Kandavalli Vinodh, Zikrin Spartak, Elf Johan, Jones Daniel
Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Nat Commun. 2025 Jan 17;16(1):764. doi: 10.1038/s41467-025-56053-z.
The rate at which transcription factors (TFs) bind their cognate sites has long been assumed to be limited by diffusion, and thus independent of binding site sequence. Here, we systematically test this assumption using cell-to-cell variability in gene expression as a window into the in vivo association and dissociation kinetics of the model transcription factor LacI. Using a stochastic model of the relationship between gene expression variability and binding kinetics, we performed single-cell gene expression measurements to infer association and dissociation rates for a set of 35 different LacI binding sites. We found that both association and dissociation rates differed significantly between binding sites, and moreover observed a clear anticorrelation between these rates across varying binding site strengths. These results contradict the long-standing hypothesis that TF binding site strength is primarily dictated by the dissociation rate, but may confer the evolutionary advantage that TFs do not get stuck in near-operator sequences while searching.
长期以来，人们一直认为转录因子（TFs）与其同源位点的结合速率受扩散限制，因此与结合位点序列无关。在此，我们利用基因表达中的细胞间变异性作为窗口，系统地测试这一假设，以深入了解模型转录因子LacI在体内的结合和解离动力学。利用基因表达变异性与结合动力学之间关系的随机模型，我们进行了单细胞基因表达测量，以推断一组35个不同LacI结合位点的结合和解离速率。我们发现，不同结合位点之间的结合和解离速率均存在显著差异，而且在不同结合位点强度下，这些速率之间存在明显的反相关关系。这些结果与长期存在的假说相矛盾，该假说认为TF结合位点强度主要由解离速率决定，但可能赋予了TF在搜索时不会被困在近操纵子序列中的进化优势。
