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

Morita, Sumiyo; Noguchi, Hirofumi; Horii, Takuro; Nakabayashi, Kazuhiko; Kimura, Masashi; Okamura, Koji; Sakai, Atsuhiko; Nakashima, Hideyuki; Hata, Kenichiro; Nakashima, Kinichi; Hatada, Izuho

doi:10.1038/nbt.3658

Cited by 431 publications

(436 citation statements)

References 32 publications

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“…Furthermore, with more complete regulatory element sequences, one could use CRISPRa/i to regulate gene expression levels. Finally, tools can be deployed that modify the methylation of endogenous promoters to activate or silence gene expression [Morita et al, 2016], [Vojta et al, 2016]. Overall, these strategies enhance our control over cell phenotype.…”

Section: Discussionmentioning

confidence: 99%

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

103

119

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Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

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Section: Discussionmentioning

confidence: 99%

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

103

119

View full text Add to dashboard Cite

show abstract

“…For example, Morita and colleagues used this system to recruit multiple copies of the catalytic domain of ten-eleven translocation methylcytosine dioxygenase (TET1CD) which induces DNA demethylation at the target region. Their results showed increased demethylation activity when SunTag was used compared to direct fusions of TET1CD to dCas9 [52]. It is important to note that the linker length between the GCN4 peptide and the copy number in the peptide repeat should be optimized depending on the specific CME.…”

Section: Biochemical-specificitymentioning

confidence: 99%

Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities

Sen

Keung

2018

Methods in Molecular Biology

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The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical- and locus-specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.

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“…The examinations of epigenome editing with DNA methylation/demethylation have been reported by many groups, where TET1 demethylase [36,41,58,59,61] and DNMT3A methyltransferase [31,32,41,43,44,[62][63][64] have been used as the epigenetic effectors.…”

Section: Targeted Dna Methylation and Demethylationmentioning

confidence: 99%

“…Most studies have utilized simple linking of DNA-binding module and epigenetic effector, but some groups recently reported the application of the second-generation architecture, SAM [58] and SunTag [59], in epigenome editing. From here we selectively introduce various milestone studies of cancer induction and suppression, mediated by epigenome editing technologies.…”

Section: Cancer Induction and Suppression With Bona Fide Epigenome Edmentioning

confidence: 99%

Cancer induction and suppression with transcriptional control and epigenome editing technologies

2017

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Cancer epigenetics is one of the most important research subjects in dissecting cancer mechanisms and therapeutic targets because the emergence and malignant transformation of various cancers are caused by unnatural expression of cancer-related genes attributed to their epigenetic errors. The original concept of cancer epigenetics basically stands on the analysis of the epigenetic status in naturally occurring cancer cells; however, the rapidly emerging technology called epigenome editing would change this situation drastically. Epigenome editing, the most promising derivative technology of genome editing, can modify the epigenetic states at the pre-defined genomic locus using the programmable effectors, consisting of various epigenetic factors combined with site-specific DNA-binding domains. This technology can be utilized in a reversible manner; i.e., cancer modeling can be achieved by introducing aberrant epigenetic marks in normal cells, and cancer suppression can be achieved by correcting the epigenetic errors in cancer cells. In this review, we summarize the basics of epigenome editing and cancer epigenetics, followed by the current examples of cancer induction and suppression with the transcriptional control and epigenome editing technologies.

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

Cited by 431 publications

References 32 publications

A reference genome of the Chinese hamster based on a hybrid assembly strategy

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities

Cancer induction and suppression with transcriptional control and epigenome editing technologies

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