Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

NMD-mediated posttranscriptional regulation fine-tunes the NLR-WRKY regulatory module to modulate bacterial defense response

Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance system that maintains transcriptome integrity by degrading aberrant RNA transcripts. NMD ensures proper growth and development by preventing autoimmunity through the direct regulation of nucleotide-binding, leucine-rich repeat (NLR) genes. Whether NMD directly regulates WRKY genes remains unclear, despite their upregulation in NMD-deficient plants, and potential feedback between NLRs and WRKYs is also poorly understood. In this study, we showed that NMD also directly regulates a subset of WRKY (WRKY15, 18, 25, 33, 46, 60, and 70) genes, particularly at lower temperatures (16°C). NMD signature-containing transcripts of WRKY46 and WRKY70, selected as representative NMD-regulated WRKY genes, showed increased half-lives in NMD-deficient mutants. Transcriptome analyses showed that these seven NMD-regulated WRKY genes are induced in response to bacterial infection. Potential homologues of these seven NMD-regulated WRKY genes in maize and rice showed similar induction in response to bacterial pathogen infection. Furthermore, these NMD-regulated WRKY genes are induced in plants overexpressing RESISTANT TO P. SYRINGAE 4 (RPS4) in a temperature-dependent manner. By using ChIP-seq and DAP-seq data of WRKY transcription factors, we showed that WRKYs potentially regulate a significant number of NLR genes by directly binding to the W-box in their promoter regions. Taken together, our findings revealed that in addition to the NLRs, the NMD machinery also regulates WRKY genes to keep the basal defense levels in check and the WRKY transcription factors directly regulate NLR genes to constitutes a positive feedback regulatory loop to optimize the plant response to invading pathogens.

The WRC domain of GRF transcription factors: Structure and DNA recognition

Growth-regulating factors (GRFs) belong to a family of transcription factors found in plants which display important roles in growth and development. GRF transcriptional activity is finely tuned by regulatory processes involving post-transcriptional repression exerted by microRNA miR396, and protein-protein interactions involving a family of co-transcriptional regulators known as GRF-interacting factors (GIFs). In this way, the activity of GRF target genes is modulated by a highly complex interplay between GRF/GIF isoform diversity and expression patterns along with miR396 and GIF gradients throughout plant tissues. At the protein level, GRFs are composed of two highly evolutionarily conserved domains known as QLQ and WRC and a less conserved C-terminal trans-activation domain. Whereas QLQ mediates GRF-GIF interaction by forming a complex with a conserved domain called SNH (by SYT N-terminal homology) found in GIFs' N-terminal region, the WRC has been proposed as a putative zinc finger domain responsible for target DNA recognition and nuclear import. However, the structural aspects governing GRF transcriptional activity and target recognition remain unknown. In this work, we applied bioinformatic and biophysical analysis to comprehensively characterize the structural features that modulate the biological function of this protein family with a focus on the WRC domain. We provide insights into the structure of the WRC domain in GRFs and explore the WRC features driving GRFs:DNA complex formation. These findings offer new insights into how WRC domains modulate the biological functions of GRFs, laying the groundwork for future studies on their structure-function relationship in gene regulation and development of plants.

ZmHB53, a Maize Homeodomain-Leucine Zipper I Transcription Factor Family Gene, Contributes to Abscisic Acid Sensitivity and Confers Seedling Drought Tolerance by Promoting the Activity of ZmPYL4

Plant-specific homeodomain-leucine zipper I (HD-Zip I) transcription factors (TFs) crucially regulate plant drought tolerance. However, their specific roles in maize (Zea mays L.) regulating drought tolerance remain largely unreported. Here, we screened a maize HD-Zip I TF family gene, ZmHB53, and clarified its role in drought stress. ZmHB53 overexpression maize plants exhibited sensitivity to abscisic acid (ABA), tolerant to polyethylene glycol (PEG 6000)-induced stress during germination, along with improved seedling drought resistance. Compared to the wild-type, ZmHB53 overexpression lines show higher water retention, biomass, and survival rates, and reduced water loss and stomatal size under drought, suggesting ZmHB53's role in drought adaptation. DNA affinity purification sequencing (DAP-Seq), yeast one hybrid, electrophoretic mobility shift assay (EMSA), and dual luciferase showed that ZmHB53 directly bound to and upregulated the expression of ABA receptor ZmPYL4. Meanwhile, transgenic plants overexpressing ZmPYL4 also exhibit ABA sensitivity and drought tolerance. The research results provide novel insights into the regulatory role of ZmHB53 and ZmPYL4 in enhancing maize's drought tolerance, establishing a foundation for future validation and potential application of ZmHB53 in strategies to improve maize resistance to drought.

