The functions of lncRNAs extend well beyond the traditional gene-to-protein paradigm, highlighting their ability to fine-tune gene expression without encoding proteins. Notably, lncRNAs participate in a wide range of regulatory processes, including epigenetic modifications, chromatin organization, transcriptional control, and post-transcriptional regulation. These molecules have emerged as key regulators of gene expression, playing crucial roles in modulating plant plasticity in response to environmental cues. This review discusses the current understanding of lncRNAs in shaping the three-dimensional conformation of plant chromatin, exploring their mechanisms of action and functional relevance in development and environmental responses. We also situate these findings within a broader cross-kingdom context by integrating insights from other eukaryotic systems.

Across all biological life, cells in the same environment, with exposure to the same signals and cues exhibit differences in gene expression patterns. This phenomenon is deemed noise and it has long been a question whether it serves a functional role. In plants, recent advances indicate that noise enables many cell fate decisions and thus triggers organogenesis. Additionally, evidence suggests that noise allows organisms to adapt to dynamic environmental conditions and stressors. Given these recent findings and the increasing pressures of climate change on agriculture, efforts to understand the sources and effects of noise are crucial for future projects in engineering resilient, adaptable crops. In this review, we discuss how plants manage noisy gene expression, in some cases buffering and in some cases amplifying natural transcriptional noise. We also discuss the downstream implications of cell to cell heterogeneity on developmental outcomes and robustness. We describe recent progress in this area and present the possibility of using gene expression variability as an engineering target.

In recent years, single-cell and single-nuclei-omic technologies have advanced rapidly in plant research, with RNA sequencing being widely adopted, and chromatin accessibility profiling through assay for transposase-accessible chromatin with sequencing steadily expanding. These approaches have provided unprecedented insight into plant development, cell identity, and stress responses. Integrating transcriptomic and chromatin accessibility data has made it possible to link regulatory elements with gene expression across diverse plant tissues. The goal of this review is to provide a practical guide synthetizing current methods, bioinformatic tools, and applications for a clear perspective on the opportunities and challenges of implementing these technologies in plants. We place particular emphasis on the technical aspects of single-cell/single-nuclei methods, with the aim of enabling informed decisions regarding the choice of protocol. We also highlight emerging multi-omic strategies, the bioinformatic frameworks that enable their analysis, and applications across diverse plant species. In light of the current progress, we discuss that expanding the use of these technologies in plants will advance fundamental biology and generate actionable insights for crop improvement, driving the translation of single-cell discoveries into agricultural innovation.

Hydathodes are tiny plant organs that form an interface between the leaf surface and xylem vasculature. They facilitate excretion of xylem fluid under conditions when leaf transpiration is low and root pressure high-a process known as guttation. Guttation fluid facilitates the entry of (opportunistic) bacterial pathogens into hydathodes. The notorious vascular pathogens of the bacterial genera Xanthomonas and Clavibacter have evolved unique mechanisms to colonize hydathodes and gain access to xylem and then spread systemically throughout the plant causing disease. For a long time, hydathodes were overlooked as plant immune barrier. Recent studies found that plants mount a defense response in hydathodes via known plant immune signaling hubs indicating that hydathode immunity involves both cell surface and intracellular immune receptors to restrict bacterial colonization. In hydathode-adapted Xanthomonas pathovars, the type III secretion system (T3SS) is critical for hydathode colonization. Through the T3SS, bacteria inject effector proteins into plant cells, indicating a role for type III-secreted effectors of Xanthomonas in promoting hydathode colonization. In addition, the type II secretion system (T2SS) and plant cell wall degrading enzymes secreted by Xanthomonas are required for bacterial translocation from the hydathode to the xylem, which indicates the presence of a physical barrier between these tissues. Future research using advanced molecular techniques give now the opportunity to deepen our understanding of hydathode colonization and hydathode immunity in order to develop novel breeding strategies against these devastating vascular bacterial pathogens.

Telomeres are essential chromosomal structures that protect genome integrity and play a central role in aging and cell proliferation. In plants, the epigenetic landscape of telomeres and their adjacent subtelomeric regions has emerged as a critical component regulating telomere function and genome organization. This review summarizes current knowledge of chromatin modifications at plant telomeres, and the impact of chromatin-associated factors on telomere stability. We also discuss experimental tools for studying telomere epigenetics, and identify key open questions in the field.

