CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome [CERES]. Homo sapiens

Large genome mapping consortia and thousands of genome-wide association studies have identified non-protein coding elements in the genome as a having a central role in tissue development, cell-type specification, response to environmental or pharmacologic signals, and susceptibility to most common diseases. However, decoding the function of the millions of putative regulatory elements discovered in these studies remains a primary challenge. New CRISPR/Cas9-based epigenome editing technologies have enabled the precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR/Cas9-based Epigenomic Regulatory Element Screening (CERES) for high-throughput screening of regulatory element activity within the native genomic context. We perform both loss- and gain-of-function screens with complementary epigenome editing tools to identify known and unknown regulatory elements of medically relevant genes in human cells. The high-throughput functional annotation of putative regulatory elements by CERES constitutes a new platform for screening biological mechanisms that cannot be perturbed by traditional methods. Overall design: Pooled gRNA screens with dCas9 based epigenome editing tools for regulatory element discovery.

大型基因组图谱联盟与数千项全基因组关联研究（genome-wide association studies）已证实，基因组中的非蛋白质编码元件在组织发育、细胞类型特化、对环境或药物信号的响应，以及大多数常见疾病的易感性中发挥核心作用。然而，解析这些研究中发现的数百万个潜在调控元件的功能，仍是当前的核心挑战。基于CRISPR/Cas9的新型表观基因组编辑（epigenome editing）技术已实现对特定调控元件活性的精准扰动。本文介绍了基于CRISPR/Cas9的表观基因组调控元件筛选技术（CRISPR/Cas9-based Epigenomic Regulatory Element Screening，缩写CERES），用于在天然基因组背景下对调控元件活性开展高通量筛选。本研究使用互补的表观基因组编辑工具，同时实施功能缺失与功能获得性筛选，以识别人类细胞中与医学相关基因的已知及未知调控元件。CERES可对潜在调控元件进行高通量功能注释，为筛选传统方法无法扰动的生物学机制提供了全新研究平台。总体实验设计：采用基于dCas9的表观基因组编辑工具开展向导RNA（gRNA）混合筛选，以发现调控元件。