ArticlePlant physiology2023
Rice transformation treatments leave specific epigenome changes beyond tissue culture.
Article in Plant physiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 7 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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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.
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Who cites it
7 citing papers in PubMed, 8 citations in OpenAlex.
- Computational Workflow for Genome-Wide DNA Methylation Profiling and Differential Methylation Analysis.Bio-protocol · 2025Article
- Morphogenetic Factors as a Tool for Enhancing Plant Regeneration Capacity During In Vitro Transformation.International journal of molecular sciences · 2025Review
- A Truncated Mutation of TP53 Promotes Chemoresistance in Tongue Squamous Cell Carcinoma.International journal of molecular sciences · 2025Article
- Poplar transformation with variable explant sources to maximize transformation efficiency.Scientific reports · 2025Article
- Article
- Genomic consequences associated with Agrobacterium-mediated transformation of plants.The Plant journal : for cell and molecular biology · 2024Review
- RNA-Seq Data Analysis for Differential Gene Expression Using HISAT2-StringTie-Ballgown Pipeline.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 4 institutions in 1 country.
Funding
Abstract
During transgenic plant production, tissue culture often carries epigenetic, and genetic changes that underlie somaclonal variations, leading to unpredictable phenotypes. Additionally, specific treatments for rice (Oryza sativa) transformation processes may individually or jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes toward transcriptional variations remain unknown. Here, the impact of individual transformation treatments on genome-wide DNA methylation and the transcriptome were examined. In addition to activating stress-responsive genes, individual transformation components targeted different gene expression modules that were enriched in specific functional categories. The transformation treatments strongly impacted DNA methylation and expression; 75% were independent of tissue culture. Furthermore, our genome-wide analysis showed that the transformation treatments consistently resulted in global hypo-CHH methylation enriched at promoters highly associated with downregulation, particularly when the promoters were colocalized with miniature inverted-repeat transposable elements. Our results clearly highlight the specificity of impacts triggered by individual transformation treatments during rice transformation with the potential association between DNA methylation and gene expression. These changes in gene expression and DNA methylation resulting from rice transformation treatments explain a significant portion of somaclonal variations, that is, way beyond the tissue culture effect.
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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.