ArticleThe Plant cell2021
Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions.
Article in The Plant cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 45 citations in OpenAlex.
- Epigenetic Control of Cold Stress Tolerance in Plants: Emerging Mechanisms and Applications for Crop Improvement.International journal of molecular sciences · 2026Review
- The landscape of cotton DNA methylation and its epigenetic regulation in Verticillium wilt resistance.Plant cell reports · 2026Article
- Reconfiguration of DNA methylation at growth resumption after winter dormancy in Kiwifruit.Scientific reports · 2025Article
- DNA methylation dynamics: patterns, regulation, and function.Current opinion in plant biology · 2025Review
- dCas-Based Tools to Visualize Chromatin or Modify Epigenetic Marks at Specific Plant Genomic Loci.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Genome-wide identification and characterization of DNA methyltransferases and demethylases inFrontiers in plant science · 2025Article
- Impact of Abiotic Stress on Rice and the Role of DNA Methylation in Stress Response Mechanisms.Plants (Basel, Switzerland) · 2024Review
- Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler.Nature communications · 2024Article
- Non-CG DNA hypomethylation promotes photosynthesis and nitrogen fixation in soybean.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- DNA Methylation Dynamics in Response to Drought Stress in Crops.Plants (Basel, Switzerland) · 2024Review
- Genome-wide characterization of DNA methyltransferase family genes implies GhDMT6 improving tolerance of salt and drought on cotton.BMC plant biology · 2024Article
- DNA methylation remodeling and the functional implication during male gametogenesis in rice.Genome biology · 2024Article
- Domains Rearranged Methylase 2 maintains DNA methylation at large DNA hypomethylated shores and long-range chromatin interactions in rice.Plant biotechnology journal · 2023Article
- Article
- Factor of DNA methylation 1 affects woodland strawberry plant stature and organ size via DNA methylation.Plant physiology · 2023Article
- Review
- Genome-wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants.The Plant journal : for cell and molecular biology · 2022Article
- Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits.Biochemical Society transactions · 2022Article
- Structure and Mechanism of Plant DNA Methyltransferases.Advances in experimental medicine and biology · 2022Article
- Which factors shape the rice DNA methylome?The Plant cell · 2021Article
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
15 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation in the non-CG context is widespread in the plant kingdom and abundant in mammalian tissues such as the brain and pluripotent cells. Non-CG methylation in Arabidopsis thaliana is coordinately regulated by DOMAINS REARRANGED METHYLTRANSFERASE (DRM) and CHROMOMETHYLASE (CMT) proteins but has yet to be systematically studied in major crops due to difficulties in obtaining genetic materials. Here, utilizing the highly efficient multiplex CRISPR-Cas9 genome-editing system, we created single- and multiple-knockout mutants for all the nine DNA methyltransferases in rice (Oryza sativa) and profiled their whole-genome methylation status at single-nucleotide resolution. Surprisingly, the simultaneous loss of DRM2, CHROMOMETHYLASE3 (CMT2), and CMT3 functions, which completely erases all non-CG methylation in Arabidopsis, only partially reduced it in rice. The regions that remained heavily methylated in non-CG contexts in the rice Os-dcc (Osdrm2/cmt2/cmt3a) triple mutant had high GC contents. Furthermore, the residual non-CG methylation in the Os-dcc mutant was eliminated in the Os-ddccc (Osdrm2/drm3/cmt2/cmt3a/cmt3b) quintuple mutant but retained in the Os-ddcc (Osdrm2/drm3/cmt2/cmt3a) quadruple mutant, demonstrating that OsCMT3b maintains non-CG methylation in the absence of other major methyltransferases. Our results showed that OsCMT3b is subfunctionalized to accommodate a distinct cluster of non-CG-methylated sites at highly GC-rich regions in the rice genome.
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