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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Abstract 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.
AbstractList 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.
Site-specific modification of epigenetic marks such as DNA methylation to regulate gene expression is a unique approach to enhance economically important crop traits. This approach allows for the maintenance of the introduced modifications in the absence of the initial transgene inducer in subsequent generations and relies largely on methylation of cytosines in the CG-specific sequence context. We have developed a targeted DNA methylation tool based on a bacterial methyltransferase and the CRISPR-Cas9 platform to directly methylate cytosines at CG sites in Arabidopsis . These tools expand the currently available CRISPR-based targeted DNA methylation tools and provide an approach for the establishment of heritable targeted DNA methylation in plants. 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.
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.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.
Author Ghoshal, Basudev
Picard, Colette L.
Vong, Brandon
Jacobsen, Steven E.
Feng, Suhua
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  surname: Ghoshal
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  givenname: Steven E.
  surname: Jacobsen
  fullname: Jacobsen, Steven E.
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Copyright Copyright © 2021 the Author(s). Published by PNAS.
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Keywords DNA methylation
SunTag
Arabidopsis
CRISPR-Cas9
Language English
License Copyright © 2021 the Author(s). Published by PNAS.
This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).
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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.
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Snippet CRISPR-based targeted modification of epigenetic marks such as DNA cytosine methylation is an important strategy to regulate the expression of genes and their...
Site-specific modification of epigenetic marks such as DNA methylation to regulate gene expression is a unique approach to enhance economically important crop...
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SubjectTerms 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
Title CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase
URI https://www.jstor.org/stable/27040924
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