PDF(Pubmed)
Abstract：
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
摘要：
非CpG甲基化与几个细胞过程相关，尤其是神经元发育和癌症，而其对DNA结构的影响尚不清楚。我们已经将含有-CGCCG-区的DNA双链体的晶体结构确定为包含非CpG位点且具有或不具有胞嘧啶甲基化的CCG重复基序。晶体结构分析表明，mC：G碱基对可以同时形成两种由非CpG甲基化产生的替代构象。包括一个独特的水介导的顺式Watson-Crick/Hoogsteen，(w)cWH,和沃森-克里克(WC)几何形状，部分占用率分别为0.1和0.9。NMR研究表明，甲基化mC：G碱基对在非CpG步骤中的另一种构象表现出cWH在溶液中具有顺式鸟苷构象的特征。与DNA结合药物棘霉素复合的DNA双链体导致（w）cWH几何结构在甲基化碱基对中的占有率增加（从0.1到0.3）。我们的结构结果表明，非CpG步骤的胞嘧啶甲基化会导致其互补鸟苷残基向（w）cWH几何结构的反→syntransition，作为WC的部分种群，在药物结合和裸mC：G碱基对中。这种特定的几何形状对B型DNA中的非CpG甲基化二核苷酸位点是特异性的。总的来说,当前的研究为表观遗传调控过程中的DNA构象提供了新的见解。