Gene regulatory network analysis of silver birch reveals the ancestral state of secondary cell wall biosynthesis in core eudicots

The compact genome and lack of recent whole-genome multiplication (WGM) events make the boreal pioneer tree silver birch (Betula pendula) a promising model for primary and secondary cell wall (PCW and SCW) regulation in forest trees. Here, we constructed regulatory networks through combined co-expression and promoter motif analysis and carried out a tissue-wide analysis of xylan using mass spectrometry. Analyses confirm the evolutionarily conserved model of superimposed layers of regulation and suggest a relatively simple ancestral state still retained in birch. Multispecies network analysis, including birch, poplar, and eucalyptus, identified conserved regulatory interactions, highlighting lignin biosynthesis as least conserved. The SCW biosynthesis co-expression module was enriched with WGM duplicates. While regulator genes were under positive selection, others evolved under relaxed purifying selection, possibly linked with diversification, as indicated by expression and regulatory motif differences. Xylan composition varied between PCW and SCW, revealing unique acetylation patterns. PCW xylan biosynthesis genes showed distinct expression and regulatory motifs, with a novel acetyl transferase potentially involved. This work highlights birch as a valuable model for understanding wood formation, vascular development, and cell wall composition in eudicots.

Diurnal Regulation of SOS Pathway and Sodium Excretion Underlying Salinity Tolerance of Vigna marina

Vigna marina (Barm.) Merr. is adapted to tropical marine beaches and has an outstanding tolerance to salt stress. Given there are growing demands for cultivating crops in saline soil or with saline water, it is important to understand how halophytic species are adapted to the saline environments. Here we revealed by positron-emitting tracer imaging system (PETIS) that V. marina actively excretes sodium from the root during the light period but not the dark period. The following whole genome sequencing accompanied with forward genetic study identified a QTL region harbouring SOS1, encoding plasma membrane Na+/H+ antiporter, which was associated with not only salt tolerance but also the ability of sodium excretion. We also found the QTL region contained a large structural rearrangement that suppressed recombination across ~14 Mbp, fixing multiple gene loci potentially involved in salt tolerance. RNA-seq and promoter analyses revealed SOS1 in V. marina was highly expressed even without salt stress and its promoter shared common cis-regulatory motifs with those exhibiting similar expression profiles. Interestingly, the cis-regulatory motifs seemed installed by a transposable element (TE) insertion. Though not identified by genetic analysis, the transcriptome data also revealed SOS2 transcription was under diurnal regulation, explaining the pattern of sodium excretion together with upregulated expression of SOS1. Altogether, the study elucidated one aspect of the strategy adopted by V. marina to adapt to marine beach, which is highly saline and transpiring.

Synthetic deconvolution of an auxin-dependent transcriptional code

How developmental signals program gene expression in space and time is still poorly understood. Here, we addressed this question for the plant master regulator, auxin. Transcriptional responses to auxin rely on a large multigenic transcription factor family, the auxin response factors (ARFs). We deconvoluted the complexity of ARF-regulated transcription using auxin-inducible synthetic promoters built from cis-element pair configurations differentially bound by ARFs. We demonstrate using cellular systems that ARF transcriptional properties are not only intrinsic but also depend on the cis-element pair configurations they bind to, thus identifying a bi-layer ARF/cis-element transcriptional code. Auxin-inducible synthetic promoters were expressed differentially in planta showing at single-cell resolution how this bi-layer code patterns transcriptional responses to auxin. Combining cis-element pair configurations in synthetic promoters created distinct patterns, demonstrating the combinatorial power of the auxin bi-layer code in generating diverse gene expression patterns that are not simply a direct translation of auxin distribution.

Dancing molecules: group A bZIPs and PEBPs at the heart of plant development and stress responses

Group A basic leucine zipper (bZIP) transcription factors play critical roles in abscisic acid (ABA) signaling and plant development. In Arabidopsis thaliana, these factors are defined by a highly conserved core bZIP domain, and four conserved domains throughout their length: three at the N-terminus (C1-C3) and a phosphorylatable C-terminal SAP motif located at the C4 domain. Initially, members such as ABI5 and ABFs were studied for their roles in ABA signaling during seed germination or stress responses. Later, a sub-clade of group A bZIPs, including FD, was found to play important roles in floral induction by interacting with the florigen FLOWERING LOCUS T (FT) at the shoot apical meristem. Recent research has expanded our understanding of these transcription factors by identifying intriguing parallels between those involved in ABA signaling and those promoting floral induction, and revealing dynamic interactions with FT and other phosphatidylethanolamine-binding proteins (PEBPs) such as TERMINAL FLOWER 1. Studies in crop plants and non-model species demonstrate broader roles, functions, and molecular targets of group A bZIPs. This review highlights common features of group A bZIPs and their post-translational regulation in enabling the activation of gene regulatory networks with important functions in plant development and stress responses.

