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bioRxiv · 10.1101/761247

Interrogation of Enhancer Function by Enhanced CRISPR Epigenetic Editing

Li, K.·Liu, Y.·Cao, H.·Zhang, Y.·Gu, Z.·Liu, X.·Yu, A.·Kaphle, P.·Dickerson, K.·Ni, M.·Xu, J.
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Abstract

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 enhanced CRISPR/dCas9-based epigenetic editing systems, enCRISPRa and enCRISPRi, for multiplexed 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 new systems display more robust perturbation 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. Multiplexed perturbations of lineage-specific enhancers using an enCRISPRi knock-in mouse establish in vivo evidence for lineage-restricted essentiality of developmental enhancers during hematopoietic lineage specification. Hence, enhanced CRSIPR epigenetic editing provides opportunities for interrogating enhancer function in native biological contexts.

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Li, K., Liu, Y., Cao, H., Zhang, Y., Gu, Z., Liu, X., Yu, A., Kaphle, P., Dickerson, K., Ni, M., Xu, J.. 2019-09-08. Interrogation of Enhancer Function by Enhanced CRISPR Epigenetic Editing. https://doi.org/10.1101/761247

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