Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing,Cell

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Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing
Cell ( IF 45.5 ) Pub Date : 2021-04-09 , DOI: 10.1016/j.cell.2021.03.025
James K Nuñez ₁ , Jin Chen ₁ , Greg C Pommier ₂ , J Zachery Cogan ₃ , Joseph M Replogle ₄ , Carmen Adriaens ₅ , Gokul N Ramadoss ₆ , Quanming Shi ₇ , King L Hung ₇ , Avi J Samelson ₆ , Angela N Pogson ₈ , James Y S Kim ₉ , Amanda Chung ₁₀ , Manuel D Leonetti ₉ , Howard Y Chang ₁₁ , Martin Kampmann ₁₂ , Bradley E Bernstein ₅ , Volker Hovestadt ₁₃ , Luke A Gilbert ₁₄ , Jonathan S Weissman ₁₅

Affiliation

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA.
Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA.
Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA.
Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158.
Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA.
Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Department of Urology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA.
Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA.

A general approach for heritably altering gene expression has the potential to enable many discovery and therapeutic efforts. Here, we present CRISPRoff—a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks establishes rules for heritable gene silencing. We identify single guide RNAs (sgRNAs) capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. The broad ability of CRISPRoff to initiate heritable gene silencing even outside of CGIs expands the canonical model of methylation-based silencing and enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.

中文翻译：

通过基于 CRISPR 的表观基因组编辑实现全基因组可编程转录记忆

遗传性改变基因表达的通用方法有可能实现许多发现和治疗工作。在这里，我们推出了 CRISPRoff——一种可编程表观遗传记忆写入器，由单个死 Cas9 融合蛋白组成，可建立 DNA 甲基化和抑制性组蛋白修饰。瞬时 CRISPRoff 表达启动高度特异性的 DNA 甲基化和基因抑制，这种抑制通过细胞分裂和干细胞分化为神经元来维持。将 CRISPRoff 与全基因组筛选和染色质标记分析相结合，建立了可遗传基因沉默的规则。我们确定了能够沉默大多数基因（包括那些缺乏规范 CpG 岛 (CGI) 的基因）的单向导 RNA (sgRNA)，并揭示了超出注释 CGI 的广泛靶向窗口。CRISPRoff 甚至在 CGI 之外启动可遗传基因沉默的广泛能力扩展了基于甲基化的沉默的规范模型，并实现了多种应用，包括全基因组筛选、多重细胞工程、增强子沉默和表观遗传的机制探索。

更新日期：2021-04-29

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