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Nat Commun DOI:10.1038/s41467-019-12166-w

Epigenome editing strategies for the functional annotation of CTCF insulators.

Publication TypeJournal Article
Year of Publication2019
AuthorsTarjan, DR, Flavahan, WA, Bernstein, BE
JournalNat Commun
Date Published2019 Sep 18

The human genome is folded into regulatory units termed 'topologically-associated domains' (TADs). Genome-wide studies support a global role for the insulator protein CTCF in mediating chromosomal looping and the topological constraint of TAD boundaries. However, the impact of individual insulators on enhancer-gene interactions and transcription remains poorly understood. Here, we investigate epigenome editing strategies for perturbing individual CTCF insulators and evaluating consequent effects on genome topology and transcription. We show that fusions of catalytically-inactive Cas9 (dCas9) to transcriptional repressors (dCas9-KRAB) and DNA methyltransferases (dCas9-DNMT3A, dCas9-DNMT3A3L) can selectively displace CTCF from specific insulators, but only when precisely targeted to the cognate motif. We further demonstrate that stable, partially-heritable insulator disruption can be achieved through combinatorial hit-and-run epigenome editing. Finally, we apply these strategies to simulate an insulator loss mechanism implicated in brain tumorigenesis. Our study provides strategies for stably modifying genome organization and gene activity without altering the underlying DNA sequence.


Alternate JournalNat Commun
PubMed ID31534142
PubMed Central IDPMC6751197
Grant ListDP1CA216873 / / U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) /