Spatiotemporal-specific DNA methylation and small RNAs are involved to regulate cell cycle progression and organ development of cucumber (Cucumis sativus L.).
Jul 2026· Journal of Advanced Research· 0 citations· 79 references
Medicine
TL;DR
A dual mechanism in which DNA methylation and CsRDR1a-related small RNAs coordinately regulate cucumber organ development is unveiled, highlighting the importance of epigenetic regulation in cucumber.
Abstract
INTRODUCTION
Cucumber fruits, with a relatively high rate of fruit expansion, are harvested at an early developmental stage once moderately expanded. Although DNA methylation regulating fruit ripening has been well studied, its function in organ development of cucumber remains unknown.
Objectives
In this study, the regulation and underlying mechanism of DNA methylation in cucumber fruit development were investigated.
Methods
Chemical treatment with DNA methylation inhibitor 5-aza, together with whole genome bisulfite sequencing (WGBS), flow cytometry, small RNA sequencing, and functional validation via virus-induced gene silencing (VIGS), were comprehensively employed.
Results
Treating cucumber fruits with 5-aza at 0 or 4 days after anthesis (DAA) caused stage-dependent inhibition of fruit expansion, with stronger inhibition observed at 0 DAA. WGBS revealed that DNA methylation at CG and CHG contexts remained at high levels before 4 DAA, while mCG levels peaked at 20 DAA and mCHH levels increased throughout. Before 4 DAA, DNA methylation levels at CHG and CG contexts were higher in fruit than fruit neck, revealing spatiotemporal dynamics of DNA methylation during the development of cucumber fruit. These dynamics were functionally enriched in genes related to cell cycle transition, and this finding was further confirmed by impaired endoreduplication observed in 5-aza treated fruits when compared with control. In addition, CsRDR1a, an RNA-dependent RNA polymerase 1 homolog, displayed fruit stage-specific expression patterns, accompanied by significant accumulation of 19---23 nt small RNAs. Cross-tissue validation by silencing CsCMT3 or CsRDR1a showed reduced leaf size, inhibited endoreduplication, and increased expression of cell-cycle genes with decreased DNA methylation levels at their promoter regions, demonstrating that DNA methylation was essential for cell cycle transition during cucumber organ development.
Conclusion
Our results unveil a dual mechanism in which DNA methylation and CsRDR1a-related small RNAs coordinately regulate cucumber organ development, highlighting the importance of epigenetic regulation in cucumber.
The data show the RdDM pathway is a major regulatory contributor to generative development and heat stress responses in barley and demonstrates that rdr2 mutant shows reduced heat stress memory capacity rendering the mutant plants more vulnerable to high temperature.
Auwalu Abdu, H. Szaker, András Kis et al.· bioRxiv· 0 citations
It is found that heat-induced CHH methylation targets specific genomic loci in a developmental stage-specific manner, with a differentially methylated window located within 6 kb of AT5G44410, an F-box protein-encoding gene.
Methylation of the cytosine bases of DNA as a regulator of chromatin structure and gene expression in the stems of rice supports methylation of the cytosine bases of DNA as a regulator of chromatin structure and gene expression in the stems of rice.
Niharika Nonavinakere Chandrakanth, M. McGowan, Nicolás Gaitán et al.· bioRxiv· 0 citations
This study focused on addressing molecular mechanisms of maize response to HAT-NSD by multi-level approaches, and provided new insights into mechanisms for maize responses to HAT-NSD through WGDM.
Y. Pei, Ya-Xing Liu, Jia-Ming Song et al.· Plant, Cell and Environment· 1 citation
Background/Objectives: Whole-genome duplication (WGD) and transposed duplication (TRD) are two principal evolutionary drivers of plant genome expansion, yet the molecular mechanisms underlying their divergent co-expression patterns remain poorly characterized. Methods: In this study, based on the reference genome of tea plant (Camellia sinensis ‘Yunkang 10’, YK10), we integrated publicly available transcriptomic, ATAC-seq, H3K27ac ChIP-seq, whole-genome bisulfite sequencing (WGBS), and SNP data from eight tissues and performed a multi-layered analysis of co-expression divergence across 4071 WGD and 10,174 TRD gene pairs. Results: WGD gene pairs exhibited significantly higher co-expression rates (44.3%) than TRD pairs (33.0%), with gene length and sequence similarity jointly promoting co-expression. Chromatin accessibility and H3K27ac modification were each positively correlated with expression and co-expression; however, under equivalent chromatin accessibility conditions, TRD gene expression remained systematically attenuated, and this reduced expression state was significantly associated with elevated levels of CG, CHG, and CHH methylation, suggesting that these epigenetic marks may collectively participate in the transcriptional repression of TRD genes. Promoter-proximal SNPs exerted disproportionately deleterious effects on TRD co-expression, demonstrating that the combined effects of genetic variation and epigenetic modifications are associated with enhanced transcriptional divergence. Weighted gene co-expression network analysis (WGCNA) revealed that WGD modules showed significant associations with EC, GC, and EGC accumulation, whereas WRKY and bHLH transcription factors in the TRD MEblue module exhibited strong associations with EGCG and ECG. Conclusions: This study systematically characterizes multi-omics association patterns related to duplicate gene co-expression divergence, providing insights into potential hierarchical regulation. It offers mechanistic clues for catechin metabolic regulation and provides candidate targets for metabolite-directed breeding.
Background: Glutathione peroxidases (GPXs) regulate peroxide detoxification and redox signaling, but their relationship with DNA methylation remains unclear in Oryza sativa. This study evaluated whether silencing mitochondrial GPX1 and GPX3 is associated with changes in growth, antioxidant activity, and DNA methylation-related profiles. Methods: Non-transformed plants (NT) and five GPX-silenced lines were evaluated in a randomized complete block design. Morphophysiological traits, antioxidant enzyme activities, total 5-methylcytosine content, and methylation-sensitive restriction profiles were analyzed. Results: GPX silencing impaired early establishment and significantly affected flowering time and leaf, root, seed, and total biomass. Total dry biomass decreased by 62.1% in the most affected GPX1 lines and by 29.2% in GPX3 lines relative to NT plants. Root biomass declined by up to 86.1%, and flowering was delayed by up to 30.7 days. Genotype significantly affected GPX-associated and glutathione reductase activities, whereas no significant genotype effects were detected for catalase, ascorbate peroxidase, or superoxide dismutase activities. GPX-associated and glutathione reductase activities were strongly correlated (r = 0.85, p < 0.001), consistent with selective alteration of GPX-associated and glutathione-linked redox metabolism. Total 5-methylcytosine content decreased by 41–42% in GPX-silenced groups. However, increased McrBC digestion and unchanged HpaII/MspI profiles indicated that methylation-related changes were nonuniform and depended on the genomic sites recognized by each enzymatic assay. Conclusions: These findings show that mitochondrial GPX knockdown is associated with impaired rice growth and reproductive development, as well as with altered total 5-methylcytosine content and restriction-sensitive methylation profiles, suggesting a potential relationship among redox homeostasis, developmental regulation, and epigenetic plasticity that requires further validation using locus-resolved and mechanistic approaches.
P. A. Velasquez-Vasconez, Marina de Lima Nogueira, Carlos Betancourth García et al.· Epigenomes· 0 citations
