Involvement of JMJ15 in the dynamic change of genome-wide H3K4me3 in response to salt stress

A systematic review to identify target genes that modulate root system architecture in response to abiotic stress

The exposure of plant roots to soil-related stresses, including drought, high temperatures, salinization, and nutrient deficiency, is on the rise due to climate change caused by human activities. A systematic literature review was conducted, which revealed evidence for conserved genes that modulate root system architecture under specific stress conditions. A collection of Arabidopsis thaliana mutants displaying a root phenotype distinct from the wild type is available in The Arabidopsis Information Resource database. Gene expression data was gathered for specific genes in response to selected abiotic stress treatments. K-means clustering, and fold change analyses identified 118 genes that were upregulated and 185 genes that were downregulated. A dedicated phenotyping approach was used to ascertain that lack of nutrients induced the transition from a 'steep, cheap, and deep' root morphotype to a 'topsoil foraging' root morphotype in the Columbia- 0 reference genotype. The anticipated role of ISOPENTENYLTRANSFERASE 3, LIPOXYGENASE 1, and WEE1 KINASE HOMOLOG as negative regulators of root growth in response to multiple stress signals was assayed. Further research with the candidate genes identified in this study may reveal promising targets for crop improvement.

Genetic responses of plants to urban environmental challenges

MAIN CONCLUSION

This review aims to describe the main genetic adaptations of plants to abiotic and biotic stressors in urban landscapes through modulation of gene expression and genotypic changes. Urbanization deeply impacts biodiversity through ecosystem alteration and habitat fragmentation, creating novel environmental challenges for plant species. Plants have evolved cellular, molecular, and biochemical strategies to cope with the diverse biotic and abiotic stresses associated with urbanization. However, many of these defense and resistance mechanisms remain poorly understood. Addressing these knowledge gaps is crucial for advancing our understanding of urban biodiversity and elucidating the ecological and evolutionary dynamics of species in urban landscapes. As sessile organisms, plants depend heavily on modifications in gene expression as a rapid and efficient strategy to survive urban stressors. At the same time, the urban environment pressures induced plant species to evolve genotypic adaptations that enhance their survival and growth in these contexts. This review explores the different genetic responses of plants to urbanization. We focus on key abiotic challenges, such as air pollution, elevated CO2 levels, heavy metal contamination, heat and drought stress, salinity, and biotic stresses caused by herbivorous insects. By examining these genetic mechanisms induced by urban stressors, we aim to analyze the molecular pathways and genetic patterns underlying the adaptation of plant species to urban environments. This knowledge is a valuable tool for enhancing the selection and propagation of adaptive traits in plant populations, supporting species conservation efforts, and promoting urban biodiversity.

The SnRK1-JMJ15-CRF6 module integrates energy and mitochondrial signaling to balance growth and the oxidative stress response in Arabidopsis

Mitochondria support plant growth and adaptation via energy production and signaling pathways. However, how mitochondria control the transition between growth and stress response is largely unknown in plants. Using molecular approaches, we identified the histone H3K4me3 demethylase JMJ15 and the transcription factor CRF6 as targets of SnRK1 in Arabidopsis. By analyzing antimycin A (AA)-triggered mitochondrial stress, we explored how SnRK1, JMJ15, and CRF6 form a regulatory module that gauges mitochondrial status to balance growth and the oxidative stress response. SnRK1a1, a catalytic α-subunit of SnRK1, phosphorylates and destabilizes JMJ15 to inhibit its H3K4me3 demethylase activity. While SnRK1a1 does not phosphorylate CRF6, it promotes its degradation via the proteasome pathway. CRF6 interacts with JMJ15 and prevents its SnRK1a1 phosphorylation-dependent degradation, forming an antagonistic feedback loop. SnRK1a1, JMJ15, and CRF6 are required for transcriptional reprogramming in response to AA stress. The transcriptome profiles of jmj15 and crf6 mutants were highly correlated with those of plants overexpressing SnRK1a1 under both normal and AA stress conditions. Genetic analysis revealed that CRF6 acts downstream of SnRK1 and JMJ15. Our findings identify the SnRK1-JMJ15-CRF6 module that integrates energy and mitochondrial signaling for the growth-defense trade-off, highlighting an epigenetic mechanism underlying mitonuclear communication.

