ArticleBMC plant biology2025
Dynamic changes in DNA methylation play a regulatory role in gene expression during the formation of callus from immature barley embryos.
Article in BMC plant biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 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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3 citing papers in PubMed.
- The mirage of DNA methylation in transcriptional regulation of plants.The plant genome · 2026Review
- Productive chaos and precision engineering: decoupling discovery from manufacturing to revolutionize plant-inspired therapeutics.Frontiers in plant science · 2026Article
- DNA methylation and prediction of biological age.Frontiers in molecular biosciences · 2025Review
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7 authors.
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Abstract
backgroundInducing embryogenic callus with regenerative potential is a pivotal step in barley transformation. Our previous research suggests that epigenetic regulatory factors might influence barley callus formation and regeneration capacity, though the exact mechanisms remain unclear.
resultsIn this study, we utilized RNA sequencing (RNA-seq) and whole-genome bisulfite sequencing (WGBS) to examine transcriptional and DNA methylome alterations during callus induction from immature embryos of the barley cultivar Golden Promise. Our findings revealed a slight decline in overall DNA methylation content and distinct 5-methylcytosine (5mC) enrichment patterns in CG, CHG, and CHH sequence contexts within genes and transposable elements. By integrating DNA methylation and transcriptome data, we identified differentially expressed genes (DEGs) associated with differentially methylated regions (DMRs) in the CG (879 DEGs), CHG (229 DEGs), and CHH (2020 DEGs) contexts. Notably, DMRs linked to 210, 94, and 1,214 DEGs were located in the 2 kb upstream regions in the CG, CHG, and CHH contexts, respectively. A negative correlation was observed between promoter methylation levels and transcript abundances of key regeneration-associated genes, such as HvKRP4, HvCYCD1;1, HvSCR, HvRAP2.6L/ERF113, HvWIND4, HvWOX5, HvE2Fa, HvPHV, and HvLBD16. This indicates a regulatory function of DNA methylation in transcriptional regulation during callus induction. Furthermore, treatment with the DNA methylation inhibitor 5-Aza-2'-deoxycytidine (5-Aza-dC) suppressed callus formation. Comparative RNA sequencing analysis between control and treated groups revealed 2,628 and 1,224 DEGs potentially regulated by DNA methylation, at 2- and 9-days post-induction, respectively. These genes were primarily associated with cell cycle and abscisic acid signalling pathways, influenced directly and indirectly by the global reduction in DNA methylation induced by 5-Aza-dC treatment.
conclusionsThis study provides insights into the intricate relationship between DNA methylation and gene expression during barley callus formation. It could inform future efforts to enhance regeneration and transformation in this significant crop species. CLINICAL TRIAL NUMBER: Not applicable.
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