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Genome Biol. 2017 Sep 18;18(1):176. doi: 10.1186/s13059-017-1306-z.

DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A.

Huang YH1,2,3, Su J4, Lei Y2,3, Brunetti L2,3, Gundry MC2,3,5, Zhang X2,3, Jeong M2,3, Li W6, Goodell MA7,8,9,10.

Author information

1
Department of Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
2
Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.
3
Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA.
4
Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
5
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
6
Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. wl1@bcm.edu.
7
Department of Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. goodell@bcm.edu.
8
Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA. goodell@bcm.edu.
9
Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA. goodell@bcm.edu.
10
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. goodell@bcm.edu.

Abstract

BACKGROUND:

DNA methylation has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global patterns of DNA methylation and gene expression.

RESULTS:

Here, we utilize nuclease-deactivated Cas9 protein fused to repetitive peptide epitopes (SunTag) recruiting multiple copies of antibody-fused de novo DNA methyltransferase 3A (DNMT3A) (dCas9-SunTag-DNMT3A) to amplify the local DNMT3A concentration to methylate genomic sites of interest. We demonstrate that dCas9-SunTag-DNMT3A dramatically increases CpG methylation at the HOXA5 locus in human embryonic kidney (HEK293T) cells. Furthermore, using a single guide RNA, dCas9-SunTag-DNMT3A is able to methylate a 4.5-kb genomic region and repress HOXA5 gene expression. Reduced representation bisulfite sequencing and RNA-seq show that dCas9-SunTag-DNMT3A methylates regions of interest with minimal impact on the global DNA methylome and transcriptome.

CONCLUSIONS:

This effective and precise tool enables site-specific manipulation of DNA methylation and may be used to address the relationship between DNA methylation and gene expression.

PMID:
28923089
PMCID:
PMC5604343
DOI:
10.1186/s13059-017-1306-z
[Indexed for MEDLINE]
Free PMC Article

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