deepTFBS: Improving within- and Cross-Species Prediction of Transcription Factor Binding Using Deep Multi-Task and Transfer Learning

The precise prediction of transcription factor binding sites (TFBSs) is crucial in understanding gene regulation. In this study, deepTFBS, a comprehensive deep learning (DL) framework that builds a robust DNA language model of TF binding grammar for accurately predicting TFBSs within and across plant species is presented. Taking advantages of multi-task DL and transfer learning, deepTFBS is capable of leveraging the knowledge learned from large-scale TF binding profiles to enhance the prediction of TFBSs under small-sample training and cross-species prediction tasks. When tested using available information on 359 Arabidopsis TFs, deepTFBS outperformed previously described prediction strategies, including position weight matrix, deepSEA and DanQ, with a 244.49%, 49.15%, and 23.32% improvement of the area under the precision-recall curve (PRAUC), respectively. Further cross-species prediction of TFBS in wheat showed that deepTFBS yielded a significant PRAUC improvement of 30.6% over these three baseline models. deepTFBS can also utilize information from gene conservation and binding motifs, enabling efficient TFBS prediction in species where experimental data availability is limited. A case study, focusing on the WUSCHEL (WUS) transcription factor, illustrated the potential use of deepTFBS in cross-species applications, in our example between Arabidopsis and wheat. deepTFBS is publically available at https://github.com/cma2015/deepTFBS.

Enhancers in Plant Development, Adaptation and Evolution

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants. This review provides an overview of how enhancers function to control gene regulation, methods to predict DNA sequences that may have enhancer activity, methods utilized to functionally validate enhancers and the current knowledge of enhancers in plants, including how they impact plant development, response to environment and evolutionary adaptation.

Molecular Mimicry of Transposable Elements in Plants

Transposable elements (TEs) are mobile DNA elements that are particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests that TE insertions promote genetic diversity that is essential for the adaptive evolution of a species. Thus far, studies have mainly investigated the cis-acting regulatory roles of TEs generated by their insertions nearby or within the host genes. However, the trans-acting effects of TE-derived RNA and DNA remained obscure to date. TEs contain various regulatory elements within their sequences that can accommodate the binding of specific RNAs and proteins. Recently, it was suggested that some of these cellular regulators are shared between TEs and the host genes, and the competition for the common host factors underlies the fine-tuned developmental reprogramming. In this review, we will highlight and discuss the latest discoveries on the biological functions of plant TEs, with a particular focus on their competitive binding with specific developmental regulators.

Inheritance of acquired adaptive cold tolerance in rice through DNA methylation

Epigenetic pathways could provide a mechanistic explanation for the inheritance of acquired characteristics, as proposed by Lamarck in 1802, but epigenetic alterations that endow adaptive hereditary traits have rarely been observed. Here, in cultivated Asian rice (Oryzasativa L.), we identified an epiallele conferring acquired and heritable cold tolerance, an adaptive trait enabling northward spread from its tropical origins. We subjected cold-sensitive rice to multigenerational cold stress and identified a line with acquired stable inheritance of cold tolerance. DNA-hypomethylation variation in the acquiredcoldtolerance 1 (ACT1) promoter region rendered its expression insensitive to cold. This change is, in large part, responsible for the acquired cold tolerance, as confirmed by DNA-methylation editing. Natural variation in ACT1 DNA hypomethylation is associated with cold tolerance and rice geographic distribution. Hypomethylation at ACT1 triggers adaptive cold tolerance, presenting a route to epigenetic-variation-driven inheritance of acquired characteristics.

Arabidopsis as a model for translational research

Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage laboratory and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, and molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.

A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation

The periderm provides a protective barrier in many seed plant species. The development of the suberized phellem, which forms the outermost layer of this important tissue, has become a trait of interest for enhancing both plant resilience to stresses and plant-mediated CO2 sequestration in soils. Despite its importance, very few genes driving phellem development are known. Employing single-nuclei sequencing, we have generated an expression census capturing the complete developmental progression of Arabidopsis root phellem cells, from their progenitor cell type, the pericycle, through to their maturation. With this, we identify a whole suite of genes underlying this process, including MYB67, which we show has a role in phellem cell maturation. Our expression census and functional discoveries represent a resource, expanding our comprehension of secondary growth in plants. These data can be used to fuel discoveries and engineering efforts relevant to plant resilience and climate change.

