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Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.

Publication ,  Journal Article
Thakore, PI; D'Ippolito, AM; Song, L; Safi, A; Shivakumar, NK; Kabadi, AM; Reddy, TE; Crawford, GE; Gersbach, CA
Published in: Nat Methods
December 2015

Epigenome editing with the CRISPR (clustered, regularly interspaced, short palindromic repeats)-Cas9 platform is a promising technology for modulating gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms of gene regulation. Fusions of nuclease-inactive dCas9 to the Krüppel-associated box (KRAB) repressor (dCas9-KRAB) can silence target gene expression, but the genome-wide specificity and the extent of heterochromatin formation catalyzed by dCas9-KRAB are not known. We targeted dCas9-KRAB to the HS2 enhancer, a distal regulatory element that orchestrates the expression of multiple globin genes, and observed highly specific induction of H3K9 trimethylation (H3K9me3) at the enhancer and decreased chromatin accessibility of both the enhancer and its promoter targets. Targeted epigenetic modification of HS2 silenced the expression of multiple globin genes, with minimal off-target changes in global gene expression. These results demonstrate that repression mediated by dCas9-KRAB is sufficiently specific to disrupt the activity of individual enhancers via local modification of the epigenome.

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Published In

Nat Methods

DOI

EISSN

1548-7105

Publication Date

December 2015

Volume

12

Issue

12

Start / End Page

1143 / 1149

Location

United States

Related Subject Headings

  • Viral Proteins
  • Repressor Proteins
  • Regulatory Elements, Transcriptional
  • RNA, Guide, CRISPR-Cas Systems
  • Lentivirus
  • K562 Cells
  • Humans
  • HEK293 Cells
  • Globins
  • Gene Expression Regulation, Viral
 

Citation

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Thakore, P. I., D’Ippolito, A. M., Song, L., Safi, A., Shivakumar, N. K., Kabadi, A. M., … Gersbach, C. A. (2015). Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods, 12(12), 1143–1149. https://doi.org/10.1038/nmeth.3630
Thakore, Pratiksha I., Anthony M. D’Ippolito, Lingyun Song, Alexias Safi, Nishkala K. Shivakumar, Ami M. Kabadi, Timothy E. Reddy, Gregory E. Crawford, and Charles A. Gersbach. “Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.Nat Methods 12, no. 12 (December 2015): 1143–49. https://doi.org/10.1038/nmeth.3630.
Thakore PI, D’Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods. 2015 Dec;12(12):1143–9.
Thakore, Pratiksha I., et al. “Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.Nat Methods, vol. 12, no. 12, Dec. 2015, pp. 1143–49. Pubmed, doi:10.1038/nmeth.3630.
Thakore PI, D’Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, Reddy TE, Crawford GE, Gersbach CA. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods. 2015 Dec;12(12):1143–1149.

Published In

Nat Methods

DOI

EISSN

1548-7105

Publication Date

December 2015

Volume

12

Issue

12

Start / End Page

1143 / 1149

Location

United States

Related Subject Headings

  • Viral Proteins
  • Repressor Proteins
  • Regulatory Elements, Transcriptional
  • RNA, Guide, CRISPR-Cas Systems
  • Lentivirus
  • K562 Cells
  • Humans
  • HEK293 Cells
  • Globins
  • Gene Expression Regulation, Viral