Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells

J Mol Biol. 2019 Jan 4;431(1):111-121. doi: 10.1016/j.jmb.2018.08.001. Epub 2018 Aug 9.

Abstract

Cell-type specific gene expression programs are tightly linked to epigenetic modifications on DNA and histone proteins. Here, we used a novel CRISPR-based epigenome editing approach to control gene expression spatially and temporally. We show that targeting dCas9-p300 complex to distal non-regulatory genomic regions reprograms the chromatin state of these regions into enhancer-like elements. Notably, through controlling the spatial distance of these induced enhancers (i-Enhancer) to the promoter, the gene expression amplitude can be tightly regulated. To better control the temporal persistence of induced gene expression, we integrated the auxin-inducible degron technology with CRISPR tools. This approach allows rapid depletion of the dCas9-fused epigenome modifier complex from the target site and enables temporal control over gene expression regulation. Using this tool, we investigated the temporal persistence of a locally edited epigenetic mark and its functional consequences. The tools and approaches presented here will allow novel insights into the mechanism of epigenetic memory and gene regulation from distal regulatory sites.

Keywords: AID (auxin-inducible degron); CRISPR; enhancer-like elements; non-regulatory regions; p300.

Publication types

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

MeSH terms

  • CRISPR-Associated Proteins / genetics*
  • CRISPR-Cas Systems / genetics*
  • Cell Line
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • E1A-Associated p300 Protein / genetics*
  • Gene Editing / methods*
  • Gene Expression Regulation
  • HEK293 Cells
  • Humans
  • Promoter Regions, Genetic / genetics
  • RNA, Guide / genetics

Substances

  • CRISPR-Associated Proteins
  • RNA, Guide
  • E1A-Associated p300 Protein
  • EP300 protein, human