Jul 2026· Plant, Cell and Environment· 1 citation· 62 references
Medicine
TL;DR
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.
Abstract
Many molecular mechanism-related details for maize to respond to and tolerate combined high air temperature and natural soil drought (HAT-NSD) stress especially via whole genome-wide DNA methylation (WGDM) are not-yet known. This study focused on addressing molecular mechanisms of maize response to HAT-NSD by multi-level approaches. The main findings included 4315 differentially methylated genes (DMG); DNA motif sequences prone to differential methylation (DM); heterozygous and homozygous variations in SNPs and InDels; differential alternative splicing (AS) events of mRNAs; high- and low-density DM regions on chromosomes; positive and negative correlations between WGDM and whole-genome gene expression, depending on C (CG, CHG and CHH) contexts in gene regions; 4186 differentially expressed genes (DEG); 1607 differentially expressed proteins (DEP); the limited impacts of whole-genome DM on protein abundance via DMG-DEG-DEP type genes; reprogramming of whole-genome gene expression and flowering by whole-genome DM under HAT-NSD, involving differential AS events and feedback from the follow-up effects of the DM; and functions of ZmSOS3-3 and ZmSOS5-2 genes in both HAT-NSD tolerance and flowering. Models of DM-driven reprogramming-feedback gene expression and flowering/tasseling of maize under HAT-NSD were proposed. The findings provide new insights into mechanisms for maize responses to HAT-NSD through WGDM.
This study provides a comprehensive integrative analysis of DNA methylation and transcriptome reprogramming in ‘Shine Muscat’ grapevine under salt stress, revealing potential epigenetic mechanisms involved in transcriptional regulation and salt adaptation.
Ao Li, Ke Li, Fengxia Wang et al.· Agronomy· 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.
These findings support a model in which repeated drought consistently recruits CHH methylation to reproducible gene-proximal TEs, where it is associated with maintenance of local TE repression despite continued activation of neighboring stress-responsive genes.
It is suggested that Al stress triggers genotype- and sequence-context-specific epigenomic reprogramming in rice, and that tolerance is associated with a targeted methylation response rather than a diffuse one.
J. Gallo-Franco, Chrystian C. Sosa, F. Johannes et al.· Frontiers in Plant Science· 0 citations
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.
The results indicate that PvHsp90 genes are evolutionarily conserved and differentially regulated during heat stress, highlighting PvHsp90‑1 and PvHsp90‑2 as promising candidates for improving reproductive thermotolerance and heat resilience in common bean.
Bayram Ali Yerlikaya, Batuhan Gül, Seher Yerlikaya· Journal of Crop Health· 0 citations