Transcriptional Tuning: How Auxin Strikes Unique Chords in Gene Regulation

Auxin is a central regulator of plant growth, development, and responses to environmental cues. How a single phytohormone mediates such a diverse array of developmental responses has remained a longstanding question in plant biology. Somehow, perception of the same auxin signal can lead to divergent responses in different organs, tissues, and cell types. These responses are primarily mediated by the nuclear auxin signaling pathway, composed of ARF transcription factors, Aux/IAA repressors, and TIR1/AFB auxin receptors, which act together to regulate auxin-dependent transcriptional changes. Transcriptional specificity likely arises through the functional diversity within these signaling components, forming many coordinated regulatory layers to generate unique transcriptional outputs. These layers include differential binding affinities for cis-regulatory elements, protein-protein interaction-specificity, subcellular localization, co-expression patterns, and protein turnover. In this review, we explore the experimental evidence of functional diversity within auxin signaling machinery and discuss how these differences could contribute to transcriptional output specificity.

The GhWL1-GhH1-GhGA2OX1 Transcriptional Module Regulates Cotton Leaf Morphology

Leaf morphology critically influences photosynthetic efficiency, directly affecting crop yield and quality. In this study, a T-DNA insertion mutant (wl-D), characterized by a wrinkled-leaf phenotype, is identified. Genetic analysis reveals that this phenotype is governed by a single dominant gene, WRINKLED-LEAF 1 (GhWL1), which is highly expressed in wl-D compared to the wild type (WT). Overexpression of GhWL1 in WT caused curling at leaf edges, while suppression of GhWL1 in wl-D restored normal leaf morphology, validating its functional role. Further analysis demonstrated that GhWL1 interacts with GhH1, a protein with a KNOX1 structural domain, to regulate leaf development. Overexpression of GhH1 in WT results in a leaf shrinkage phenotype similar to wl-D, whereas suppressing GhH1 in wl-D restored normal leaf morphology, indicating that GhH1 acts downstream of GhWL1. The GhWL1-GhH1 complex directly binds to the promoter of GhGA2OX1 (gibberellin 2-beta-dioxygenase 1), positively regulating its expression. Overexpression of GhGA2OX1 in WT mimicked the leaf shrinkage phenotype observed in plants overexpressing GhH1. These findings establish the GhWL1-GhH1-GhGA2OX1 module as a critical pathway in regulating leaf development, offering valuable insights into the genetic and hormonal networks controlling leaf morphological diversity.

Hierarchical Regulatory Networks Reveal Conserved Drivers of Plant Drought Response at the Cell-Type Level

Drought is a critical environmental challenge affecting plant growth and productivity. Understanding the regulatory networks governing drought response at the cellular level remains an open question. Here, a comprehensive multi-omics integration framework that combines transcriptomic, proteomic, epigenetic, and network-based analyses to delineate cell-type-specific regulatory networks involved in plant drought response is presented. By analyzing nearly 30 000 multi-omics data samples across species, unique insights are revealed into conserved drought responses and cell-type-specific regulatory dynamics, leveraging novel integrative analytical workflows. Notably, CIPK23 emerges as a conserved protein kinase mediating drought tolerance through interactions with CBL4, as validated by yeast two-hybrid and BiFC assays. Experimental validation in Arabidopsis thaliana and Vitis vinifera confirms the functional conservation of CIPK23, which enhances drought resistance in overexpression lines. In addition, the authors' causal network analysis pinpoints critical regulatory drivers such as NLP7 and CIPK23, providing insights into the molecular mechanisms of drought adaptation. These findings advance understanding of plant drought tolerance and offer potential targets for improving crop resilience across diverse species.

Planting Genomes in the Wild: Arabidopsis from Genetics History to the Ecology and Evolutionary Genomics Era

The genetics model system Arabidopsis thaliana (L.) Heynh. lives across a vast geographic range with contrasting climates, in response to which it has evolved diverse life histories and phenotypic adaptations. In the last decade, the cataloging of worldwide populations, DNA sequencing of whole genomes, and conducting of outdoor field experiments have transformed it into a powerful evolutionary ecology system to understand the genomic basis of adaptation. Here, we summarize new insights on Arabidopsis following the coordinated efforts of the 1001 Genomes Project, the latest reconstruction of biogeographic and demographic history, and the systematic genomic mapping of trait natural variation through 15 years of genome-wide association studies. We then put this in the context of local adaptation across climates by summarizing insights from 73 Arabidopsis outdoor common garden experiments conducted to date. We conclude by highlighting how molecular and genomic knowledge of adaptation can help us to understand species' (mal)adaptation under ongoing climate change.

