仅显示短暂的枢纽相互作用。枢纽强度和相互作用持续时间与爆发幅度、RNA聚合酶II加载速率和转录输出相关。这些发现挑战了枢纽形成的全局观点，并支持了一种模型，即枢纽特性以基因特异性方式在局部进行调节以控制转录动力学。
