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.
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
A genomics‐enabled roadmap for developing heat‐resilient rice cultivars under intensifying global warming and supporting sustainable global rice production is outlined.
Prabhat Rana, Chanderkant Chaudhary, Rajat Pruthi et al.· The Plant Genome· 0 citations
Heat stress is one of the most damaging abiotic constraints on crop productivity, and its consequences are expected to intensify as extreme temperature events become more frequent and severe. Pepper (Capsicum annuum L.) is particularly vulnerable to sustained high temperatures, which can disrupt photosynthetic performance, cellular homeostasis, and redox regulation. However, the physiological and transcriptional dynamics underlying genotype-dependent responses to prolonged heat exposure remain insufficiently understood. We combined repeated physiological measurements with time-course RNA sequencing to compare GPC003240, previously identified as a candidate heat-tolerant accession, with two non-elite accessions, GPC010350 and GPC014930, which are phenotypically divergent from each other, under 40/30 °C Day/night temperatures for up to six days. GPC010350 maintained comparatively stable photosystem II performance and higher stomatal conductance, whereas GPC014930 showed progressive photochemical impairment and lower conductance; GPC003240 displayed a distinct, moderately responsive profile. Transcriptomic responses showed partial functional convergence during the early phase of stress exposure but diverged markedly after six days. When gene expression at day 6 was compared with the pre-treatment baseline separately within each genotype, 4,436 differentially expressed genes were detected in GPC010350, compared with 680 in GPC003240 and only 78 in GPC014930. The late response of GPC010350 was associated with enrichment of RNA- and ribosome-related, biosynthetic, DNA-repair, and genome-maintenance functions. By contrast, GPC014930 showed negative enrichment of photosynthesis, plastid organization, redox homeostasis, and translation-related processes. Global co-expression analysis identified a time-decreasing photosynthesis-associated module (ME5) and two time-increasing modules, ME12 and ME19, that were enriched in genes contributing to the late GPC010350 response. Integration of differential expressions, module membership, and functional annotation highlighted a heat shock transcription factor (Caz03g27980), HSP101 (Caz03g07770), and a dual-specificity phosphatase (Caz05g20970) as candidates for further investigation. Overall, the results suggest that genotype-dependent responses to prolonged heat exposure were associated not only with the magnitude of early transcriptional change, but also with differences in the temporal organization of stress-response, maintenance, and metabolic processes. The contrasting responses of the non-elite accessions GPC010350 and GPC014930 further highlight the value of phenotypically diverse germplasm for uncovering mechanisms relevant to future heat-tolerance breeding.
M. Martina, E. Vergnano, F. Secchi et al.· bioRxiv· 0 citations
A near telomere-to-telomere genome assembly of Populus wilsonii, a montane tree species endemic to the eastern Hengduan Mountains, 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
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.
