ArticlePlant physiology2016
Genomic DNA Methylation Analyses Reveal the Distinct Profiles in Castor Bean Seeds with Persistent Endosperms.
Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 45 citations in OpenAlex.
- Multi-omics analysis of the role of muskmelon mitochondria in Si-induced resistance mechanisms.Frontiers in plant science · 2026Article
- 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
- Dynamic changes in DNA methylation play a regulatory role in gene expression during the formation of callus from immature barley embryos.BMC plant biology · 2025Article
- Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant.Nature communications · 2025Article
- 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
- DNA Methylation is Involved in Sex Determination in Spinach.Biochemical genetics · 2024Article
- A DNA demethylase reduces seed size by decreasing the DNA methylation of AT-rich transposable elements in soybean.Communications biology · 2024Article
- Characteristics ofHorticulture research · 2023Article
- Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughoutFrontiers in plant science · 2023Article
- Epigenetic regulation of seed-specific gene expression by DNA methylation valleys in castor bean.BMC biology · 2022Article
- Regulation of DNA Methylation During Plant Endosperm Development.Frontiers in genetics · 2022Review
- Expression Patterns of DNA Methylation and Demethylation Genes during Plant Development and in Response to Phytohormones.International journal of molecular sciences · 2021Article
- DNA methylation-mediated modulation of rapid desiccation tolerance acquisition and dehydration stress memory in the resurrection plant Boea hygrometrica.PLoS genetics · 2021Article
- Whole genome bisulfite sequencing methylome analysis of mulberry (Morus alba) reveals epigenome modifications in response to drought stress.Scientific reports · 2020Article
- Characterization of DNA methylation variations during fruit development and ripening ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- A role of age-dependent DNA methylation reprogramming in regulating the regeneration capacity of Boea hygrometrica leaves.Functional & integrative genomics · 2020Article
- Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton.International journal of molecular sciences · 2019Article
- The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways.BMC plant biology · 2019Article
- Global Gene Expression of Seed Coat Tissues Reveals a Potential Mechanism of Regulating Seed Size Formation in Castor Bean.International journal of molecular sciences · 2019Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Investigations of genomic DNA methylation in seeds have been restricted to a few model plants. The endosperm genomic DNA hypomethylation has been identified in angiosperm, but it is difficult to dissect the mechanism of how this hypomethylation is established and maintained because endosperm is ephemeral and disappears with seed development in most dicots. Castor bean (Ricinus communis), unlike Arabidopsis (Arabidopsis thaliana), endosperm is persistent throughout seed development, providing an excellent model in which to dissect the mechanism of endosperm genomic hypomethylation in dicots. We characterized the DNA methylation-related genes encoding DNA methyltransferases and demethylases and analyzed their expression profiles in different tissues. We examined genomic methylation including CG, CHG, and CHH contexts in endosperm and embryo tissues using bisulfite sequencing and revealed that the CHH methylation extent in endosperm and embryo was, unexpectedly, substantially higher than in previously studied plants, irrespective of the CHH percentage in their genomes. In particular, we found that the endosperm exhibited a global reduction in CG and CHG methylation extents relative to the embryo, markedly switching global gene expression. However, CHH methylation occurring in endosperm did not exhibit a significant reduction. Combining with the expression of 24-nucleotide small interfering RNAs (siRNAs) mapped within transposable element (TE) regions and genes involved in the RNA-directed DNA methylation pathway, we demonstrate that the 24-nucleotide siRNAs played a critical role in maintaining CHH methylation and repressing the activation of TEs in persistent endosperm development. This study discovered a novel genomic DNA methylation pattern and proposes the potential mechanism occurring in dicot seeds with persistent endosperm.
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