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

Editing DNA Methylation in the Mammalian Genome

Cell. 2016 Sep 22;167(1):233-247.e17. doi: 10.1016/j.cell.2016.08.056.

Authors

Affiliations

¹ Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
² Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, 31-007 Kraków, Poland.
³ Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
⁴ Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address: jaenisch@wi.mit.edu.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bacterial Proteins / genetics
Bacterial Proteins / metabolism
Brain-Derived Neurotrophic Factor / genetics
CCCTC-Binding Factor
CRISPR-Associated Protein 9
Cell Line
Clustered Regularly Interspaced Short Palindromic Repeats*
CpG Islands
DNA (Cytosine-5-)-Methyltransferases / genetics
DNA (Cytosine-5-)-Methyltransferases / metabolism*
DNA Methylation / genetics*
DNA Methyltransferase 3A
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism*
Endonucleases / genetics
Endonucleases / metabolism
Enhancer Elements, Genetic
Epigenesis, Genetic*
Gene Editing / methods*
Genome
Mice
MyoD Protein / metabolism
Neurons / metabolism
Promoter Regions, Genetic
Protein Binding
Proto-Oncogene Proteins / genetics
Proto-Oncogene Proteins / metabolism*
Recombinant Fusion Proteins / genetics
Recombinant Fusion Proteins / metabolism
Repressor Proteins / metabolism

Substances

Bacterial Proteins
Brain-Derived Neurotrophic Factor
CCCTC-Binding Factor
Ctcf protein, mouse
DNA-Binding Proteins
Dnmt3a protein, mouse
MyoD Protein
Proto-Oncogene Proteins
Recombinant Fusion Proteins
Repressor Proteins
TET1 protein, mouse
DNA (Cytosine-5-)-Methyltransferases
DNA Methyltransferase 3A
CRISPR-Associated Protein 9
Cas9 endonuclease Streptococcus pyogenes
Endonucleases

Abstract

Publication types

MeSH terms

Substances

Grants and funding