Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 3200003, Israel.
Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, TN, Italy.
Nucleic Acids Res. 2021 Feb 22;49(3):1364-1382. doi: 10.1093/nar/gkaa1283.
Sequence-specific protein-DNA interactions are at the heart of the response of the tumor-suppressor p53 to numerous physiological and stress-related signals. Large variability has been previously reported in p53 binding to and transactivating from p53 response elements (REs) due, at least in part, to changes in direct (base) and indirect (shape) readouts of p53 REs. Here, we dissect p53 REs to decipher the mechanism by which p53 optimizes this highly regulated variable level of interaction with its DNA binding sites. We show that hemi-specific binding is more prevalent in p53 REs than previously envisioned. We reveal that sequences flanking the REs modulate p53 binding and activity and show that these effects extend to 4-5 bp from the REs. Moreover, we show here that the arrangement of p53 half-sites within its REs, relative to transcription direction, has been fine-tuned by selection pressure to optimize and regulate the response levels from p53 REs. This directionality in the REs arrangement is at least partly encoded in the structural properties of the REs. Furthermore, we show here that in the p21-5' RE the orientation of the half-sites is such that the effect of the flanking sequences is minimized and we discuss its advantages.
序列特异性的蛋白-DNA 相互作用是肿瘤抑制因子 p53 对众多生理和应激相关信号做出响应的核心。先前的研究表明，由于 p53 反应元件 (RE) 的直接 (碱基) 和间接 (形状) 读取发生变化，p53 与 p53 反应元件结合并反式激活的变异性很大。在这里，我们剖析 p53RE 以破译 p53 优化与 DNA 结合位点高度调控的变异性相互作用的机制。我们发现半特异性结合在 p53RE 中比以前想象的更为普遍。我们揭示了侧翼序列调节 p53 结合和活性的作用，并表明这些作用延伸到距离 RE 4-5 个碱基处。此外，我们在这里表明，相对于转录方向，p53 半位点在其 RE 内的排列方式已经通过选择压力进行了微调，以优化和调节 p53RE 的反应水平。这种在 RE 排列中的方向性至少部分地编码在 RE 的结构特性中。此外，我们在这里表明，在 p21-5'RE 中，半位点的取向使得侧翼序列的影响最小化，我们讨论了其优点。
