Heat-induced CHH methylation changes near an F-box protein gene in Arabidopsis mature-stage seeds

DNA Methylation-Mediated Reprogramming of Gene Expression and Flowering Under Combined Heat and Drought Stress in Maize.

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.

Developmental stage-dependent decoupling of molecular and phenotypic responses to heat in wheat grain

Heatwaves during flowering and grain development threaten global wheat production, yet the extent to which developmental stage shapes molecular and phenotypic responses remains unclear. Here, we investigated whether heat stress (36/29°C for 48 h) imposed at closely spaced developmental stages surrounding anthesis generates stage-specific molecular responses that are associated with subsequent effects on grain properties. Heat exposure increased floret abortion most strongly when it was imposed at the trinucleate stage (TN; ∼48%) compared with the binucleate (BN) and early post-anthesis stages. Methylation levels were largely unaffected by prior heat treatments; however, heat induced stage- and locus-specific methylation changes, particularly at BN. Spatial RNA-seq revealed tissue-specific heat responses that were distinctively different in BN and TN. Integrated metabolomic analyses revealed stage-dependent metabolic reprogramming, including shifts towards stress-associated pathways. Despite heat stress at BN generating broader molecular reprogramming in developing grain, exposure at TN produced stronger effects on grain set and composition, revealing a decoupling between the magnitude of responses and phenotypic outcomes. Together, these findings demonstrate that subtle differences in developmental stage influence the complex molecular responses to heat and subsequent grain properties.

CHH methylation is recruited to gene-proximal transposable elements during repeated drought stress

Trees experience decades-to-centuries of environmental change within a single lifetime, requiring molecular mechanisms that enable rapid physiological and transcriptional adjustment without genetic adaptation across generations. Increasing drought frequency provides one important example of the environmental challenges faced by long-lived species. DNA methylation is a candidate regulator of such responses, but whether environmentally induced methylation primarily protects the genome, regulates nearby transcription, or both, remains an outstanding question. To address this question, we integrated methylome and transcriptome data from valley oak (Quercus lobata) seedlings exposed to drought and well-watered conditions. Drought conditions induced widespread and dynamic CHH methylation that repeatedly targeted the same gene-proximal transposable elements (TEs) across successive drought exposures despite turnover of individual methylated cytosines. This response was concentrated within specific TE families, indicating targeted recruitment of CHH methylation across the genome. Genes associated with CHH-methylated upstream TEs showed increased transcription under drought and were enriched for drought-response pathways, including abscisic acid signaling, cuticle and wax biosynthesis and cell wall remodelling. Nonetheless, the magnitude of transcriptional activation declined with increasing CHH methylation, indicating a graded regulatory effect rather than binary silencing. Despite little overall change in the TE transcriptome, greater CHH methylation was specifically associated with reduced expression of intragenic TEs, consistent with maintenance of local TE repression. 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. Increasing CHH methylation is associated with progressively weaker transcriptional responses, suggesting that high levels of CHH methylation may simultaneously suppress TE activity and constrain nearby gene expression. Such a mechanism may influence how long-lived trees repeatedly adjust transcriptional responses to fluctuating climates throughout their lifespan. Teaser Genome protection during drought may carry an associated cost to stress-responsive gene expression.

Integrative methylome and transcriptome analysis reveals genotype and sequence context-specific responses to aluminum stress in rice

Introduction Aluminum (Al) toxicity in acidic soils is a major constraint to rice production worldwide. However, the epigenetic mechanisms underlying genotypic differences in Al tolerance remain largely unexplored. Methods We integrated whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to characterize DNA methylation dynamics and their relationship with gene expression in two contrasting Oryza sativa genotypes, Al-tolerant Azucena and Al-susceptible BGI, exposed to prolonged Al stress (10 days). Results Genome-wide analysis revealed pronounced context-specific methylation changes that differed markedly between genotypes. CHG methylation was broadly reduced under stress in both genotypes, with a stronger response in BGI, whereas CHH methylation showed a genome-wide increase in BGI but only modest changes in Azucena, indicating more extensive epigenomic perturbation in the susceptible background. At the local level, differentially methylated regions (DMRs) were predominantly hypomethylated across all cytosine contexts and, particularly within the CHG and CHH contexts, were significantly enriched within transposable elements and upstream regulatory regions relative to genomic background, suggesting that stress-induced relaxation of TE silencing and regulatory reprogramming of promoter regions are conserved features of the Al epigenetic response. Integration of DMR and differential expression data identified 71 and 93 genes with both methylation and transcriptional changes in Azucena and BGI, respectively, with only three genes shared between genotypes, all showing opposite transcriptional responses, underscoring the near-complete genotype specificity of the methylation–expression interface. In Azucena, the Al-tolerant genotype, methylation and expression changes were targeted in genes directly linked to Al exclusion, including organic acid and MATE transporters, whereas BGI showed a broader and less specific epigenomic response. Discussion These results suggest 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. This positions DNA methylation as an additional regulatory layer shaping Al tolerance, and pinpoints a short list of candidate genes as priority targets for epigenome-informed breeding strategies in Al-tolerant rice.

Identification of specific transcripts for plant heat stress tolerance through genome-wide analysis of SIZ1-dependent alternative polyadenylation

Heat stress (HS) has emerged as a significant environmental factor affecting plant growth and agricultural productivity. Alternative polyadenylation (APA) is a crucial co-transcriptional process that regulates developmental processes and stress responses in plants. However, the distinct roles of its resultant transcripts in plant HS response remain to be investigated. In this study, we employed poly(A) tag sequencing (PAT-seq) to identify over 1500 transcripts whose expression exhibited significant alterations in response to HS, mediated by SIZ1, a SUMO E3 ligase in Arabidopsis. Further analysis revealed that more than 300 switch genes with varying poly(A) site usages were differentially expressed under HS conditions. Compared to non-canonical poly(A) sites, more genes utilize 3’UTR sites to regulate transcript expression by altering the usage of poly(A) signals. Based on the information of APA genes regulated by SIZ1, we selected two genes, Galactinol synthase enzyme (GolS2) and Tetratricopeptide repeat (TPR) like 3 (TTL3), for characterizing their novel functions. Overexpression of the distal transcript of GolS2 or the proximal transcript of TTL3 enhanced heat tolerance in Arabidopsis. Collectively, our current study elucidates the regulation of APA mediated by SIZ1 during HS response and establishes a strategy for identifying specific transcripts arising from APA for plant heat tolerance.

Genome-Wide Characterization and Reproductive Tissue-Specific Heat-Responsive Expression Analysis of the HSP90 Gene Family in Common Bean (Phaseolus Vulgaris L.)