The formation and function of highly specialized cells and tissues in a multicellular organism from a single genome are enabled through differential spatiotemporal access to the information contained in the genomic DNA. The epigenome plays an essential role in how DNA information can be accessed, and in the last decade the link between epigenetic aberrations and pathologies has become increasingly clear. Methods to precisely modify the epigenome are hence attracting interest as potential novel therapeutics. We recently described a platform, designer epigenome modifier (DEM), capable of precisely editing the epigenome of a cell to control the expression of selected genes. Here, we provide a detailed protocol to streamline the process of identifying DEMs that efficiently and selectively bind to their intended target site and inactivate expression of the target gene. Further, we describe the procedure to simultaneously regulate the expression of up to three genes in a multiplexed fashion. The protocol is divided into four stages that guide the user through the generation of the multicolor reporter cell line and its use for selecting functional DEMs. The duration of the whole procedure described varies from ~6 weeks when using a single reporter up to 13 weeks for fine-tuning the multiplex epigenome editing abilities of selected DEMs using three reporters. Given the great interest in epigenome editing in various fields of biomedical research, this protocol will help scientists to explore these novel technologies for their research.

通过对基因组 DNA 中包含的信息的不同时空访问，能够从单个基因组中形成多细胞生物体中高度特化的细胞和组织。表观基因组在如何获取 DNA 信息方面发挥着重要作用，在过去十年中，表观遗传畸变与病理之间的联系变得越来越清晰。因此，精确修饰表观基因组的方法作为潜在的新疗法引起了人们的兴趣。我们最近描述了一个平台，设计表观基因组修饰符 (DEM)，能够精确编辑细胞的表观基因组以控制所选基因的表达。这里，我们提供了一个详细的协议来简化识别 DEM 的过程，这些 DEM 有效地和选择性地结合到其预期的目标位点并使目标基因的表达失活。此外，我们描述了以多重方式同时调节多达三个基因表达的程序。该协议分为四个阶段，指导用户生成多色报告细胞系及其用于选择功能 DEM。所描述的整个过程的持续时间从使用单个记者时约 6 周到 13 周不等，使用三个记者微调所选 DEM 的多重表观基因组编辑能力。鉴于生物医学研究的各个领域对表观基因组编辑的极大兴趣，