CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase

CRISPR-based targeted modification of epigenetic marks such as DNA cytosine methylation is an important strategy to regulate the expression of genes and their associated phenotypes. Although plants have DNA methylation in all sequence contexts (CG, CHG, CHH, where H = A, T, C), methylation in the sy...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 118; no. 23; pp. 1 - 8
Main Authors Ghoshal, Basudev, Picard, Colette L., Vong, Brandon, Feng, Suhua, Jacobsen, Steven E.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 08.06.2021
Subjects
Arabidopsis - enzymology
Arabidopsis - genetics
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biological Sciences
CRISPR
CRISPR-Cas Systems
Cytosine
Deoxyribonucleic acid
DNA
DNA Methylation
DNA methyltransferase
DNA, Plant - genetics
DNA, Plant - metabolism
DNA-Cytosine Methylases - genetics
DNA-Cytosine Methylases - metabolism
Epigenetics
Gene expression
Gene silencing
Meiosis
Nucleotide sequence
Phenotypes
Plants, Genetically Modified - genetics
Plants, Genetically Modified - metabolism
Tenericutes - enzymology
Tenericutes - genetics
DNA methylation
SunTag
Arabidopsis
CRISPR-Cas9
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Summary:CRISPR-based targeted modification of epigenetic marks such as DNA cytosine methylation is an important strategy to regulate the expression of genes and their associated phenotypes. Although plants have DNA methylation in all sequence contexts (CG, CHG, CHH, where H = A, T, C), methylation in the symmetric CG context is particularly important for gene silencing and is very efficiently maintained through mitotic and meiotic cell divisions. Tools that can directly add CG methylation to specific loci are therefore highly desirable but are currently lacking in plants. Here we have developed two CRISPR-based CG-specific targeted DNA methylation systems for plants using a variant of the bacterial CG-specific DNA methyltransferase MQ1 with reduced activity but high specificity. We demonstrate that the methylation added by MQ1 is highly target specific and can be heritably maintained in the absence of the effector. These tools should be valuable both in crop engineering and in plant genetic research.
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Reviewers: S.P., New England Biolabs; and N.M.S., University of Minnesota.
1B.G. and C.L.P. contributed equally to this work.
Contributed by Steven E. Jacobsen, April 27, 2021 (sent for review January 28, 2021; reviewed by Sriharsa Pradhan and Nathan M. Springer)
Author contributions: B.G. and S.E.J. designed research; B.G., C.L.P., B.V., and S.F. performed research; B.G., C.L.P., and S.E.J. contributed new reagents/analytic tools; B.G., C.L.P., and S.E.J. analyzed data; and B.G. and S.E.J. wrote the paper.
ISSN:0027-8424
1091-6490
1091-6490
DOI:10.1073/pnas.2125016118