美国斯坦福大学William J. Greenleaf等研究人员合作发现，单分子状态将转录因子结合与基因表达联系起来。相关论文于2024年11月20日在线发表在《自然》杂志上。

研究人员应用单分子足迹分析技术，测量了在具有不同数量转录因子（TF）结合位点的工程增强子–启动子构建体上。其中，TF、核小体和其他调控蛋白的同时结合，这些构建体涉及合成TF和参与I型干扰素反应的内源性TF。尽管在无核小体DNA上的TF结合事件是独立的，但激活域招募共同因子，这些共同因子不稳定核小体，从而驱动了观察到的TF结合协同作用。

平均TF占据量线性地决定了启动子活性，研究人员将TF的强度分解为可分离的结合和激活项。最后，研究人员发展了热力学和动力学模型，定量预测了增强子结合微状态和基因表达动态。这项工作为定量剖析基因表达的不同贡献者提供了模板，包括TF激活域、浓度、结合亲和力、结合位点配置和染色质调控因子的招募。

据悉，多个TF结合到基因组增强子上，驱动哺乳动物细胞中的基因表达。然而，链接增强子序列、TF结合、启动子状态和转录水平的分子细节仍不清楚。

附：英文原文

Title: Single-molecule states link transcription factor binding to gene expression

Author: Doughty, Benjamin R., Hinks, Michaela M., Schaepe, Julia M., Marinov, Georgi K., Thurm, Abby R., Rios-Martinez, Carolina, Parks, Benjamin E., Tan, Yingxuan, Marklund, Emil, Dubocanin, Danilo, Bintu, Lacramioara, Greenleaf, William J.

Issue&Volume: 2024-11-20

Abstract: The binding of multiple transcription factors (TFs) to genomic enhancers drives gene expression in mammalian cells1. However, the molecular details that link enhancer sequence to TF binding, promoter state and transcription levels remain unclear. Here we applied single-molecule footprinting2,3 to measure the simultaneous occupancy of TFs, nucleosomes and other regulatory proteins on engineered enhancer–promoter constructs with variable numbers of TF binding sites for both a synthetic TF and an endogenous TF involved in the type I interferon response. Although TF binding events on nucleosome-free DNA are independent, activation domains recruit cofactors that destabilize nucleosomes, driving observed TF binding cooperativity. Average TF occupancy linearly determines promoter activity, and we decompose TF strength into separable binding and activation terms. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the enhancer binding microstates and gene expression dynamics. This work provides a template for the quantitative dissection of distinct contributors to gene expression, including TF activation domains, concentration, binding affinity, binding site configuration and recruitment of chromatin regulators.

DOI: 10.1038/s41586-024-08219-w

Source: https://www.nature.com/articles/s41586-024-08219-w