Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing.,Nature Communications

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Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing.
Nature Communications ( IF 14.7 ) Pub Date : 2020-01-24 , DOI: 10.1038/s41467-020-14362-5
Kailong Li _{1,

2} , Yuxuan Liu _{1,

2} , Hui Cao _{1,

2} , Yuannyu Zhang _{1,

2} , Zhimin Gu _{1,

2} , Xin Liu _{1,

2} , Andy Yu _{1,

3} , Pranita Kaphle _{1,

2} , Kathryn E Dickerson _{1,

2} , Min Ni _{1,

2} , Jian Xu _{1,

2}

Affiliation

Tissue-specific gene expression requires coordinated control of gene-proximal and -distal cis-regulatory elements (CREs), yet functional analysis of gene-distal CREs such as enhancers remains challenging. Here we describe CRISPR/dCas9-based enhancer-targeting epigenetic editing systems, enCRISPRa and enCRISPRi, for efficient analysis of enhancer function in situ and in vivo. Using dual effectors capable of re-writing enhancer-associated chromatin modifications, we show that enCRISPRa and enCRISPRi modulate gene transcription by remodeling local epigenetic landscapes at sgRNA-targeted enhancers and associated genes. Comparing with existing methods, the improved systems display more robust perturbations of enhancer activity and gene transcription with minimal off-targets. Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Single or multi-loci perturbations of lineage-specific enhancers using an enCRISPRi knock-in mouse establish in vivo evidence for lineage-restricted essentiality of developmental enhancers during hematopoiesis. Hence, enhancer-targeting CRISPR epigenetic editing provides opportunities for interrogating enhancer function in native biological contexts.

中文翻译：

通过增强子靶向 CRISPR 表观遗传编辑来探究增强子功能。

组织特异性基因表达需要基因近端和远端顺式调控元件（CRE）的协调控制，但基因远端CRE（例如增强子）的功能分析仍然具有挑战性。在这里，我们描述了基于 CRISPR/dCas9 的增强子靶向表观遗传编辑系统 enCRISPRa 和 enCRISPRi，用于有效分析原位和体内增强子功能。使用能够重写增强子相关染色质修饰的双效应器，我们证明 enCRISPRa 和 enCRISPRi 通过重塑 sgRNA 靶向增强子和相关基因的局部表观遗传景观来调节基因转录。与现有方法相比，改进的系统显示出增强子活性和基因转录的更强大的扰动，并且脱靶率最小。 enCRISPRa 等位基因特异性靶向致癌 TAL1 超级增强子可调节异种移植中 TAL1 的表达和癌症进展。使用 enCRISPRi 敲入小鼠对谱系特异性增强子进行单或多位点扰动，为造血过程中发育增强子的谱系限制重要性建立了体内证据。因此，增强子靶向 CRISPR 表观遗传编辑为在天然生物环境中探究增强子功能提供了机会。

更新日期：2020-01-24

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