Epigenome editing is a promising technology, potentially allowing the stable reprogramming of gene expression profiles without alteration of the DNA sequence. Targeted DNA methylation has been successfully documented by many groups for silencing selected genes, but recent publications have raised concerns regarding its specificity. In the current work, we developed new EpiEditors for programmable DNA methylation in cells with a high efficiency and improved specificity. First, we demonstrated that the catalytically deactivated Cas9 protein (dCas9)-SunTag scaffold, which has been used earlier for signal amplification, can be combined with the DNMT3A-DNMT3L single-chain effector domain, allowing for a strong methylation at the target genomic locus. We demonstrated that off-target activity of this system is mainly due to untargeted freely diffusing DNMT3A-DNMT3L subunits. Therefore, we generated several DNMT3A-DNMT3L variants containing mutations in the DNMT3A part, which reduced their endogenous DNA binding. We analyzed the genome-wide DNA methylation of selected variants and confirmed a striking reduction of untargeted methylation, most pronounced for the R887E mutant. For all potential applications of targeted DNA methylation, the efficiency and specificity of the treatment are the key factors. By developing highly active targeted methylation systems with strongly improved specificity, our work contributes to future applications of this approach.

译文

表观基因组编辑是一项有前途的技术,可能允许基因表达谱的稳定重编程而不改变DNA序列。靶向DNA甲基化已被许多小组成功地记录为沉默选定的基因,但最近的出版物引起了人们对其特异性的关注。在当前的工作中,我们开发了用于细胞中可编程DNA甲基化的新型EpiEditors,具有高效率和改进的特异性。首先,我们证明了较早用于信号扩增的催化失活Cas9蛋白 (dCas9)-SunTag支架可以与DNMT3A-DNMT3L的单链效应结构域结合,从而在靶基因组基因座处实现强甲基化。我们证明了该系统的脱靶活动主要是由于未靶向的自由扩散DNMT3A-DNMT3L亚基。因此,我们在DNMT3A部分产生了几个包含突变的DNMT3A-DNMT3L变体,这降低了它们的内源性DNA结合。我们分析了所选变体的全基因组DNA甲基化,并证实了未靶向甲基化的显着降低,对于R887E突变体最为明显。对于靶向DNA甲基化的所有潜在应用,治疗的效率和特异性是关键因素。通过开发具有高度改善的特异性的高活性靶向甲基化系统,我们的工作为该方法的未来应用做出了贡献。

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