ArticleGenome biology2017
The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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89 citing papers in PubMed, 180 citations in OpenAlex.
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- Synonymous Codons as Potential Contributors to Chromatin Stability and Gene Body Methylation in Plants.Journal of molecular evolution · 2026Article
- Evolution of Epigenetic Regulation in Plant Reproduction.Epigenomes · 2026Review
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- A high-resolution 3D genome map of kiwifruit provides insights into chromatin architecture and transcriptional activity.Horticulture research · 2026Article
- Strain, procedures, and tools for reproducible genetic transformation and genome editing of the emerging plant model Spirodela polyrhiza.The New phytologist · 2026Article
- Identification of DNA Methyltransferase/Demethylase Genes and 5-Azacytidine's Impact on β-Elemene and Methylation inBiology · 2025Article
- Genome-Wide Identification and Expression Pattern Analysis of the DNA Methyltransferase Gene Family Revealed the DNA Methylation Response to Tapping in Rubber Tree.Plants (Basel, Switzerland) · 2025Article
- Accelerated growth increases the somatic epimutation rate in trees.Nature communications · 2025Article
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Review
- Repressive Cytosine Methylation is a Marker of Viral Gene Transfer Across Divergent Eukaryotes.Molecular biology and evolution · 2025Article
- Harnessing neo-domestication of wild pigmented rice for enhanced nutrition and sustainable agriculture.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingGenome research · 2025Article
- Epigenetic odyssey to decrypt the hidden code for sustainable brassica production: enhancing yield, stress resilience and nutritional quality.Frontiers in plant science · 2025Review
- Characterization of DNA methylation reader proteins inGenome research · 2024Article
- Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases.Science advances · 2024Article
- DNA Methylation is Involved in Sex Determination in Spinach.Biochemical genetics · 2024Article
- DNA methylation enables recurrent endogenization of giant viruses in an animal relative.Science advances · 2024Article
- Dynamic evolution of the heterochromatin sensing histone demethylase IBM1.PLoS genetics · 2024Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe evolution of gene body methylation (gbM), its origins, and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridiplantae, we provide novel insights into the evolution of gbM and its relationship to CHROMOMETHYLASE (CMT) proteins.
resultsCMTs are evolutionary conserved DNA methyltransferases in Viridiplantae. Duplication events gave rise to what are now referred to as CMT1, 2 and 3. Independent losses of CMT1, 2, and 3 in eudicots, CMT2 and ZMET in monocots and monocots/commelinids, variation in copy number, and non-neutral evolution suggests overlapping or fluid functional evolution of this gene family. DNA methylation within genes is widespread and is found in all major taxonomic groups of Viridiplantae investigated. Genes enriched with methylated CGs (mCG) were also identified in species sister to angiosperms. The proportion of genes and DNA methylation patterns associated with gbM are restricted to angiosperms with a functional CMT3 or ortholog. However, mCG-enriched genes in the gymnosperm Pinus taeda shared some similarities with gbM genes in Amborella trichopoda. Additionally, gymnosperms and ferns share a CMT homolog closely related to CMT2 and 3. Hence, the dependency of gbM on a CMT most likely extends to all angiosperms and possibly gymnosperms and ferns.
conclusionsThe resulting gene family phylogeny of CMT transcripts from the most diverse sampling of plants to date redefines our understanding of CMT evolution and its evolutionary consequences on DNA methylation. Future, functional tests of homologous and paralogous CMTs will uncover novel roles and consequences to the epigenome.
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