Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants

Trevor Weiss, Peter A. Crisp, Krishan M. Rai, Meredith Song, Nathan M. Springer, Feng Zhang

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


CRISPR–Cas9-mediated genome editing has been widely adopted for basic and applied biological research in eukaryotic systems. While many studies consider DNA sequences of CRISPR target sites as the primary determinant for CRISPR mutagenesis efficiency and mutation profiles, increasing evidence reveals the substantial role of chromatin context. Nonetheless, most prior studies are limited by the lack of sufficient epigenetic resources and/or by only transiently expressing CRISPR–Cas9 in a short time window. In this study, we leveraged the wealth of high-resolution epigenomic resources in Arabidopsis (Arabidopsis thaliana) to address the impact of chromatin features on CRISPR–Cas9 mutagenesis using stable transgenic plants. Our results indicated that DNA methylation and chromatin features could lead to substantial variations in mutagenesis efficiency by up to 250-fold. Low mutagenesis efficiencies were mostly associated with repressive heterochromatic features. This repressive effect appeared to persist through cell divisions but could be alleviated through substantial reduction of DNA methylation at CRISPR target sites. Moreover, specific chromatin features, such as H3K4me1, H3.3, and H3.1, appear to be associated with significant variation in CRISPR–Cas9 mutation profiles mediated by the non-homologous end joining repair pathway. Our findings provide strong evidence that specific chromatin features could have substantial and lasting impacts on both CRISPR–Cas9 mutagenesis efficiency and DNA double-strand break repair outcomes.

Original languageEnglish (US)
Pages (from-to)1153-1164
Number of pages12
JournalPlant physiology
Issue number2
StatePublished - Oct 2022

Bibliographical note

Funding Information:
M.S. was supported by the Undergraduate Research Opportunities Program (UROP) from the University of Minnesota. Funding from NSF IOS-1934384 to N.M.S. partially supported this work. P.A.C. was supported by an ARC Discovery Early Career Award (DE200101748). F.Z. was supported by the startup fund from the Department of Plant and Microbial Biology, University of Minnesota.

Publisher Copyright:
© The Author(s) 2022. Published by Oxford University Press on behalf of American Society of Plant Biologists.


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