Epigenetic control of plant abiotic stress responses

On top of genetic information, organisms have evolved complex and sophisticated epigenetic regulation to adjust gene expression in response to developmental and environmental signals. Key epigenetic mechanisms include DNA methylation, histone modifications and variants, chromatin remodeling, and chemical modifications of RNAs. Epigenetic control of environmental responses is particularly important for plants, which are sessile and unable to move away from adverse environments. Besides enabling plants to rapidly respond to environmental stresses, some stress-induced epigenetic changes can be maintained, providing plants with a pre-adapted state to recurring stresses. Understanding these epigenetic mechanisms offers valuable insights for developing crop varieties with enhanced stress tolerance. Here, we focus on abiotic stresses and summarize recent progress in characterizing stress-induced epigenetic changes and their regulatory mechanisms and roles in plant abiotic stress resistance.

Genome-wide mapping of main histone modifications and coordination regulation of metabolic genes under salt stress in pea (Pisum sativum L)

Pea occupy a key position in modern biogenetics, playing multifaceted roles as food, vegetable, fodder, and green manure. However, due to the complex nature of its genome and the prolonged unveiling of high-quality genetic maps, research into the molecular mechanisms underlying pea development and stress responses has been significantly delayed. Furthermore, the exploration of its epigenetic modification profiles and associated regulatory mechanisms remains uncharted. This research conducted a comprehensive investigation of four specific histone marks, namely H3K4me3, H3K27me3, H3K9ac, and H3K9me2, and the transcriptome in pea under normal conditions, and established a global map of genome-wide regulatory elements, chromatin states, and dynamics based on these major modifications. Our analysis identified epigenomic signals across ~82.6% of the genome. Each modification exhibits distinct enrichment patterns: H3K4me3 is predominantly associated with the gibberellin response pathway, H3K27me3 is primarily associated with auxin and ethylene responses, and H3K9ac is primarily associated with negative regulatory stimulus responses. We also identified a novel bivalent chromatin state (H3K9ac-H3K27me3) in pea, which is related to their development and stress response. Additionally, we unveil that these histone modifications synergistically regulate metabolic-related genes, influencing metabolite production under salt stress conditions. Our findings offer a panoramic view of the major histone modifications in pea, elucidate their interplay, and highlight their transcriptional regulatory roles during salt stress.

Insights into the Epigenetic Basis of Plant Salt Tolerance

The increasing salinity of agricultural lands highlights the urgent need to improve salt tolerance in crops, a critical factor for ensuring food security. Epigenetic mechanisms are pivotal in plant adaptation to salt stress. This review elucidates the complex roles of DNA methylation, histone modifications, histone variants, and non-coding RNAs in the fine-tuning of gene expression in response to salt stress. It emphasizes how heritable changes, which do not alter the DNA sequence but significantly impact plant phenotype, contribute to this adaptation. DNA methylation is notably prevalent under high-salinity conditions and is associated with changes in gene expression that enhance plant resilience to salt. Modifications in histones, including both methylation and acetylation, are directly linked to the regulation of salt-tolerance genes. The presence of histone variants, such as H2A.Z, is altered under salt stress, promoting plant adaptation to high-salinity environments. Additionally, non-coding RNAs, such as miRNAs and lncRNAs, contribute to the intricate gene regulatory network under salt stress. This review also underscores the importance of understanding these epigenetic changes in developing plant stress memory and enhancing stress tolerance.

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

BACKGROUND

Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress.

RESULTS

In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls.

CONCLUSION

Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.