Stable and dynamic gene expression patterns over diurnal and developmental timescales in Arabidopsis thaliana

Developmental processes are known to be circadian-regulated in plants. For instance, the circadian clock regulates genes involved in the photoperiodic flowering pathway and the initiation of leaf senescence. Furthermore, signals that entrain the circadian clock, such as energy availability, are known to vary in strength over plant development. However, diel oscillations of the Arabidopsis transcriptome have typically been measured in seedlings. We collected RNA sequencing (RNA-seq) data from Arabidopsis leaves over developmental and diel timescales, concurrently: every 4 h d-1, on three separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more over the developmental timescale than on the diel timescale, including genes related to a key energy sensor: the sucrose nonfermenting-1-related protein kinase complex. Moreover, regulatory targets of core clock genes displayed changes in rhythmicity and amplitude of expression over development. Cell-type-specific expression showed diel patterns that varied in amplitude, but not phase, over development. Some previously identified reverse transcription quantitative polymerase chain reaction housekeeping genes display undesirable levels of variation over both timescales. We identify which common reverse transcription quantitative polymerase chain reaction housekeeping genes are most stable across developmental and diel timescales. In summary, we establish the patterns of circadian transcriptional regulation over plant development, demonstrating how diel patterns of expression change over developmental timescales.

RhNIRF1-mediated ubiquitination of RhNAC31 affects drought tolerance by regulating stress-related genes in Rosa hybrida

Ubiquitin-mediated protein modification by E3 ligases is crucial for plant stress responses. Here, we demonstrate that the RING-type E3 ligase RhNIRF1 physically interacts with and ubiquitinates the NAC-domain transcription factor RhNAC31, establishing a regulatory module that governs drought tolerance in rose (Rosa hybrida). Silencing of RhNAC31 resulted in decreased dehydration tolerance, whereas its overexpression conferred enhanced photosynthetic capacity concomitant with reduced relative oxygen species accumulation. Notably, RhNIRF1 transcript levels were significantly downregulated under drought stress, while RhNAC31 exhibited an opposite trend. In vitro ubiquitination assays confirmed that the RING domain of RhNIRF1 possesses intrinsic E3 ligase activity specifically targeting RhNAC31 for polyubiquitination. Moreover, RhNAC31 directly binds to various stress-related genes in rose, including RhABI1 and RhANAC083, functioning as a transcriptional activator during dehydration responses. Luciferase assays demonstrated that RhNIRF1 accelerates the degradation of RhNAC31, thereby modulating the binding ability of downstream genes. Our findings highlight the RhNIRF1-RhNAC31 module as a novel molecular switch at the post-translational level for improving drought stress tolerance in rose plants.

Shining light on Arabidopsis regulatory networks integrating nitrogen use and photosynthesis

Nitrogen and light availability are well-known to influence photosynthesis, having both individual and synergistic effects. However, the regulatory interactions between these signaling pathways, especially the transcription factors (TFs) that perceive and integrate these cues, remain to be elucidated. Arabidopsis grown in a matrix of nitrogen and light treatments exhibited distinct physiological and transcriptomic responses. Notably, the effect of nitrogen dose on biomass, nitrogen use efficiency, carbon-to-nitrogen ratio, and gene expression was highly dependent on light intensity. Genes differentially expressed across the treatments were enriched for photosynthetic processes, including the pentose-phosphate cycle, light-harvesting, and chlorophyll biosynthesis. TFs coordinating photosynthesis, carbon-to-nitrogen balance, and nitrogen uptake were identified based on motif enrichment, validated binding data, and gene regulatory network analysis. Dynamic light-by-nitrogen responses were found for TFs previously linked to either nitrogen or light signaling, which now emerge as regulatory hubs that integrate these signals. Among these TFs, we identified bZIP and MYB-related family transcription factors as pivotal players in harmonizing photosynthesis, nitrogen assimilation, and light responses. The transcription factors unveiled in this study have the potential to unlock new strategies for optimizing photosynthetic activity and nutrient-use efficiency in plants.

