Targeted DNA demethylation of the arabidopsis genome using the human TET1 catalytic domain

Javier Gallego-Bartolomé, Jason Gardiner, Wanlu Liu, Ashot Papikian, Basudev Ghoshal, Hsuan Yu Kuo, Jenny Miao Chi Zhao, David Segal, Steven E. Jacobsen

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

DNA methylation is an important epigenetic modification involved in gene regulation and transposable element silencing. Changes in DNA methylation can be heritable and, thus, can lead to the formation of stable epialleles. A well-characterized example of a stable epiallele in plants is fwa, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the FLOWERING WAGENINGEN (FWA) gene, causing up-regulation of FWA and a heritable late-flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the FWA promoter can cause highly efficient targeted demethylation, FWA up-regulation, and a heritable late-flowering phenotype. Additional ZF-TET1cd fusions designed to target methylated regions of the CACTA1 transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCas9-based targeted demethylation system using the TET1cd and a modified SunTag system. Similar to the ZF-TET1cd fusions, the SunTag-TET1cd system is able to target demethylation and activate gene expression when directed to the FWA or CACTA1 loci. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal offtarget effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons.

Original languageEnglish (US)
Pages (from-to)E2125-E2134
JournalProceedings of the National Academy of Sciences of the United States of America
Volume115
Issue number9
DOIs
StatePublished - Feb 27 2018

Fingerprint

Zinc Fingers
Human Genome
DNA Methylation
Arabidopsis
Catalytic Domain
DNA
Up-Regulation
Clustered Regularly Interspaced Short Palindromic Repeats
Genes
Phenotype
DNA Transposable Elements
Cytosine
Transgenes
Epigenomics
Genome
Gene Expression

Keywords

  • Arabidopsis
  • Artificial zinc finger
  • Crispr/dCas9 suntag
  • Targeted demethylation
  • TET1

ASJC Scopus subject areas

  • General

Cite this

Gallego-Bartolomé, J., Gardiner, J., Liu, W., Papikian, A., Ghoshal, B., Kuo, H. Y., ... Jacobsen, S. E. (2018). Targeted DNA demethylation of the arabidopsis genome using the human TET1 catalytic domain. Proceedings of the National Academy of Sciences of the United States of America, 115(9), E2125-E2134. https://doi.org/10.1073/pnas.1716945115

Targeted DNA demethylation of the arabidopsis genome using the human TET1 catalytic domain. / Gallego-Bartolomé, Javier; Gardiner, Jason; Liu, Wanlu; Papikian, Ashot; Ghoshal, Basudev; Kuo, Hsuan Yu; Zhao, Jenny Miao Chi; Segal, David; Jacobsen, Steven E.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 115, No. 9, 27.02.2018, p. E2125-E2134.

Research output: Contribution to journalArticle

Gallego-Bartolomé, J, Gardiner, J, Liu, W, Papikian, A, Ghoshal, B, Kuo, HY, Zhao, JMC, Segal, D & Jacobsen, SE 2018, 'Targeted DNA demethylation of the arabidopsis genome using the human TET1 catalytic domain', Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 9, pp. E2125-E2134. https://doi.org/10.1073/pnas.1716945115
Gallego-Bartolomé, Javier ; Gardiner, Jason ; Liu, Wanlu ; Papikian, Ashot ; Ghoshal, Basudev ; Kuo, Hsuan Yu ; Zhao, Jenny Miao Chi ; Segal, David ; Jacobsen, Steven E. / Targeted DNA demethylation of the arabidopsis genome using the human TET1 catalytic domain. In: Proceedings of the National Academy of Sciences of the United States of America. 2018 ; Vol. 115, No. 9. pp. E2125-E2134.
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