Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

Ashot Papikian; Wanlu Liu; Javier Gallego-Bartolomé; Steven E Jacobsen

doi:10.1038/s41467-019-08736-7

Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

Nat Commun. 2019 Feb 13;10(1):729. doi: 10.1038/s41467-019-08736-7.

Authors

Ashot Papikian^{1

2}, Wanlu Liu^{1

3}, Javier Gallego-Bartolomé¹, Steven E Jacobsen^{4

5}

Affiliations

¹ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
² Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
³ Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
⁴ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA. jacobsen@ucla.edu.
⁵ Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA. jacobsen@ucla.edu.

Abstract

Understanding genomic functions requires site-specific manipulation of loci via efficient protein effector targeting systems. However, few approaches for targeted manipulation of the epigenome are available in plants. Here, we adapt the dCas9-SunTag system to engineer targeted gene activation and DNA methylation in Arabidopsis. We demonstrate that a dCas9-SunTag system utilizing the transcriptional activator VP64 drives robust and specific activation of several loci, including protein coding genes and transposable elements, in diverse chromatin contexts. In addition, we present a CRISPR-based methylation targeting system for plants, utilizing a SunTag system with the catalytic domain of the Nicotiana tabacum DRM methyltransferase, which efficiently targets DNA methylation to specific loci, including the FWA promoter, triggering a developmental phenotype, and the SUPERMAN promoter. These SunTag systems represent valuable tools for the site-specific manipulation of plant epigenomes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Arabidopsis / genetics*
Arabidopsis / metabolism
Arabidopsis Proteins / genetics*
Arabidopsis Proteins / metabolism
Binding Sites / genetics
CRISPR-Cas Systems*
Chromatin / genetics
Chromatin / metabolism
DNA Methylation*
Epigenesis, Genetic
Gene Editing / methods*
Gene Expression Regulation, Plant
Homeodomain Proteins / genetics
Homeodomain Proteins / metabolism
Plants, Genetically Modified
Promoter Regions, Genetic / genetics
Transcription Factors / genetics
Transcription Factors / metabolism

Substances

Arabidopsis Proteins
Chromatin
FWA protein, Arabidopsis
Homeodomain Proteins
Transcription Factors