Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Shirokanedai, Tokyo 108-8639, Japan.
Nucleic Acids Res. 2011 Jul;39(13):5489-98. doi: 10.1093/nar/gkr153. Epub 2011 Mar 26.
Epigenetic DNA methylation is involved in many biological processes. An epigenetic status can be altered by gain or loss of a DNA methyltransferase gene or its activity. Repair of DNA damage can also remove DNA methylation. In response to such alterations, DNA endonucleases that sense DNA methylation can act and may cause cell death. Here, we explored the possibility that McrBC, a methylation-dependent DNase of Escherichia coli, cleaves DNA at a replication fork. First, we found that in vivo restriction by McrBC of bacteriophage carrying a foreign DNA methyltransferase gene is increased in the absence of homologous recombination. This suggests that some cleavage events are repaired by recombination and must take place during or after replication. Next, we demonstrated that the enzyme can cleave a model DNA replication fork in vitro. Cleavage of a fork required methylation on both arms and removed one, the other or both of the arms. Most cleavage events removed the methylated sites from the fork. This result suggests that acquisition of even rarely occurring modification patterns will be recognized and rejected efficiently by modification-dependent restriction systems that recognize two sites. This process might serve to maintain an epigenetic status along the genome through programmed cell death.
表观遗传 DNA 甲基化参与许多生物学过程。表观遗传状态可以通过获得或丧失 DNA 甲基转移酶基因或其活性来改变。DNA 损伤的修复也可以去除 DNA 甲基化。为了应对这些变化，能够感知 DNA 甲基化的 DNA 内切酶可能会发挥作用，并可能导致细胞死亡。在这里，我们探讨了大肠杆菌依赖甲基化的 McrBC 内切酶在复制叉处切割 DNA 的可能性。首先，我们发现体内限制噬菌体携带外源 DNA 甲基转移酶基因的 McrBC 在没有同源重组的情况下增加。这表明一些切割事件是通过重组修复的，必须发生在复制过程中或之后。接下来，我们证明了该酶可以在体外切割模型 DNA 复制叉。切割叉需要两条臂上的甲基化，并且去除一条、另一条或两条臂。大多数切割事件将甲基化位点从叉上移除。该结果表明，即使是很少发生的修饰模式的获得也会被识别并被识别两个位点的依赖修饰的限制系统有效地拒绝。这个过程可能通过程序性细胞死亡来维持基因组上的表观遗传状态。
