Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

Nat Commun. 2020 Jan 24;11(1):485. doi: 10.1038/s41467-020-14362-5.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CRISPR-Cas Systems
  • Cell Line
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Enhancer Elements, Genetic*
  • Epigenesis, Genetic*
  • Female
  • Gene Editing / methods*
  • HEK293 Cells
  • Hematopoiesis / genetics
  • Humans
  • Jurkat Cells
  • K562 Cells
  • Mice
  • Mice, Inbred NOD
  • Mice, SCID
  • Mice, Transgenic
  • Neoplasms / genetics
  • RNA, Guide, Kinetoplastida / genetics
  • T-Cell Acute Lymphocytic Leukemia Protein 1 / genetics


  • RNA, Guide
  • T-Cell Acute Lymphocytic Leukemia Protein 1
  • TAL1 protein, human