A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing

Cells must accurately sense and respond to nutrients to compete for resources and establish growth. Phosphate is a critical nutrient source necessary for signaling, energy metabolism, and synthesis of nucleic acids, phospholipids, and cellular metabolites. During phosphate limitation, fungi import phosphate from the environment and liberate phosphate from phosphate-containing molecules in the cell. In the model filamentous fungus Neurospora crassa , the phosphate starvation response is regulated by the conserved transcription factor NUC-1. The activity of NUC-1 is repressed by a complex of the cyclin-dependent kinase MDK-1 and the cyclin PREG when phosphate is plentiful. When phosphate is limiting, NUC-1 repression by MDK-1/PREG is relieved by the cyclin-dependent kinase inhibitor NUC-2. We investigated the global response of N. crassa to phosphate starvation. During phosphate starvation, NUC-1 directly activated expression of genes encoding phosphatases, nucleases, and a phosphate transporter and directly repressed genes associated with the ribosome. Additionally, NUC-1 indirectly activated the expression of an uncharacterized transcription factor, which we named nuc-3 . NUC-3 directly repressed the expression of genes involved in phosphate acquisition and liberation after an extended period of phosphate starvation. Additionally, NUC-3 directly repressed expression of the cyclin-dependent kinase inhibitor nuc-2 . Thus, through the combination of NUC-3 direct repression of genes in the phosphate starvation response and nuc-2 , an activator of the phosphate starvation response, NUC-3 serves to act as a brake on the phosphate starvation response after an extended period of phosphate starvation. This braking mechanism could reduce transcription, a phosphate-intensive process, in conditions when phosphate is limiting.

IMPORTANCE

Fungi evolved regulatory networks to respond to available nutrients. Phosphate is frequently a limiting nutrient for fungi critical for many cellular functions, including nucleic acid and phospholipid biosynthesis, cell signaling, and energy metabolism. The fungal response to phosphate limitation is important in interactions with plants and animals. We investigated the global transcriptional response to phosphate starvation and the role of a major transcriptional regulator, NUC-1, in the model filamentous fungus Neurospora crassa . Our data shows NUC-1 is a bifunctional transcription factor that directly activates phosphate acquisition genes, while directly repressing genes associated with phosphate-intensive processes. NUC-1 indirectly regulates an uncharacterized transcription factor, which we named nuc-3 . NUC-3 directly represses phosphate acquisition genes and nuc-2 , an activator of the phosphate starvation response, during extended periods of phosphate starvation. Thus, NUC-3 acts as a brake on the phosphate starvation response to reduce phosphate-intensive activities, like transcriptional activation, when phosphate starvation persists.

A conserved ARF-DNA interface underlies auxin-triggered transcriptional response

Auxin Response Factor (ARF) plant transcription factors are the key effectors in auxin signaling. Their DNA-Binding Domain (DBD) contains a B3 domain that allows base-specific interactions with Auxin Response Elements (AuxREs) in DNA target sites. Land plants encode three phylogenetically distinct ARF classes: the closely related A- and B-classes have overlapping DNA binding properties, contrasting with the different DNA-binding properties of the divergent C-class ARFs. ARF DNA-binding divergence likely occurred early in the evolution of the gene family, but the molecular determinants underlying it remain unclear. Here, we show that the B3 DNA-binding residues are deeply conserved in ARFs, and variability within these is only present in tracheophytes, correlating with greatly expanded ARF families. Using the liverwort Marchantia polymorpha, we confirm the essential role of conserved DNA-contacting residues for ARF function. We further show that ARF B3-AuxRE interfaces are not mutation-tolerant, suggesting low evolvability that has led to the conservation of the B3-DNA interface between ARF classes. Our data support the almost complete interchangeability between A/B-class ARF B3 by performing interspecies domain swaps in M. polymorpha, even between ARF lineages that diverged over half a billion years ago. Our analysis further suggests that C-class ARF DNA-binding specificity diverged early during ARF evolution in a common streptophyte ancestor, followed by strong selection in A and B-class ARFs as part of a competition-based auxin response system.

Role of an endodermis-specific miR858b-MYB1L module in the regulation of Taxol biosynthesis in Taxus mairei

Taxol, a chemotherapeutic agent widely used for treating various cancers, is extracted from the stems of Taxus mairei. However, current knowledge regarding the effects of stem tissue and age on Taxol accumulation is limited. We employed matrix-assisted laser desorption/ionization mass spectrometry to visualize taxoids in stem section sections of varying ages from T. mairei. Laser capture microdissection integrated with data-dependent acquisition-MS/MS analysis identified that several Taxol biosynthesis pathway-related enzymes were predominantly produced in the endodermis, elucidating the molecular mechanisms underlying endodermis-specific Taxol accumulation. We identified an endodermis-specific MYB1-like (MYB1L) protein and proposed a potential function for the miR858-MYB1L module in regulating secondary metabolic pathways. DNA affinity purification sequencing analysis produced 92 506 target peaks for MYB1L. Motif enrichment analysis identified several de novo motifs, providing new insights into MYB recognition sites. Four target peaks of MYB1L were identified within the promoter sequences of Taxol synthesis genes, including TBT, DBTNBT, T13OH, and BAPT, and were confirmed using electrophoretic mobility shift assays. Dual-luciferase assays showed that MYB1L significantly activated the expression of TBT and BAPT. Our data indicate that the miR858b-MYB1L module plays a crucial role in the transcriptional regulation of Taxol biosynthesis by up-regulating the expression of TBT and BAPT genes in the endodermis.

Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding

Paralogous transcription factors (TFs) frequently recognize highly similar DNA motifs. Homodimerization can help distinguish them according to their different dimeric configurations. Here, by studying R2R3-MYB TFs, we show that homodimerization can also directly change the recognized DNA motifs to distinguish between similar TFs. By high-throughput SELEX, we profiled the specificity landscape for 40 R2R3-MYBs of subfamily VIII and curated 833 motif models. The dimeric models show that homodimeric binding has evoked specificity changes for AtMYBs. Focusing on AtMYB2 as an example, we show that homodimerization has modified its specificity and allowed it to recognize additional cis-regulatory sequences that are different from the closely related CCWAA-box AtMYBs and are unique among all AtMYBs. Genomic sites described by the modified dimeric specificities of AtMYB2 are conserved in evolution and involved in AtMYB2-specific transcriptional activation. Collectively, this study provides rich data on sequence preferences of VIII R2R3-MYBs and suggests an alternative mechanism that guides closely related TFs to respective cis-regulatory sites.

Abundant clock proteins point to missing molecular regulation in the plant circadian clock

Understanding the biochemistry behind whole-organism traits such as flowering time is a longstanding challenge, where mathematical models are critical. Very few models of plant gene circuits use the absolute units required for comparison to biochemical data. We refactor two detailed models of the plant circadian clock from relative to absolute units. Using absolute RNA quantification, a simple model predicted abundant clock protein levels in Arabidopsis thaliana, up to 100,000 proteins per cell. NanoLUC reporter protein fusions validated the predicted levels of clock proteins in vivo. Recalibrating the detailed models to these protein levels estimated their DNA-binding dissociation constants (Kd). We estimate the same Kd from multiple results in vitro, extending the method to any promoter sequence. The detailed models simulated the Kd range estimated from LUX DNA-binding in vitro but departed from the data for CCA1 binding, pointing to further circadian mechanisms. Our analytical and experimental methods should transfer to understand other plant gene regulatory networks, potentially including the natural sequence variation that contributes to evolutionary adaptation.

NAA enhances armillaria gallica growth by modulating nitrogen metabolism through AgZFP48

Armillaria gallica (A. gallica) is a fungus with both medicinal and edible properties. Previous transcriptome analysis has identified the C2H2-type zinc finger transcription factor as a candidate gene involved in the NAA-induced growth promotion of A. gallica. However, the molecular mechanism underlying the enhancement of A. gallica growth by C2H2 transcription factor in response to NAA treatment remains unclear. In this study, we identified a C2H2-type zinc finger transcription factor gene in A. gallica and investigated its function, aiming to elucidate the mechanism by which C2H2-type zinc finger transcription factors regulate the growth of A. gallica. We identified and characterized a novel C2H2-type zinc finger transcription factor, AgZFP48, in A. gallica and found that AgZFP48 is located in the nucleus, where it acts as a transcription activator. AgZFP48 positively regulated the growth of A. gallica. The potential targets of AgZFP48 were identified by using DNA affinity purification sequencing (DAP-seq). In addition, four candidate genes were selected for Electrophoretic Mobility Shift Assays (EMSA) and luciferase reporter activity assessment. The results showed that AgZFP48 activated the expression of ammonium transporter (AgAMT), glutamine synthetase (AgGS), acetylornithine aminotransferase (AgAcOAT), and amino acid permease (AgAAP) by binding to their promoters or exons. In summary, our results suggest that AgZFP48 promotes nitrogen metabolism in A. gallica by activating the expression of nitrogen metabolism-related genes, thereby regulating the growth of the fungus.

The Expansion and Diversification of Epigenetic Regulatory Networks Underpins Major Transitions in the Evolution of Land Plants

