Transcriptional memories mediate the plasticity of cold stress responses to enable morphological acclimation in Brachypodium distachyon

Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression

Variation in complex traits is controlled by multiple genes. The prevailing assumption is that such polygenic complex traits are underpinned by variation in elementary molecular traits, such as gene expression, which themselves have a simple genetic basis. Here, we review recent advances that reveal the captivating complexity of gene regulation: the cell type, time point, and magnitude of gene expression are not merely dependent on a couple of regulators; rather, they result from a probabilistic process shaped by cis- and trans-regulatory elements collaboratively integrating internal and external cues with the tightly regulated dynamics of DNA. In addition, the finding that genetic variants linked to complex diseases in humans often do not co-localize with quantitative trait loci modulating gene expression, along with the role of nonfunctional transcription factor (TF) binding sites, suggests that some of the genetic effects influencing gene expression variation may be indirect. If the number of genomic positions responsible for TF binding, TF binding site search time, DNA conformation and accessibility as well as regulation of all trans-acting factors is indeed vast, is it plausible that the complexity of elementary molecular traits approaches the complexity of higher-level organismal traits? Although it is hard to know the answer to this question, we motivate it by reviewing the complexity of the molecular machinery further.

RESPIRATORY BURST OXIDASE HOMOLOG 5.1 regulates H3K4me3 deposition and transcription after cold priming in cucumber

Plants can maintain acquired cold tolerance for a long period after cold priming, even after the resumption of warmer temperatures. However, the transcriptional mechanisms active during the recovery period after cold priming remain unknown. Here, we found that in cucumber (Cucumis sativus), cold priming altered the Histone H3 lysine 4 trimethylation (H3K4me3) signal of sustainably-induced (memory) and non-sustainably-induced (NSI) genes during recovery. In addition, H3K4me3 marks on upregulated memory genes exhibited a specific epigenetic memory during recovery. However, the rank of the H3K4me3 signal on memory and NSI genes in the genome was independent of cold priming, which always contributed to and inhibited the formation of transcription patterns of memory and NSI genes, respectively. Furthermore, the short-lived increase of RESPIRATORY BURST OXIDASE HOMOLOG 5.1 (CsRBOH5.1) expression during recovery after cold priming was essential to maintain high levels of NADPH oxidase activity and apoplastic H2O2, causing cucumber to acquire cold priming and enhancing the maintenance of acquired cold tolerance (MACT). Interestingly, the expression of some key H3K4me3 methyltransferase genes and the accumulation of H3K4me3 on memory genes depended on CsRBOH5.1. Surprisingly, CsRBOH5.1 was essential for almost all genes to form the normal H3K4me3 signaling patterns during recovery, and the necessity was more obvious as recovery progressed. Moreover, transcriptional memory was completely lost in Csrboh5.1 mutants, and the transcriptional patterns of about 80% of NSI genes were disrupted. Overall, our results show that CsRBOH5.1 governs H3K4me3 deposition and cold-induced transcription during recovery after cold priming, affecting the acquisition of cold priming and the intensity of MACT.

Involvement of epigenetic factors in flavonoid accumulation during plant cold adaptation

Plant responses to cold stress include either induction of flavonoid biosynthesis as part of defense responses or initially elevated levels of these substances to mitigate sudden temperature fluctuations. The role of chromatin modifying factors and, in general, epigenetic variability in these processes is not entirely clear. In this work, we review the literature to establish the relationship between flavonoids, cold and chromatin modifications. We demonstrate the relationship between cold acclimation and flavonoid accumulation, and then describe the cold adaptation signaling pathways and their relationship with chromatin modifying factors. Particular attention was paid to the cold signaling module OST1-HOS1-ICE1 and the novel function of the E3 ubiquitin protein ligase HOS1 (a protein involved in chromatin modification during cold stress) in flavonoid regulation.

Transcriptome analysis reveals key regulatory networks and genes involved in the acquisition of cold stress memory in pepper seedlings

Temperature is an important limiting factor in the counter-seasonal cultivation of pepper. Currently, there are no studies on transcriptomic analysis of 'cold stress memory' in pepper. In this study, in order to understand the mechanism of 'cold stress memory' in pepper (Capsicum annuum L.), seedlings were subjected to the following treatments: normal temperature treatment (P0), the first cold treatment for 3 days (P3), the recovery temperature treatment for 3 days (R3), and another cold treatment for 3 days (RP3). The results showed that P3 plants wilted the most, RP3 the second and R3 the least. Leaf reactive oxygen species (ROS) and electrolyte leakage were the most in P3, the second in RP3 and the least in R3. In addition, RP3 had the highest accumulation of zeaxanthin, violaxanthin and β-cryptoxanthin, followed by P3, and R3 had the least. These results suggest that pepper seedlings are characterized by 'cold stress memory'. Transcriptomics was used to analyze the key genes and transcription factors involved in the biosynthesis of zeaxanthin, violaxanthin and β-cryptoxanthin during the formation of 'cold stress memory'. This study provides candidate genes and transcription factors for an in-depth study of the cold tolerance mechanism in pepper.

