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.
Abstract
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.
Rising temperatures increasingly threaten plant survival, particularly for long-lived forest trees that face repeated exposure to extreme climatic events. However, the specific mechanisms underlying transient transcriptomic and epigenetic responses to thermal stress, and how these relate to evolutionary selection, remain poorly understood. Here, we present a near telomere-to-telomere genome assembly of Populus wilsonii, a montane tree species endemic to the eastern Hengduan Mountains. To investigate the multi-omic responses related to thermotolerance, we integrated transcriptomic, methylomic, and small RNAome profiling under control, heat-stress, and recovery conditions, alongside population-scale genome resequencing. In addition to an extensive transcriptomic response to heat stress, our findings uncover immediate regulatory mechanisms-including transposable element (TE) activation and repression, CHH methylation reprogramming, and small RNA-mediated pathways-that collectively modulate heat-responsive gene expression. Furthermore, population genomic analyses revealed that these heat-induced genes are under stronger purifying selection and exhibit epigenetic priming that may be maintained over evolutionary timescales. We infer that the epigenetic plasticity provided by dynamic CHH methylation and TEs likely acts as a crucial short-term buffer for plant survival, modulating vital stress-response genes that are further maintained by strict evolutionary constraints over long timescales. This study offers novel insights into how forest trees balance transient epigenetic flexibility with enduring genetic stability to survive accelerating climate change.
Xinxin Zhang, Jiajun Feng, Zeng Wang et al.· Plant Communications· 0 citations
Populus deltoides is a key species for industrial timber and ecological construction in temperate regions, where increasingly frequent and persistent heat waves pose serious challenges to its survival. However, the epigenetic mechanisms by which DNA methylation regulates environmental responses remain poorly understood. Here, whole-genome bisulfite sequencing and RNA-seq were performed on five P. deltoides genotypes grown in temperate and tropical regions. Results revealed that CG/CHG methylation stability is closely correlated with environmental sensitivity. Significant CG/CHG methylation variations may occur specifically in sensitive genotypes with large provenance-environment differences, thereby threatening the survival of P. deltoides by inhibiting the expression of key genes involved in life processes. CHH methylation variation may act as a potential epigenetic regulator of environmental adaptation. Promoter CHH-hypermethylation appears to represent a general response of P. deltoides under high-temperature and short-photoperiod (HS) stress, potentially regulating the expression of 56 genes to activate Ca2+ influx and heat shock proteins, repressing auxin, cytokinin, and cell cycle pathways, thereby initiating stress-protective responses. PdeCNGC13, PdeARF6, PdeLOG3, and PdeHSP15.7 were identified as potential regulatory genes of HS adaptation that are associated with DNA methylation. The mechanism of PdeLOG3 may involve HS-induced CHH-hypermethylation at its PdeLOG3 promoter, which may be associated with suppressed expression, reduced dihydrozeatin levels, and growth. This effect was partially reversed by 5-Azacytidine administration, accompanying increased cytokinin synthesis, enhanced antioxidant capacity, and coinciding with alleviation of HS stress. Our work preliminarily reveals the molecular mechanisms underlying DNA methylation-associated environmental adaptation in poplar, providing potential genetic targets for breeding climate-resilient trees.
Zhengsai Yuan, Weixi Zhang, Xiaohua Su et al.· Forestry Research· 0 citations
Drought increasingly constrains global rice productivity, yet how water deficit remodels cis-regulatory activity in plants remains poorly resolved. Here we used precision run-on sequencing (PRO-seq) to profile nascent transcription in rice leaves under well-watered and drought conditions and mapped transcription-initiation regions with the tool dREG, which detects genome-wide peaks of bidirectional transcription displaying active-enhancer behaviour. PRO-seq captured a robust drought response at genes and revealed extensive remodelling of initiation landscapes. We detected 85,764 consensus dREG sites, of which 17,193 changed significantly under drought and were predominantly intergenic. Because plant intergenic space is rich in transposable elements and silencing-associated transcription, we integrated transposable-element overlap and small-RNA loci with chromatin accessibility and DNA methylation to prioritize 2,428 drought-responsive intergenic sites (841 induced and 1,308 repressed) that are accessible, locally hypomethylated, and bidirectionally transcribed - features consistent with enhancer-like elements. Activity at proximal candidates correlated with elevated nascent transcription of nearby genes, and a subset overlapped gene-connected chromatin loop anchors, supporting candidate enhancer–target relationships. Motif enrichment further supported the involvement of drought-responsive regulatory programs, and hundreds of candidates overlapped rice STARR-seq enhancers. Together, these data define a drought-responsive atlas of candidate enhancer-like nascent transcription in rice and provide prioritized cis-regulatory candidates for mechanistic validation and crop improvement.
Fabian Ortner-Krause, Marina Goliasse, John Gitau 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.
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