Rodriguez Kevin, Do Albert, Senay-Aras Betul, Perales Mariano, Alber Mark, Chen Weitao, Reddy G Venugopala
Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA.
Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA.
Sci Adv. 2022 Aug 12;8(32):eabo6157. doi: 10.1126/sciadv.abo6157. Epub 2022 Aug 10.
Gene expression specificity of homeobox transcription factors has remained paradoxical. WUSCHEL activates and represses transcription at lower and higher concentrations, respectively. We use computational modeling and experimental analysis to investigate the properties of the cis-regulatory module. We find that intrinsically each cis-element can only activate at a higher WUSCHEL concentration. However, together, they repress at higher WUSCHEL and activate only at lower WUSCHEL, showing that the concentration-dependent interactions among cis-elements regulate both activation and repression. Biochemical experiments show that two adjacent functional cis-elements bind WUSCHEL with higher affinity and dimerize at relatively lower levels. Moreover, increasing the distance between cis-elements prolongs WUSCHEL monomer binding window, resulting in higher activation. Our work showing a constellation of optimally spaced cis-elements of defined affinities determining activation and repression thresholds in regulating transcription provides a previously unknown mechanism of cofactor-independent regulation of transcription factor binding in mediating gene expression specificity.
同源异型框转录因子的基因表达特异性一直存在矛盾之处。WUSCHEL蛋白在较低和较高浓度时分别激活和抑制转录。我们运用计算建模和实验分析来研究顺式调控模块的特性。我们发现，本质上每个顺式元件仅能在较高的WUSCHEL浓度下激活转录。然而，这些顺式元件共同作用时，在较高的WUSCHEL浓度下会抑制转录，仅在较低的WUSCHEL浓度下激活转录，这表明顺式元件之间浓度依赖性的相互作用同时调控着激活和抑制过程。生化实验表明，两个相邻的功能性顺式元件以更高的亲和力结合WUSCHEL蛋白，并在相对较低的水平上形成二聚体。此外，增加顺式元件之间的距离会延长WUSCHEL单体的结合窗口，从而导致更高的激活水平。我们的研究表明，一组具有确定亲和力且间隔最佳的顺式元件决定了调控转录时的激活和抑制阈值，这为转录因子结合的辅因子非依赖性调控提供了一种前所未知的机制，该机制在介导基因表达特异性中发挥作用。