Fine-tuning eukaryotic gene expression heavily relies on chromatin regulatory mechanisms involving dynamic exchanges and modifications of histones. Here, we review the main pathways that mediate histone H2A and H2B monoubiquitination and ubiquitination in Arabidopsis thaliana. These histone post-translational modifications are linked to multiple chromatin regulatory layers, enabling distinct functional outcomes across the genome and in response to developmental and environmental signals. Indeed, while H2A ubiquitination primarily attenuates transcription either independently or together with PRC2-mediated H3K27 trimethylation, H2B monoubiquitination facilitates nucleosome dynamics and RNA polymerase II progression during gene activation. Given the widespread role of histone ubiquitination mechanisms in plant development, we also discuss how H2Aub and H2Bub homeostasis influences genome regulation. Finally, by referencing yeast and metazoans, we highlight examples of distinctive plant molecular mechanisms and epigenetic interplays involving histone ubiquitination.

Pangenomics significantly expands our understanding of genetic diversity in plants beyond single reference genomes by capturing extensive genomic variations. In this review, we discuss recent methodological breakthroughs in pangenomics, including advances in long-read sequencing, graph-based pangenome tools, artificial intelligence, and multiomics approaches that have collectively enabled pangenomes to become more accurate and prevalent. We review the broad applications of pangenomics in plant science, particularly focusing on crop breeding, including haplotype-based selection, improved prediction for genomic selection, multiomics guided marker discovery, precise identification of genome-editing targets, association of genes with agronomic traits, understanding transposable element dynamics, and providing valuable insights to guide crop improvement. Furthermore, we discuss current challenges and future directions for pangenomics studies.

Nutrients are essential regulators of growth and development across all life forms, serving not only as energetic resources and structural building blocks but also as dynamic signals that govern cell proliferation, metabolism, growth and development. Nutrients and metabolic processes orchestrate plant developmental programs and plasticity via the coordination with dynamic changes in the epigenomic landscape, which is fundamental for governing gene expression programs and developmental transitions in multicellular organisms. In this review, we explore the interplay between nutrition, metabolism, and epigenetic reprogramming in plants, with a particular focus on the novel mechanisms, including nuclear localized metabolic enzymes, moonlighting functions of metabolic enzymes, epigenetic regulators as metabolic sensors, and nutrient sensing and signaling pathways. Elucidating these mechanisms holds significant implications for understanding plant growth and development and improving crop yield and quality.

Plants rely on a two-tiered innate immune system to detect and fend off microorganism infections. This system comprises cell-surface pattern recognition receptors (PRRs) and intracellular nucleotide-binding leucine-rich repeat receptors (NLRs), both of which have been extensively characterized in the model plant Arabidopsis thaliana (hereafter Arabidopsis) and various crop species. Historically, NLR-mediated immunity has been more intensively studied in the context of plant-oomycete interactions compared to PRR-mediated immunity, primarily due to conferring stronger resistance. Recently, however, the identification of novel PRRs and elucidation of their underlying molecular mechanisms in crops have significantly heightened interest in PRR-mediated immunity against oomycetes. Meanwhile, recent advances reveal that oomycete PRRs can perceive host-derived molecules that contribute to virulence. Therefore, this review provides an overview of recent notable advances in understanding PRR-mediated immunity and signal perception during plant-oomycete interactions, with a specific emphasis on the receptor identification, signaling cascades, and molecular mechanisms governing PRR responses to oomycete infection.

Histone variants alter the core properties of the nucleosomes they decorate and hence constitute a significant epigenetic layer to control cellular processes. Historically, histone variants have been studied using classical genetics to implicate the functions associated with them. However, over the last few years, advanced (epi)genomics and structural investigations have revealed the fine molecular steps involved in histone variant-specific genome regulation. This review outlines the key mechanistic findings that uncovered both structural and functional aspects of plant histone variants in unprecedented resolution. We also highlight the key avenues that might hold potential for future studies, including chromatin engineering using histone variants.

In plants, altering the accessibility to DNA through chromatin modification is a key component of transcriptome regulation, crucial for normal development and environmental response. In recent years, our understanding of how and why plants engineer their chromatin has greatly improved, leading to strategies that now enable us to engineer chromatin through both targeted and non-targeted approaches. Although new and improved systems for chromatin engineering are continually emerging, it is evident that developing a diverse toolbox of strategies to tackle various unique challenges is necessary. This review outlines different methods for non-targeted and targeted chromatin engineering, enabling the manipulation of the transcriptome through chromatin engineering. It also discusses particular challenges in the field of chromatin engineering in plants and offers a brief outlook on potential future directions.

