ArticleThe Plant cell2008
High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression.
Article in The Plant cell, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
139 citing papers in PubMed.
- H3K4 Methylation Readers in Plants: Recognition Mechanisms and Biological Functions.International journal of molecular sciences · 2026Review
- Response of DNA methylation and gene expression to light treatments in Norway spruce [Picea abies (L.) Karst.].BMC genomics · 2026Article
- CUT&tag analysis reveals a crucial role of H3K4 trimethylation occupancy in cold-related genes by cold stress on cotton.BMC plant biology · 2026Article
- Epigenetics in forest trees- key driver to phenotypic plasticity and adaptation under stress.Functional & integrative genomics · 2025Review
- A comprehensive allele specific expression resource for the equine transcriptome.BMC genomics · 2025Article
- The highly dynamic satellitomes of cultivated wheat species.Annals of botany · 2024Article
- EPO modified MSCs protects SH-SY5Y cells against ischemia/hypoxia-induced apoptosis via REST-dependent epigenetic remodeling.Scientific reports · 2024Article
- A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome.Research square · 2024Article
- Epigenetic and metabolic reprogramming in inflammatory bowel diseases: diagnostic and prognostic biomarkers in colorectal cancer.Cancer cell international · 2023Review
- Targeting Epigenetic Changes Mediated by Members of the SMYD Family of Lysine Methyltransferases.Molecules (Basel, Switzerland) · 2023Review
- Research on Xiaoyao Powder in the treatment of depression based on epigenetics and quality markers.Frontiers in neuroscience · 2023Review
- TheProceedings of the National Academy of Sciences of the United States of America · 2022Article
- The establishment of CDK9/RNA PolII/H3K4me3/DNA methylation feedback promotes HOTAIR expression by RNA elongation enhancement in cancer.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- The potential role of DNA methylation as preventive treatment target of epileptogenesis.Frontiers in cellular neuroscience · 2022Review
- Drought induces variation in the DNA methylation status of the barley HvDME promoter.Journal of plant research · 2021Article
- Leveraging histone modifications to improve genome annotations.G3 (Bethesda, Md.) · 2021Article
- Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica).Plant methods · 2021Article
- DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus.Horticulture research · 2021Article
- The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles.International journal of molecular sciences · 2021Review
- The role of epigenetics, particularly DNA methylation, in the evolution of caste in insect societies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Review
79 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present high-resolution maps of DNA methylation and H3K4 di- and trimethylation of two entire chromosomes and two fully sequenced centromeres in rice (Oryza sativa) shoots and cultured cells. This analysis reveals combinatorial interactions between these epigenetic modifications and chromatin structure and gene expression. Cytologically densely stained heterochromatin had less H3K4me2 and H3K4me3 and more methylated DNA than the less densely stained euchromatin, whereas centromeres had a unique epigenetic composition. Most transposable elements had highly methylated DNA but no H3K4 methylation, whereas more than half of protein-coding genes had both methylated DNA and di- and/or trimethylated H3K4. Methylation of DNA but not H3K4 was correlated with suppressed transcription. By contrast, when both DNA and H3K4 were methylated, transcription was only slightly reduced. Transcriptional activity was positively correlated with the ratio of H3K4me3/H3K4me2: genes with predominantly H3K4me3 were actively transcribed, whereas genes with predominantly H3K4me2 were transcribed at moderate levels. More protein-coding genes contained all three modifications, and more transposons contained DNA methylation in shoots than cultured cells. Differential epigenetic modifications correlated to tissue-specific expression between shoots and cultured cells. Collectively, this study provides insights into the rice epigenomes and their effect on gene expression and plant development.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.