Transgenerational plasticity in salinity tolerance of rice: unraveling non-genetic phenotypic modifications and environmental influences

Transgenerational plasticity in plants enables rapid adaptation to environmental changes, allowing organisms and their offspring to adapt to the environment without altering their underlying DNA. In this study, we investigated the transgenerational plasticity in salinity tolerance of rice plants using a reciprocal transplant experimental strategy. Our aim was to assess whether non-genetic environment-induced phenotypic modifications and transgenerational salinity affect the salinity tolerance of progeny while excluding nuclear genomic factors for two generations. Using salt-tolerant and salt-sensitive rice genotypes, we observed that the parentally salt-stressed salt-sensitive genotype displayed greater growth performance, photosynthetic activity, yield performance, and transcriptional responses than the parentally non-stressed salt-sensitive plants under salt stress conditions. Surprisingly, salt stress-exposed salt-tolerant progeny did not exhibit as much salinity tolerance as salt stress-exposed salt-sensitive progeny under salt stress. Our findings indicate that the phenotypes of offspring plants differed based on the environment experienced by their ancestors, resulting in heritable transgenerational phenotypic modifications in salt-sensitive genotypes via maternal effects. These results elucidated the mechanisms underlying transgenerational plasticity in salinity tolerance, providing valuable insights into how plants respond to changing environmental conditions.

High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

BACKGROUND

The adaptation of plants to cold stress involves changes in gene expression profiles that are associated with epigenetic regulation. Although the three-dimensional (3D) genome architecture is considered an important epigenetic regulator, the role of 3D genome organization in the cold stress response remains unclear.

RESULTS

In this study, we developed high-resolution 3D genomic maps using control and cold-treated leaf tissue of the model plant Brachypodium distachyon using Hi-C to determine how cold stress affects the 3D genome architecture. We generated ~ 1.5 kb resolution chromatin interaction maps and showed that cold stress disrupts different levels of chromosome organization, including A/B compartment transition, a reduction in chromatin compartmentalization and the size of topologically associating domains (TADs), and loss of long-range chromatin loops. Integrating RNA-seq information, we identified cold-response genes and revealed that transcription was largely unaffected by the A/B compartment transition. The cold-response genes were predominantly localized in compartment A. In contrast, transcriptional changes are required for TAD reorganization. We demonstrated that dynamic TAD events were associated with H3K27me3 and H3K27ac state alterations. Moreover, a loss of chromatin looping, rather than a gain of looping, coincides with alterations in gene expression, indicating that chromatin loop disruption may play a more important role than loop formation in the cold-stress response.

CONCLUSIONS

Our study highlights the multiscale 3D genome reprogramming that occurs during cold stress and expands our knowledge of the mechanisms underlying transcriptional regulation in response to cold stress in plants.

Maintenance of abiotic stress memory in plants: Lessons learned from heat acclimation

Plants acquire enhanced tolerance to intermittent abiotic stress by employing information obtained during prior exposure to an environmental disturbance, a process known as acclimation or defense priming. The capacity for stress memory is a critical feature in this process. The number of reports related to plant stress memory (PSM) has recently increased, but few studies have focused on the mechanisms that maintain PSM. Identifying the components involved in maintaining PSM is difficult due in part to the lack of clear criteria to recognize these components. In this review, based on what has been learned from genetic studies on heat acclimation memory, we propose criteria for identifying components of the regulatory networks that maintain PSM. We provide examples of the regulatory circuits formed by effectors and regulators of PSM. We also highlight strategies for assessing PSMs, update the progress in understanding the mechanisms of PSM maintenance, and provide perspectives for the further development of this exciting research field.

Priming crops for the future: rewiring stress memory

The agricultural sector must produce resilient and climate-smart crops to meet the increasing needs of global food production. Recent advancements in elucidating the mechanistic basis of plant stress memory have provided new opportunities for crop improvement. Stress memory-coordinated changes at the organismal, cellular, and various omics levels prepare plants to be more responsive to reoccurring stress within or across generation(s). The exposure to a primary stress, or stress priming, can also elicit a beneficial impact when encountering a secondary abiotic or biotic stress through the convergence of synergistic signalling pathways, referred to as cross-stress tolerance. 'Rewired plants' with stress memory provide a new means to stimulate adaptable stress responses, safeguard crop reproduction, and engineer climate-smart crops for the future.

