Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains
Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains
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DOI：
10.1093/nar/gkw528
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发表时间：
2016-10-14
影响因子：
14.9
通讯作者：
Poon, Gregory M. K.
中科院分区：
文献类型：
--
作者：
Stephens, Dominique C.;Poon, Gregory M. K.
转录因子ETS家族的成员共享结构保守的DNA结合结构域，其反式激活对靶基因的甲基化非常敏感。DNA甲基化控制ETS蛋白的机制仍然知之甚少。不确定性也弥漫在半甲基化DNA的影响，这发生在DNA复制和低甲基化剂，对ETS蛋白的网站识别。为了解决这些问题，我们测量了两个序列不同的ETS同源物，PU.1和Ets-1的亲和力，以DNA位点窝藏半甲基化和完全甲基化的CpG二核苷酸。虽然这两种蛋白质结合未甲基化的DNA具有不可区分的亲和力，但它们对甲基化DNA的亲和力是显著异质的，并且在两个CpG甲基胞嘧啶之间表现出主要的能量耦合。模拟的DNA和现有的共晶结构的分析表明，半甲基化诱导的非本地的骨干和槽的几何形状，在完全甲基化的状态不保守。这些扰动的间接读出是差异实现的两个ETS同系物，与独特的界面水合PU.1/DNA结合缓和DNA甲基化结合的抑制作用。这些数据为与PU.1相关的开创性特性建立了生物物理学基础，PU.1牢固地结合完全甲基化的DNA，而不是Ets-1，Ets-1基本上被抑制。
Transactivation by the ETS family of transcription factors, whose members share structurally conserved DNA-binding domains, is variably sensitive to methylation of their target genes. The mechanism by which DNA methylation controls ETS proteins remains poorly understood. Uncertainly also pervades the effects of hemi-methylated DNA, which occurs following DNA replication and in response to hypomethylating agents, on site recognition by ETS proteins. To address these questions, we measured the affinities of two sequence-divergent ETS homologs, PU.1 and Ets-1, to DNA sites harboring a hemi- and fully methylated CpG dinucleotide. While the two proteins bound unmethylated DNA with indistinguishable affinity, their affinities to methylated DNA are markedly heterogeneous and exhibit major energetic coupling between the two CpG methylcytosines. Analysis of simulated DNA and existing co-crystal structures revealed that hemi-methylation induced non-local backbone and groove geometries that were not conserved in the fully methylated state. Indirect readout of these perturbations was differentially achieved by the two ETS homologs, with the distinctive interfacial hydration in PU.1/DNA binding moderating the inhibitory effects of DNA methylation on binding. This data established a biophysical basis for the pioneering properties associated with PU.1, which robustly bound fully methylated DNA, but not Ets-1, which was substantially inhibited.