Hörberg Johanna, Hallbäck Björn, Moreau Kevin, Reymer Anna
Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
QRB Discov. 2022 Nov 28;3:e23. doi: 10.1017/qrd.2022.21. eCollection 2022.
Selective DNA binding by transcription factors (TFs) is crucial for the correct regulation of DNA transcription. In healthy cells, promoters of active genes are hypomethylated. A single CpG methylation within a TF response element (RE) may change the binding preferences of the protein, thus causing the dysregulation of transcription programs. Here, we investigate a molecular mechanism driving the downregulation of the gene, due to hypermethylation, which is associated with multiple cancers. Using bioinformatic analyses of breast cancer cell line MCF7, we identify a hypermethylated region containing the binding sites of two TFs dimers, CEBPB and E2F1-DP1, located 130 b.p. from the gene transcription start site. All-atom extended MD simulations of wild type and methylated DNA alone and in complex with either one or both TFs dimers provide mechanistic insights into the cooperative asymmetric binding order of the two dimers; the CEBPB binding should occur first to facilitate the E2F1-DP1-DNA association. The CpG methylation within the E2F1-DP1 RE and the linker decrease the cooperativity effects and renders the E2F1-DP1 binding site less recognizable by the TF dimer. Taken together, the identified CpG methylation site may contribute to the downregulation of the gene.
转录因子（TFs）对DNA的选择性结合对于正确调控DNA转录至关重要。在健康细胞中，活跃基因的启动子处于低甲基化状态。TF反应元件（RE）内的单个CpG甲基化可能会改变蛋白质的结合偏好，从而导致转录程序失调。在此，我们研究了一种由于高甲基化导致基因下调的分子机制，这种高甲基化与多种癌症相关。通过对乳腺癌细胞系MCF7进行生物信息学分析，我们确定了一个高甲基化区域，该区域包含两个TF二聚体CEBPB和E2F1-DP1的结合位点，位于距基因转录起始位点130个碱基对处。对野生型和甲基化DNA单独以及与一个或两个TF二聚体形成复合物的全原子扩展分子动力学模拟，为两个二聚体的协同不对称结合顺序提供了机制性见解；CEBPB的结合应首先发生，以促进E2F1-DP1与DNA的结合。E2F1-DP1 RE内的CpG甲基化和连接子降低了协同效应，并使E2F1-DP1结合位点更难被TF二聚体识别。综上所述，所确定的CpG甲基化位点可能导致该基因的下调。