Effector-triggered immunity (ETI) can be defined as immune responses activated upon specific recognition of a pathogen effector protein by its cognate plant immune receptor protein. This classic gene-for-gene model of the interaction of one pathogen effector, also known as an Avirulence (Avr) gene, with one plant immune receptor gene, known as a Resistance (R) gene has been documented since the 1950s. Since then, different types of recognition that deviate from the gene-for-gene model, for example, immune receptor pairs and immune receptor networks, have been identified. In addition, while many R genes encode NLR (nucleotide binding, leucine rich repeat) proteins, R genes that encode only parts of NLR domains, and non-NLR encoding R genes such as tandem kinases have been identified, broadening the immune receptor repertoire in plants. In recent years, there have been significant advances in understanding the molecular mechanisms of NLR intracellular immune receptors in plants, including how they are inhibited, activated, and regulated. This review covers recent developments in ETI initiation mechanisms and in plant NLR biology.

Grass stomata provide an exemplary model of how form can improve functionality and promote the success of a plant family. The four-celled grass stomata are composed of dumbbell-shaped guard cells, each flanked by a single parallel subsidiary cell-arguably the most derived and fastest stomatal morphotype. The grasses' breathing pores develop in a strictly linear gradient within a stereotypically patterned epidermis, making it a highly accessible and spatiotemporally predictable developmental study system. Here, we highlight our current understanding of how vein-associated establishment of stomatal identity, tightly regulated asymmetric and symmetric cell division programs and extraordinary morphogenetic processes orchestrate the development of these uniquely shaped graminoid stomata. The innovative geometry and cellular composition of grass stomata have been repeatedly linked to rapid stomatal opening and closing kinetics, thus contributing to the grasses' water-use-efficient photosynthesis. Therefore, besides revealing fundamental aspects of plant development and plant cell biology, the dissection of the developmental processes forming grass stomata can also highlight strategies to engineer stomatal morphology for improved plant-atmosphere gas exchange.

Histone acetyltransferase (HAT) complexes are pivotal regulators of chromatin dynamics, orchestrating transcriptional programs essential for plant development and stress responses in plants. This review synthesizes recent advances in the classification, subunit composition, and functional mechanisms of plant HAT complexes, emphasizing plant-specific characteristics compared to the conserved architecture of HAT complexes. By integrating genetic, biochemical, and structural studies, we delineate how these complexes modulate histone acetylation and coordinate with other chromatin modifications to regulate gene expression. Further research should focus on deciphering the spatiotemporal regulation of HAT complex composition and histone acetylation, and determining the targeting mechanisms of these complexes.

In plants, meiotic crossovers preferentially occur near and within genes, reshuffling preexisting genetic variation from parental genomes and thereby generating diversity in offspring. However, crossovers are generally limited to one to three per chromosome pair, tend to be widely spaced, and are rare in heterochromatic pericentromeric regions. These constraints on crossover number and distribution limit the genetic variation available for crop improvement and hinder the fine mapping of quantitative trait loci (QTLs). Unleashing meiotic crossovers has, therefore, become a key objective in plant genetics and breeding. Here, we review recent findings on pro- and anti-crossover factors that regulate crossover numbers, along with epigenetic mechanisms that suppress pericentromeric crossover recombination. We then explore genetic strategies to manipulate these regulators to maximize crossovers in both chromosomal arms and pericentromeric regions. Finally, we consider the implications of substantially elevating crossover frequency for enhancing QTL mapping resolution and accelerating plant breeding.

Plastids are multifunctional plant organelles, acting as crucial environmental sensors and metabolic hubs that influence plant development and responses to environmental cues. This integration depends on bidirectional communication between plastids and the nucleus. While anterograde regulation is extensively characterized, biogenic retrograde signaling arising during plastid differentiation, remains incompletely understood. Traditionally focused on chloroplasts, studies have identified tetrapyrroles such as heme as key signals. However, recent findings support carotenoid-derived apocarotenoids, particularly those from acyclic cis-carotenes, as emerging retrograde signals. These signals function not only under stress but also during normal chloroplast developmental transitions, such as de-etiolation, and can act as either positive or negative regulators depending on the context. Evidence from grasses suggests that chloroplast differentiation proceeds through sequential, stage-specific signals serving as developmental checkpoints. Moreover, biogenic signaling tunes nuclear gene expression through transcription factors, chromatin remodeling and posttranslational regulation. This review synthesizes current knowledge on biogenic retrograde signaling, highlighting its role in plastid differentiation, development and adaptation. We emphasize the emerging roles of apocarotenoids, highly sensitive to metabolic and environmental conditions, as potential retrograde signals. We highlight that broader studies on different plastid types, novel metabolites and regulatory networks are essential to unravel the complexity of plastid-to-nucleus communication and its key roles in plant morphogenesis and adaptation to environmental changes.

