Accurate gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a TF binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Recent studies suggest TP53 functions as a pioneer factor that can target its TFBS within nucleosomes, but it remains unclear how TP53 binds to nucleosomal DNA. To comprehensively examine TP53 nucleosome binding, we competitively bound TP53 to multiple in vitro–formed nucleosomes containing a high- or low-affinity TP53 TFBS located at differing translational and rotational positions within the nucleosome. Stable TP53–nucleosome complexes were isolated and quantified using next-generation sequencing. Our results demonstrate TP53 binding is limited to nucleosome edges with significant binding inhibition occurring within 50 bp of the nucleosome dyad. Binding site affinity only affects TP53 binding for TFBSs located at the same nucleosomal positions; otherwise, nucleosome position takes precedence. Furthermore, TP53 has strong nonspecific nucleosome binding facilitating its interaction with chromatin. Our in vitro findings were confirmed by examining TP53-induced binding in a cell line model, showing induced binding at nucleosome edges flanked by a nucleosome-free region. Overall, our results suggest that the pioneering capabilities of TP53 are driven by nonspecific nucleosome binding with specific binding at nucleosome edges.

准确的基因表达需要将转录因子（TFs）靶向经常被核小体封闭的调节序列。靶向核小体中TF结合位点（TFBS）的能力一直是称为先驱因子的特殊类型TF的定义特征。最近的研究表明，TP53是可以靶向其TFBS的核糖体中的先驱因子，但目前尚不清楚TP53如何与核小体DNA结合。为了全面检查TP53核小体的结合，我们将TP53竞争性结合了多个体外形成的核小体，这些核小体包含位于核小体内不同翻译和旋转位置的高亲和力或低亲和力TP53 TFBS。稳定的TP53–核小体复合物已被分离，并使用下一代测序技术进行了定量。我们的结果表明，TP53的结合仅限于核小体边缘，在核小体二聚体的50 bp内发生了显着的结合抑制作用。结合位点亲和力仅影响位于相同核小体位置的TFBS的TP53结合。否则，核小体位置优先。此外，TP53具有很强的非特异性核小体结合，有助于其与染色质的相互作用。通过在细胞系模型中检查TP53诱导的结合，证实了我们的体外发现，结果显示诱导的结合在侧翼为无核小体区域的核小体边缘。总的来说，我们的结果表明TP53的开拓能力是由非特异性核小体结合和核小体边缘的特异性结合所驱动的。结合位点亲和力仅影响位于相同核小体位置的TFBS的TP53结合。否则，核小体位置优先。此外，TP53具有很强的非特异性核小体结合，有助于其与染色质的相互作用。通过在细胞系模型中检查TP53诱导的结合，证实了我们的体外发现，结果显示诱导的结合在侧翼为无核小体区域的核小体边缘。总的来说，我们的结果表明TP53的开拓能力是由非特异性核小体结合和核小体边缘的特异性结合所驱动的。结合位点亲和力仅影响位于相同核小体位置的TFBS的TP53结合。否则，核小体位置优先。此外，TP53具有很强的非特异性核小体结合，有助于其与染色质的相互作用。通过在细胞系模型中检查TP53诱导的结合，证实了我们的体外发现，结果显示诱导的结合在侧翼为无核小体区域的核小体边缘。总的来说，我们的结果表明TP53的开拓能力是由非特异性核小体结合和核小体边缘的特异性结合所驱动的。通过在细胞系模型中检查TP53诱导的结合，证实了我们的体外发现，结果显示诱导的结合在侧翼为无核小体区域的核小体边缘。总的来说，我们的结果表明TP53的开拓能力是由非特异性核小体结合以及在核小体边缘具有特异性结合所驱动的。通过在细胞系模型中检查TP53诱导的结合，证实了我们的体外发现，结果显示诱导的结合在侧翼为无核小体区域的核小体边缘。总的来说，我们的结果表明TP53的开拓能力是由非特异性核小体结合和核小体边缘的特异性结合所驱动的。