Editing DNA Methylation in the Mammalian Genome

X Shawn Liu; Hao Wu; Xiong Ji; Yonatan Stelzer; Xuebing Wu; Szymon Czauderna; Jian Shu; Daniel Dadon; Richard A Young; Rudolf Jaenisch

doi:10.1016/j.cell.2016.08.056

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Editing DNA Methylation in the Mammalian Genome

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Editing DNA Methylation in the Mammalian Genome

X Shawn Liu, Hao Wu, Xiong Ji, Yonatan Stelzer, Xuebing Wu, Szymon Czauderna, Jian Shu, Daniel Dadon, Richard A Young and Rudolf Jaenisch

Cell (Cambridge), Vol.167(1), pp.233-247.e17

22/Sep/2016

DOI: https://doi.org/10.1016/j.cell.2016.08.056

PMCID: PMC5062609

PMID: 27662091

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Abstract

Mammalian DNA methylation is a critical epigenetic mechanism orchestrating gene expression networks in many biological processes. However, investigation of the functions of specific methylation events remains challenging. Here, we demonstrate that fusion of Tet1 or Dnmt3a with a catalytically inactive Cas9 (dCas9) enables targeted DNA methylation editing. Targeting of the dCas9-Tet1 or -Dnmt3a fusion protein to methylated or unmethylated promoter sequences caused activation or silencing, respectively, of an endogenous reporter. Targeted demethylation of the BDNF promoter IV or the MyoD distal enhancer by dCas9-Tet1 induced BDNF expression in post-mitotic neurons or activated MyoD facilitating reprogramming of fibroblasts into myoblasts, respectively. Targeted de novo methylation of a CTCF loop anchor site by dCas9-Dnmt3a blocked CTCF binding and interfered with DNA looping, causing altered gene expression in the neighboring loop. Finally, we show that these tools can edit DNA methylation in mice, demonstrating their wide utility for functional studies of epigenetic regulation.

Brain-Derived Neurotrophic Factor - genetics

Endonucleases - genetics

Epigenesis, Genetic

Endonucleases - metabolism

Recombinant Fusion Proteins - metabolism

DNA (Cytosine-5-)-Methyltransferases - metabolism

DNA-Binding Proteins - metabolism

Clustered Regularly Interspaced Short Palindromic Repeats

Neurons - metabolism

Repressor Proteins - metabolism

Proto-Oncogene Proteins - metabolism

Cell Line

Promoter Regions, Genetic

Bacterial Proteins - genetics

Proto-Oncogene Proteins - genetics

DNA Methylation - genetics

MyoD Protein - metabolism

DNA-Binding Proteins - genetics

DNA (Cytosine-5-)-Methyltransferases - genetics

Animals

Enhancer Elements, Genetic

CCCTC-Binding Factor

CpG Islands

Protein Binding

Recombinant Fusion Proteins - genetics

Bacterial Proteins - metabolism

Gene Editing - methods

Mice

Genome

Details

Title: Editing DNA Methylation in the Mammalian Genome
Creators: X Shawn Liu - Whitehead Institute for Biomedical Research
Hao Wu - Whitehead Institute for Biomedical Research
Xiong Ji - Whitehead Institute for Biomedical Research
Yonatan Stelzer - Whitehead Institute for Biomedical Research
Xuebing Wu - Whitehead Institute for Biomedical Research
Szymon Czauderna - Jagiellonian University
Jian Shu - Whitehead Institute for Biomedical Research
Daniel Dadon - Massachusetts Institute of Technology
Richard A Young - Massachusetts Institute of Technology
Rudolf Jaenisch (Corresponding Author) - Massachusetts Institute of Technology
Resource Type: Journal article
Publication Details: Cell (Cambridge), Vol.167(1), pp.233-247.e17; 22/Sep/2016
Language: English
DOI: https://doi.org/10.1016/j.cell.2016.08.056
PMID: 27662091
PMCID: PMC5062609
Grant note: R01 HD045022 / NICHD NIH HHS R01 NS088538 / NINDS NIH HHS R01 HG002668 / NHGRI NIH HHS T32 GM007287 / NIGMS NIH HHS R37 CA084198 / NCI NIH HHS R01 GM114864 / NIGMS NIH HHS R37 HD045022 / NICHD NIH HHS P30 CA014051 / NCI NIH HHS
Record Identifier: 993277020003596

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