ArticleScientific reports2017
Gene-body CG methylation and divergent expression of duplicate genes in rice.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- DNA methylation around transcription start sites is not globally associated with transcription in the grain of natural and synthetic hexaploid wheat.BMC plant biology · 2026Article
- How to improve crop pathogen resistance with epigenetics.Phytopathology research · 2026Review
- The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato.Plant biotechnology journal · 2023Article
- DNA methylation signatures of duplicate gene evolution in angiosperms.Plant physiology · 2023Article
- 6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication.Plants (Basel, Switzerland) · 2023Article
- Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (International journal of molecular sciences · 2022Article
- Interplay between gene expression and gene architecture as a consequence of gene and genome duplications: evidence from metabolic genes ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Genome-Wide Identification and Characterization of theInternational journal of molecular sciences · 2022Article
- Whole-Genome DNA Methylation Analysis inFrontiers in plant science · 2022Article
- Article
- Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants.Molecular biology and evolution · 2020Article
- Understanding epigenomics based on the rice model.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- OsZIP1 functions as a metal efflux transporter limiting excess zinc, copper and cadmium accumulation in rice.BMC plant biology · 2019Article
- Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.).BMC plant biology · 2018Article
- Parental experience modifies the Mimulus methylome.BMC genomics · 2018Article
- Combinatorial Interactions of Biotic and Abiotic Stresses in Plants and Their Molecular Mechanisms: Systems Biology Approach.Molecular biotechnology · 2018Review
- The gymnastics of epigenomics in rice.Plant cell reports · 2018Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene and genome duplication fosters genetic novelty, but redundant gene copies would undergo mutational decay unless preserved via selective or neutral forces. Molecular mechanisms mediating duplicate preservation remain incompletely understood. Several recent studies showed an association between DNA methylation and expression divergence of duplicated genes and suggested a role of epigenetic mechanism in duplicate retention. Here, we compare genome-wide gene-body CG methylation (BCGM) and duplicate gene expression between a rice mutant null for OsMet1-2(a major CG methytransferase in rice) and its isogenic wild-type. We demonstrate a causal link between BCGM divergence and expression difference of duplicate copies. Interestingly, the higher- and lower-expressing copies of duplicates as separate groups show broadly different responses with respect to direction of expression alteration upon loss of BCGM. A role for BCGM in conditioning expression divergence between copies of duplicates generally holds for duplicates generated by whole genome duplication (WGD) or by small-scale duplication processes. However, differences are evident among these categories, including a higher proportion of WGD duplicates manifesting expression alteration, and differential propensities to lose BCGM by the higher- and lower-expression copies in the mutant. Together, our results support the notion that differential epigenetic marking may facilitate long-term retention of duplicate genes.
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