Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
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DOI：
10.1038/nature14482
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发表时间：
2015-07-30
期刊：
影响因子：
64.8
通讯作者：
Wang D
中科院分区：
文献类型：
--
作者：
Wang L;Zhou Y;Xu L;Xiao R;Lu X;Chen L;Chong J;Li H;He C;Fu XD;Wang D
选择性胞嘧啶残基(5mC)的DNA甲基化和Tet介导的DNA去甲基化是在早期胚胎发育中建立多潜能状态的关键。Tet酶依次将5mC、5fC和5caC转化为5hmC、5fC和5caC，后两种酶在碱基切除修复的同时被胸腺嘧啶DNA糖基酶(TDG)清除。早期报道表明，5fC和5caC可以稳定地存在于增强子、启动子和基因体上，对基因表达有不同的影响，但其机制尚不清楚。在这里，我们测定了延长的Pol II与含有氧化的5-甲基胞嘧啶(oxi-MCS)的DNA模板络合物的X射线晶体结构，揭示了5caC的5-羧基与聚合酶中保守的表观DNA识别环之间的特异性氢键。这会导致进入的NTP的位置移动，从而影响核苷酸加成。为了测试这一结构洞察的体内意义，我们确定了5fC/5caC水平增加对转录的整体影响，发现这种DNA修饰确实延缓了Pol II在基因体上的延伸。这些结果证明了oxi-MCS对基因表达的功能影响，并暗示了POL II在转录延伸过程中作为一种特异和直接的表观遗传感受器的新作用。
DNA methylation at selective cytosine residues (5mC) and their removal by TET-mediated DNA demethylation are critical for setting up pluripotent states in early embryonic development. TET enzymes successively convert 5mC to 5hmC, 5fC, and 5caC, the latter two of which are subject to removal by thymine DNA glycosylase (TDG) in conjunction with base excision repair. Early reports indicate that 5fC and 5caC could be stably detected on enhancers, promoters, and gene bodies with distinct effects on gene expression, but the mechanisms have remained elusive. Here we determined the X-ray crystal structure of elongating Pol II in complex with DNA template containing oxidized 5-methylcytosines (oxi-mCs), revealing specific hydrogen bonds between the 5-carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase. This causes a positional shift for incoming NTP thus compromising nucleotide addition. To test the in vivo significance of this structural insight, we determined the global effect of increased 5fC/5caC levels on transcription, finding that such DNA modifications indeed retarded Pol II elongation on gene bodies. These results demonstrate the functional impact of oxi-mCs on gene expression and suggest a novel role for Pol II to function as a specific and direct epigenetic sensor during transcription elongation.