ArticleBMC genomics2012
Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
165 citing papers in PubMed, 316 citations in OpenAlex.
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- Methylome differences among barley inbreds and their association with genomic, transcriptomic, and phenotypic variation.Journal of experimental botany · 2026Article
- How to improve crop pathogen resistance with epigenetics.Phytopathology research · 2026Review
- Regulation of gene expression by 5mC DNA methylation during the bolting process of cabbage (Frontiers in plant science · 2026Article
- Epigenetic Regulation of Salt Stress Responses in Rice: Mechanisms and Prospects for Enhancing Tolerance.Epigenomes · 2025Review
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- Whole-Genome DNA Methylation Analysis of Inoculation withJournal of fungi (Basel, Switzerland) · 2025Article
- Epigenetic regulation of organ-specific functions in Mikania micrantha and Mikania cordata: insights from DNA methylation and siRNA integration.BMC plant biology · 2024Article
- A Novel Single Base Mutation inInternational journal of molecular sciences · 2024Article
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- Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum.BMC genomics · 2024Article
- Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar.The plant genome · 2024Article
- DNA Methylation Analysis of Growth Differences between Upright and Inverted Cuttings ofInternational journal of molecular sciences · 2024Article
- Multi-omic analysis of the extension of broccoli quality during storage by folic acid.Journal of advanced research · 2024Article
- The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet.International journal of molecular sciences · 2024Article
- The Sink-Source Relationship in Cucumber (Plants (Basel, Switzerland) · 2023Article
- Article
105 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
20 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara.
resultsThe overall methylation level of rice genomes is four times higher than that of Arabidopsis. Consistent with the results reported for Arabidopsis, methylation in promoters represses gene expression while gene-body methylation generally appears to be positively associated with gene expression. Interestingly, we discovered that methylation in gene transcriptional termination regions (TTRs) can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Through integrated analysis of genomic, DNA methylomic and transcriptomic differences between cultivated and wild rice, we found that primary DNA sequence divergence is the major determinant of methylational differences at the whole genome level, but DNA methylational difference alone can only account for limited gene expression variation between the cultivated and wild rice. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice.
conclusionsThe single-base resolution methylomes of rice obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice.
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