ArticleJournal of experimental botany2015
Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes.
Article in Journal of experimental botany, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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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
24 citing papers in PubMed, 35 citations in OpenAlex.
- Gene regulatory mechanisms downstream of DNA methylation.Nature reviews. Genetics · 2026Review
- Article
- Methylcytosine oxidation derivatives are preferentially associated with repetitive chromatin and mark active rDNA inFrontiers in plant science · 2026Article
- DNA methylation in wheat: current understanding and future potential for enhancing biotic and abiotic stress tolerance.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Review
- Sexy ways: approaches to studying plant sex chromosomes.Journal of experimental botany · 2024Review
- β-Aminobutyric acid promotes stress tolerance, physiological adjustments, as well as broad epigenetic changes at DNA and RNA nucleobases in field elms (Ulmus minor).BMC plant biology · 2024Article
- Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia.Journal of experimental botany · 2024Article
- Base Excision DNA Repair in Plants:International journal of molecular sciences · 2023Review
- Uncovering plant epigenetics: new insights into cytosine methylation in rye genomes.Journal of experimental botany · 2023Article
- DNA Glycosylases Define the Outcome of Endogenous Base Modifications.International journal of molecular sciences · 2023Review
- Exploring the crop epigenome: a comparison of DNA methylation profiling techniques.Frontiers in plant science · 2023Review
- Article
- Progressive DNA demethylation in epigenetic hybrids between parental plants with and without methylation of the transgene promoter.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Epigenetic features improve TALE target prediction.BMC genomics · 2021Article
- DNA Methyltransferases Regulate Pathogenicity ofJournal of fungi (Basel, Switzerland) · 2021Article
- The Multiple Roles of Ascorbate in the Abiotic Stress Response of Plants: Antioxidant, Cofactor, and Regulator.Frontiers in plant science · 2021Review
- Induction of Radiata Pine Somatic Embryogenesis at High Temperatures Provokes a Long-Term Decrease in DNA Methylation/Hydroxymethylation and Differential Expression of Stress-Related Genes.Plants (Basel, Switzerland) · 2020Article
- DNA methylation analysis in plants: review of computational tools and future perspectives.Briefings in bioinformatics · 2020Review
- Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome.Scientific reports · 2019Article
- Regulation of transposable elements by DNA modifications.Nature reviews. Genetics · 2019Review
Corrections and comments
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Authors and funding
14 authors at 8 institutions in 4 countries.
Funding
Abstract
5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.
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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.