Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions

• Published in: Nature biotechnology 2016-10, Vol.34 (10), p.1060-1065
• Main Authors: Morita, Sumiyo, Noguchi, Hirofumi, Horii, Takuro, Nakabayashi, Kazuhiko, Kimura, Mika, Okamura, Kohji, Sakai, Atsuhiko, Nakashima, Hideyuki, Hata, Kenichiro, Nakashima, Kinichi, Hatada, Izuho
• Format: Article
• Language: English
• Subjects: 38; 38/23; 38/77; 631/1647/1513/1967/3196; 631/1647/2210/2213; Agriculture; Amino acids; Animals; Basic-Leucine Zipper Transcription Factors - genetics; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Catalysis; Clustered Regularly Interspaced Short Palindromic Repeats - genetics; CpG Islands - genetics; CRISPR-Associated Proteins - genetics; Deoxyribonucleic acid; DNA; DNA methylation; DNA Methylation - genetics; DNA sequencing; Gene Targeting - methods; Genetic Engineering - methods; Genomics; letter; Life Sciences; Methods; Methylation; Mice; Mixed Function Oxygenases - genetics; Observations; Peptides; Physiological aspects; Protein Domains; Proto-Oncogene Proteins - genetics; Saccharomyces cerevisiae Proteins - genetics; Single-Chain Antibodies - genetics; Stem cells
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.3658

DNA methyl groups are selectively removed at target loci using inactive Cas9 fused to a SunTag-based peptide repeat that recruits the enzymatic activity. Despite the importance of DNA methylation in health and disease, technologies to readily manipulate methylation of specific sequences for functional analysis and therapeutic purposes are lacking. Here we adapt the previously described dCas9–SunTag for efficient, targeted demethylation of specific DNA loci. The original SunTag consists of ten copies of the GCN4 peptide separated by 5-amino-acid linkers. To achieve efficient recruitment of an anti-GCN4 scFv fused to the ten-eleven (TET) 1 hydroxylase, which induces demethylation, we changed the linker length to 22 amino acids. The system attains demethylation efficiencies >50% in seven out of nine loci tested. Four of these seven loci showed demethylation of >90%. We demonstrate targeted demethylation of CpGs in regulatory regions and demethylation-dependent 1.7- to 50-fold upregulation of associated genes both in cell culture (embryonic stem cells, cancer cell lines, primary neural precursor cells) and in vivo in mouse fetuses.