A drought-responsive atlas of candidate enhancer-like nascent transcription in rice is defined and prioritized cis-regulatory candidates for mechanistic validation and crop improvement are provided.
Abstract
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.
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 stress is one of the most severe abiotic constraints limiting plant growth, productivity, and global food security, with its impact intensifying under climate change. Plants adapt to drought through complex physiological, transcriptional, and epigenetic regulatory networks. Among these, long non-coding RNAs (lncRNAs) have emerged as critical regulators that integrate transcriptional control with chromatin-level modulation. Once considered transcriptional noise, lncRNAs are now recognised as dynamic molecular regulators that fine-tune drought-responsive gene expression through chromatin remodelling, histone modifications, DNA methylation, RNA-directed DNA methylation (RdDM), and lncRNA-microRNA crosstalk. These mechanisms regulate key adaptive pathways, including abscisic acid (ABA) signalling, reactive oxygen species (ROS) homeostasis, osmotic adjustment, and root system plasticity. Emerging evidence further highlights the role of lncRNAs in epigenetic stress memory, enabling plants to maintain a primed transcriptional state and respond more efficiently to recurrent drought episodes. This review summarises recent advances in the epigenetic functions of lncRNAs in plant drought adaptation, with particular emphasis on chromatin dynamics, stress memory, and lncRNA-mediated regulatory networks. We also discuss insights from integrated omics approaches and highlight the translational potential of drought-responsive lncRNAs for developing climate-resilient crops.
Salt and cold stresses often occur together in nature and severely impact crop productivity, yet their transcriptional regulation remains poorly understood. Here, we conducted a time-series transcriptomic analysis of maize under salt, cold, and their combination at 0, 6, 12, and 24 h. Differential expression analysis revealed dynamic, condition-specific gene responses grouped into eight distinct temporal patterns. Promoter motif analysis of genes within each pattern identified 5–39 significantly enriched motifs, with over 40% lacking known counterparts, suggesting the involvement of previously uncharacterized cis-regulatory elements in stress-responsive transcriptional regulation. By comparing combined stress responses to the sum of single-stress effects, we found that about 74% of DEGs showed non-additive patterns, suggesting that combined stress triggers a distinct transcriptional program. Evolutionary analysis showed that additive DEGs tend to be more recently evolved, subject to weaker purifying selection, and enriched in transposed duplications, contrasting with the stronger constraint observed in non-additive DEGs. WGCNA identified 24 co-expression modules, among which 65 hub DEGs were detected in modules significantly correlated with specific stress conditions. Furthermore, we reconstructed 228, 20, and 200 sequential transcription factor cascades spanning 6 h, 12 h, and 24 h under cold, salt, and combined stress, respectively, with no cascade shared across all three conditions. Together, these results reveal that maize responses to combined salt and cold stress are largely non-additive and temporally dynamic, with distinct evolutionary patterns underlying different response types, offering insights and candidate regulators for enhancing crop stress resilience.
In miRNA–mRNA regulatory modules of Setaria italica, the candidate novel miRNAs Sit-miR74-N/APX7 and Sit-miR132-N/PEPC involved in key pathways underlying water-deficit response have been detected. In the first module, APX7 expression was directly associated with water-deficit intensity, whereas in the second module, PEPC activation occurred under moderate water deficit. Drought severely constrains plant growth and productivity, yet the underlying regulatory mechanisms remain incompletely understood. Here, we determined the miRNA-mediated post-transcriptional landscape during water deficit in the panicoid grass Setaria italica. Two independent water-deficit experiments combined with small RNA and degradome sequencing identified 159 miRNAs, including 135 candidate novel sequences, of which 20 were differentially expressed under contrasting watering regimes. In silico analysis predicted 1,612 miRNA–mRNA regulatory modules, representing a broad landscape of potential post-transcriptional regulation. Complementarily, degradome sequencing identified 19 miRNA–mRNA modules, several of which exhibited inverse expression patterns, particularly under severe water-deficit conditions. Functional annotation of target mRNAs uncovered multiple functional processes, including transcriptional regulation, photosynthesis, redox homeostasis, and solute transport. Additionally, transient expression assays validated selected miRNA–mRNA modules, confirming the interaction between candidate novel miRNAs and water deficit–related mRNA targets. These modules are involved in key water deficit–responsive pathways, including oxidative stress regulation (Sit-miR74-N/APX7), photosynthetic carbon metabolism (Sit-miR132-N/PEPC), and flavonoid biosynthetic pathways (Sit-miR39-N/OMT). Together, these findings reveal a complex regulatory network in which miRNAs contribute to the coordination of water-deficit responses in S. italica, with post-transcriptional regulation underlying plant responses to abiotic stress.
J. Rodrigues, Vitor G. B. Theodoro, Gabriel G. Carvalho et al.· Planta· 0 citations
The validated hub genes may serve as promising candidate targets for the development of functional markers in marker-assisted selection (MAS), potentially facilitating early-stage screening and pyramiding of drought-tolerant alleles in barley breeding programs, pending experimental validation.
Hossein Sabouri, B. Kazerani, Fakhtak Taliei et al.· Euphytica· 0 citations
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