DNA Methylation in Plant Responses and Adaption to Abiotic Stresses

Due to their sessile state, plants are inevitably affected by and respond to the external environment. So far, plants have developed multiple adaptation and regulation strategies to abiotic stresses. One such system is epigenetic regulation, among which DNA methylation is one of the earliest and most studied regulatory mechanisms, which can regulate genome functioning and induce plant resistance and adaption to abiotic stresses. In this review, we outline the most recent findings on plant DNA methylation responses to drought, high temperature, cold, salt, and heavy metal stresses. In addition, we discuss stress memory regulated by DNA methylation, both in a transient way and the long-term memory that could pass to next generations. To sum up, the present review furnishes an updated account of DNA methylation in plant responses and adaptations to abiotic stresses.

Integrated Transcriptomic and Metabolomic Analyses of Cold-Tolerant and Cold-Sensitive Pepper Species Reveal Key Genes and Essential Metabolic Pathways Involved in Response to Cold Stress

Cold stress, triggered by particularly low temperatures, is one of the most severe forms of abiotic stress in pepper plants and a major constraint to the global pepper industry, threatening crop production and food security. To acclimatize to extreme conditions, the plant undergoes numerous modifications, including genetic and metabolic modulations. A thorough study of both the genetic and metabolic alterations of plants in response to cold stress is vital to understanding and developing the cold stress resistance mechanism. This study implemented transcriptome and metabolome analyses to evaluate the cold stress response in cold-tolerant and cold-sensitive pepper species. The weighted gene co-expression network revealed three significant modules related to cold stress tolerance in Capsicum pubescens. We identified 17 commonly enriched genes among both species at different time points in 10 different comparisons, including the AP2 transcription factor, LRR receptor-like serine, hypersensitivity-related 4-like protein, and uncharacterized novel.295 and novel.6172 genes. A pathway enrichment analysis indicated that these DEGs were mainly associated with the MAPK signaling pathway, hormone signaling pathway, and primary and secondary metabolism. Additionally, 21 significantly differentially accumulated metabolites (DAMs) were identified in both species after 6 h of cold stress. A transcriptome and metabolome integrated analysis revealed that 54 genes correlated with metabolites enriched in five different pathways. Most genes and metabolites involved in carbohydrate metabolism, the TCA cycle, and flavonoid biosynthesis pathways were upregulated in cold-tolerant plants under cold stress. Together, the results of this study provide a comprehensive gene regulatory and metabolic network in response to cold stress and identified some key genes and metabolic pathways involved in pepper cold tolerance. This study lays a foundation for the functional characterization and development of pepper cultivars with improved cold tolerance.

Molecular basis of priming-induced acquired tolerance to multiple abiotic stresses in plants

The growth, survival, and productivity of plants are constantly challenged by diverse abiotic stresses. When plants are exposed to stress for the first time, they can capture molecular information and store it as a form of memory, which enables them to competently and rapidly respond to subsequent stress(es). This process is referred to as a priming-induced or acquired stress response. In this review, we discuss how (i) the storage and retrieval of the information from stress memory modulates plant physiological, cellular, and molecular processes in response to subsequent stress(es), (ii) the intensity, recurrence, and duration of priming stimuli influences the outcomes of the stress response, and (iii) the varying responses at different plant developmental stages. We highlight current understanding of the distinct and common molecular processes manifested at the epigenetic, (post-)transcriptional, and post-translational levels mediated by stress-associated molecules and metabolites, including phytohormones. We conclude by emphasizing how unravelling the molecular circuitry underlying diverse priming-stimuli-induced stress responses could propel the use of priming as a management practice for crop plants. This practice, in combination with precision agriculture, could aid in increasing yield quantity and quality to meet the rapidly rising demand for food.

Understanding plant stress memory response for abiotic stress resilience: Molecular insights and prospects

As sessile species and without the possibility of escape, plants constantly face numerous environmental stresses. To adapt in the external environmental cues, plants adjust themselves against such stresses by regulating their physiological, metabolic and developmental responses to external environmental cues. Certain environmental stresses rarely occur during plant life, while others, such as heat, drought, salinity, and cold are repetitive. Abiotic stresses are among the foremost environmental variables that have hindered agricultural production globally. Through distinct mechanisms, these stresses induce various morphological, biochemical, physiological, and metabolic changes in plants, directly impacting their growth, development, and productivity. Subsequently, plant's physiological, metabolic, and genetic adjustments to the stress occurrence provide necessary competencies to adapt, survive and nurture a condition known as "memory." This review emphasizes the advancements in various epigenetic-related chromatin modifications, DNA methylation, histone modifications, chromatin remodeling, phytohormones, and microRNAs associated with abiotic stress memory. Plants have the ability to respond quickly to stressful situations and can also improve their defense systems by retaining and sustaining stressful memories, allowing for stronger or faster responses to repeated stressful situations. Although there are relatively few examples of such memories, and no clear understanding of their duration, taking into consideration plenty of stresses in nature. Understanding these mechanisms in depth could aid in the development of genetic tools to improve breeding techniques, resulting in higher agricultural yield and quality under changing environmental conditions.

Regulation of alternative splicing in response to temperature variation in plants

Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.