Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism
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DOI：
10.1038/nature07249
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发表时间：
2008-10-09
期刊：
影响因子：
64.8
通讯作者：
Shirakawa, Masahiro
中科院分区：
文献类型：
--
作者：
Arita, Kyohei;Ariyoshi, Mariko;Shirakawa, Masahiro
CpG二核苷酸的DNA甲基化是哺乳动物基因组的重要表观遗传修饰，并且对于染色质结构、基因表达和基因组稳定性的调节是必不可少的（1，2）。DNA甲基化模式的差异是多种生物学过程的基础，例如基因组印记、X染色体失活、胚胎发生和癌发生（3-6）。表观遗传甲基化模式的遗传由DNA甲基转移酶1（Dnmt 1）介导，该酶在DNA复制期间甲基化新合成的CpG序列，这取决于模板链的甲基化状态（7，8）。蛋白质UHRF 1（也称为Np 95和ICBP 90）通过SET和RING相关（SRA）结构域识别半甲基化位点，并将Dnmt 1引导至这些位点（9-11）。在这里，我们报告的晶体结构的SRA结构域在自由和半甲基化的DNA结合状态。SRA结构域折叠成具有由高度保守残基形成的基本凹面的球形结构。DNA与凹面的结合导致SRA结构域的环和氨基末端尾在甲基化位点的大沟和小沟处折叠成DNA界面。与甲基- CpG结合结构域识别的完全甲基化的CpG位点相反（12，13），半甲基化位点的甲基胞嘧啶碱基从SRA-DNA复合物中的DNA螺旋中翻转出来，并紧密地嵌入凹面上的蛋白质口袋中.复合物结构表明，预先存在的甲基化胞嘧啶和待甲基化的靶胞嘧啶的连续翻转与半甲基化CpG位点从UHRF 1到Dnmt 1的协调转移相关。
DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability(1,2). Differences in DNA methylation patterns underlie a wide range of biological processes, such as genomic imprinting, inactivation of the X chromosome, embryogenesis, and carcinogenesis(3-6). Inheritance of the epigenetic methylation pattern is mediated by the enzyme DNA methyltransferase 1 ( Dnmt1), which methylates newly synthesized CpG sequences during DNA replication, depending on the methylation status of the template strands(7,8). The protein UHRF1 ( also known as Np95 and ICBP90) recognizes hemi- methylation sites via a SET and RING- associated ( SRA) domain and directs Dnmt1 to these sites(9-11). Here we report the crystal structures of the SRA domain in free and hemi- methylated DNA- bound states. The SRA domain folds into a globular structure with a basic concave surface formed by highly conserved residues. Binding of DNA to the concave surface causes a loop and an amino- terminal tail of the SRA domain to fold into DNA interfaces at the major and minor grooves of the methylation site. In contrast to fully methylated CpG sites recognized by the methyl- CpG- binding domain(12,13), the methylcytosine base at the hemi- methylated site is flipped out of the DNA helix in the SRA - DNA complex and fits tightly into a protein pocket on the concave surface. The complex structure suggests that the successive flip out of the pre- existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi- methylated CpG site from UHRF1 to Dnmt1.