The plant cell wall (CW) was long thought to be a rigid barrier encasing the plant cell and protecting it against biotic and abiotic stressors. Different CW polysaccharides interact with each other, and modifications of either the components or organization of these polysaccharides result in impaired growth or immunity. Emerging evidence suggests that the CW is dynamically modified and reorganized based on internal and external cues. Thus, the CW is both the first barrier that pathogens encounter and the critical final step in defense signaling that leads to fortification of the CW. Here, we review recent findings on how CW components are remodeled to fortify the CW upon pathogen attack and propose a novel concept: layered CW remodeling as an immune strategy. Within this framework, we categorize three interconnected layers of CW remodeling upon pathogen attack: (i) rapid and reversible CW depositions that provide immediate but transient protection; (ii) flexible modifications with plausible signaling functions that integrate defense and surveillance; and (iii) irreversible fortifications that encase pathogen, delimiting infected cells from uninfected cells. This layered framework provides a cohesive view of how different CW modifications are integrated into, and contribute to, plant defense. We also discuss the challenges in studying CW modifications during biotic stresses and highlight important questions that remain unanswered.

Transposons are DNA sequences capable of self-mobilization, which occupy large fractions of plant genomes. Due to their repetitive nature, complete maps of transposon diversity have been challenging to obtain. The advent of long-read sequencing now provides high-quality pangenomic assemblies, revealing transposon diversity within and between species. Transposons are major targets of epigenetic and post-transcriptional silencing, which provide the capacity for cryptic transmission, and facilitate environmental and developmental regulation. Transposon distributions are highly structured along plant chromosomes and we examine genomic niches that specific families are adapted to occupy. Here, we review new insights into transposon core and accessory proteins, and how these can regulate activity in vivo. Finally, we consider the role of transposons in host genome adaptation and evolution, as well as how they are selected on their own terms.

The spatially constrained nature of plant cells makes them highly reliant on targeted membrane vesicle trafficking, which sustains proper cellular function, tissue organization, and overall plant growth and development. These mechanisms are regulated by small GTPases, which function assembling tethering complexes and later serve as their effectors. Tethering factors facilitate the initial contact between the target membrane and incoming vesicles, thereby playing a pivotal role in vesicle targeting and fusion. This review focuses on two tethering complexes, the class C core vacuole/endosome tethering (CORVET) and the homotypic fusion and vacuole protein sorting (HOPS) tethering complex, which have been best studied in the model plant Arabidopsis thaliana. The activity of these complexes has been linked to the regulation of multivesicular endosomes with the vacuole membrane. However, recent reports propose additional functions for specific HOPS subunits regulating other fusion events. Despite these advances, our understanding of HOPS/CORVET function and regulation, including the input of small GTPases, remains incomplete. Thus, in this review, we emphasize the essential role of the HOPS/CORVET tethering complex in plant growth and development while identifying key gaps for future research.

Proteostasis, the regulated balance between protein synthesis and degradation, is crucial for the cellular function and survival. Disruptions in this balance caused by different internal cues and environmental stresses, including pathogen infection, lead to proteotoxicity, which can be highly detrimental or even lethal to the organisms. Pathogens, in their efforts to modulate the host physiology to accommodate their own needs, target and manipulate host proteostasis processes. The extent of pathogen-mediated manipulation of host proteostasis spans every step in the life cycle of a protein: from the transcription and maturation of its coding mRNA, to the protein turnover via the ubiquitin-proteasome system or vacuolar degradation. These diverse sophisticated strategies to manipulate the host proteostasis ultimately lead to the overaccumulation of unfunctional and misfolded proteins, causing proteotoxic stress and facilitating in most cases the pathogen colonization. In turn, plants try to cope with this pathogen-induced proteotoxicity by attenuating translation, promoting chaperon-assisted protein folding and increasing the activity of different proteolytic pathways. Here, we discuss recent advances in understanding the global picture of how pathogens modulate plant proteostasis as well as how plants counter this, which will be crucial for the future development of more tolerant crops to mitigate emerging food security threats.

Diseases caused by plant pathogens are a major factor decreasing crop yields that lead to food insecurity. To protect against pathogen threats, plants possess a multifaceted immune system that perceive threats derived from plant pathogens, resulting in the activation of immune responses. Evolutionary pressures allow plant pathogens to evolve rapidly and evade recognition by nucleotide-binding leucine-rich repeat (NLR) receptors. In recent years, advancements in our understanding of the molecular and structural basis of effector recognition by NLRs have enabled targeted strategies for engineered receptors that contain novel or expanded recognition profiles. In conjunction with advancements in structural modeling and synthetic biology tools, this has transformed our ability to manipulate plant receptors with precision. Here, we highlight structure-based approaches toward engineering plant NLRs, including integrated domain (ID) engineering and leucine-rich repeat resurfacing, discuss challenges associated with NLR engineering, and highlight future engineering approaches to enhance the plant immune system against pathogen threats.