Rewriting DNA Methylation Signatures at Will: The Curable Genome Within Reach?
- 3.5k Downloads
Epigenetic regulation of gene expression is vital for the maintenance of genome integrity and cell phenotype. In addition, many different diseases have underlying epigenetic mutations, and understanding their role and function may unravel new insights for diagnosis, treatment, and even prevention of diseases. It was an important breakthrough when epigenetic alterations could be gene-specifically manipulated using epigenetic regulatory proteins in an approach termed epigenetic editing. Epigenetic editors can be designed for virtually any gene by targeting effector domains to a preferred sequence, where they write or erase the desired epigenetic modification. This chapter describes the tools for editing DNA methylation signatures and their applications. In addition, we explain how to achieve targeted DNA (de)methylation and discuss the advantages and disadvantages of this approach. Silencing genes directly at the DNA methylation level instead of targeting the protein and/or RNA is a major improvement, as repression is achieved at the source of expression, potentially eliminating the need for continuous administration. Re-expression of silenced genes by targeted demethylation might closely represent the natural situation, in which all transcript variants might be expressed in a sustainable manner. Altogether epigenetic editing, for example, by rewriting DNA methylation, will assist in realizing the curable genome concept.
KeywordsZinc Finger Zinc Finger Protein SOX2 Promoter Heterochromatic Gene CDKN2A Locus
Artificial transcription factor
Clustered regulatory interspaced palindromic repeats
Transcription activator-like effectors
We would like to acknowledge the EU funding for D.G. (H2020-MSCA-ITN-2014-ETN 642691 EpiPredict). M.G.R. serves as vice-chair of H2020-COST CM1406, and her team is partially funded by NWO-Vidi-91786373 and EU-FP7-SNN-4D22C-T2007.
- Cano-Rodriguez D, Gjaltema RA, Jilderda LJ, Jellema P, Dokter-Fokkens J, Ruiters MH, Rots MG. Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner. Nat Commun. 2016;7:12284. (doi: 10.1038/ncomms12284. PubMed PMID: 27506838).
- Choudhury SR, Cui Y, Lubecka K, Stefanska B, Irudayaraj J. CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter. Oncotarget. 2016. (Epub ahead of print) (doi: 10.18632/oncotarget.10234. PubMed PMID: 27356740).
- McDonald JI, Celik H, Rois LE, Fishberger G, Fowler T, Rees R, et al. Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation. Biol Open. 2016;5(6):866–74. (doi: 10.1242/bio.019067. PubMed PMID: 27170255; PubMed Central PMCID: PMC4920199).Google Scholar
- Siddique AN, Nunna S, Rajavelu A, Zhang Y, Jurkowska RZ, Reinhardt R, et al. Targeted Methylation and Gene Silencing of VEGF-A in Human Cells by Using a Designed Dnmt3a-Dnmt3L Single-Chain Fusion Protein with Increased DNA Methylation Activity. J Mol Biol. 2012;425(3):479–91.CrossRefPubMedGoogle Scholar
- van der Gun BT, Maluszynska-Hoffman M, Kiss A, Arendzen AJ, Ruiters MH, McLaughlin PM, et al. Targeted DNA methylation by a DNA methyltransferase coupled to a triple helix forming oligonucleotide to down-regulate the epithelial cell adhesion molecule. Bioconjug Chem. 2010;21(7):1239–45. doi: 10.1021/bc1000388.Google Scholar
- Vojta A, Dobrinić P, Tadić V, Bočkor L, Korać P, Julg B, et al. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res. 2016;44(12):5615–28. (doi: 10.1093/nar/gkw159. Epub 2016 Mar 11; PMID: 26969735; PubMed Central PMCID: PMC4937303).Google Scholar
- Xu X, Tao Y, Gao X, Zhang L, Li X, Zou W, et al. A CRISPR- based approach for targeted DNA demethylation. Cell Discov. 2016;3;2:16009. (doi: 10.1038/celldisc.2016.9. eCollection 2016. PubMed PMID: 27462456; PubMed Central PMCID: PMC4853773).