Epigenetic silencing is essential for regulating gene expression and cellular diversity in eukaryotes. While DNA and H3K9 methylation silence transposable elements (TEs), H3K27me3 marks deposited by the Polycomb repressive complex 2 (PRC2) silence varying proportions of TEs and genes across different lineages. Despite the major development role epigenetic silencing plays in multicellular eukaryotes, little is known about how epigenetic regulatory networks were shaped over evolutionary time. Here, we analyze epigenomes from diverse species across the green lineage to infer the chronological epigenetic recruitment of genes during land plant evolution. We first reveal the nature of plant heterochromatin in the unicellular chlorophyte microalga Chlorella sorokiniana and identify several genes marked with H3K27me3, highlighting the deep origin of PRC2-regulated genes in the green lineage. By incorporating genomic phylostratigraphy, we show how genes of differing evolutionary age occupy distinct epigenetic states in plants. While young genes tend to be silenced by H3K9 methylation, genes that emerged in land plants are preferentially marked with H3K27me3, some of which form part of a common network of PRC2-repressed genes across distantly related species. Finally, we analyze the potential recruitment of PRC2 to plant H3K27me3 domains and identify conserved DNA-binding sites of ancient transcription factor families known to interact with PRC2. Our findings shed light on the conservation and potential origin of epigenetic regulatory networks in the green lineage, while also providing insight into the evolutionary dynamics and molecular triggers that underlie the adaptation and elaboration of epigenetic regulation, laying the groundwork for its future consideration in other eukaryotic lineages.

Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants

The plant hormone auxin regulates a wide variety of transcriptional responses depending on the cell type, environment and species. How this diversity is achieved may be related to the specific complement of auxin-signalling components in each cell. The levels of activators (class-A AUXIN RESPONSE FACTORS) and repressors (class-B ARFs) are particularly important. Tight regulation of ARF protein levels is probably key in determining this balance. Through comparative analysis of novel, dominant mutants in maize and the moss Physcomitrium patens, we have discovered a ~500-million-year-old mechanism of class-B ARF protein-level regulation mediated by proteasome degradation, important in determining cell fate decisions across land plants. Thus, our results add a key piece to the puzzle of how auxin regulates plant development.

MYB74 transcription factor guides de novo specification of epidermal cells in the abscission zone of Arabidopsis

The waxy cuticle layer is crucial for plant defence, growth and survival, and is produced by epidermal cells, which were thought to be specified only during embryogenesis. New surface cells are exposed during abscission, by which leaves, fruits, flowers and seeds are shed. Recent work has shown that nonepidermal residuum cells (RECs) can accumulate a protective cuticle layer after abscission, implying the potential de novo specification of epidermal cells by transdifferentiation. However, it remains unknown how this process occurs and what advantage this mechanism may offer over the other surface protection alternative, the wound healing pathways. Here we followed this transdifferentiation process with single-cell RNA sequencing analysis of RECs, showing that nonepidermal RECs transdifferentiate into epidermal cells through three distinct stages. During this vulnerable process, which involves a transient period when the protective layer is not yet formed, stress genes that protect the plant from environmental exposure are expressed before epidermis formation, ultimately facilitating cuticle development. We identify a central role for the transcription factor MYB74 in directing the transdifferentiation. In contrast to alternative protective mechanisms, our results suggest that de novo epidermal specification supports the subsequent growth of fruit at the abscission site. Altogether, we reveal a developmental programme by which plants use a transdifferentiation pathway to protect the plant while promoting growth.

Transcription factors SlNOR and SlNOR-like1 regulate steroidal glycoalkaloids biosynthesis in tomato fruit

Steroidal glycoalkaloids (SGAs) are specialized metabolites in Solanaceae that serve as defensive compounds and undergo significant compositional changes during fruit ripening. This study explored the roles of transcription factors SlNOR and SlNOR-like1 in SGAs biosynthesis during tomato fruit development. UPLC-MS/MS revealed dynamic changes in four major SGAs: tomatidine, β-tomatine, α-tomatine, and Esculeoside A. Transgenic studies with knockout and overexpression lines demonstrated that both SlNOR and SlNOR-like1 positively regulated SGAs accumulation. RT-qPCR analysis showed that these transcription factors modulated multiple GAME genes in the SGAs biosynthetic pathway. Through EMSA and DLR assays, we established that SlNOR and SlNOR-like1 directly bound to and activated GAME25 and GAME40 promoters, two key genes involved in tomatidine synthesis and α-tomatine conversion, respectively. These findings reveal a previously unknown regulatory mechanism of SGAs metabolism and suggest potential strategies for optimizing tomato fruit quality through molecular breeding.

Integration of ATAC-seq and RNA-seq reveals the dynamics of chromatin accessibility and gene expression in zoysiagrass response to drought

KEY MESSAGE

The 'X4' accession of zoysiagrass demonstrated superior drought tolerance compared to other accessions. Integration analysis of transcriptomics and epigenomics revealed a positive correlation between ATAC-seq peak intensity and gene expression levels. Six motifs involved in regulating drought responses were identified, which are similar to the domains of the ERF and C2H2 transcription factor families. Heterologous expression of Zja11G000860 in yeast enhanced tolerance to drought stress, allowing robust growth even at high PEG6000 concentrations. Zoysiagrass is renowned for its drought tolerance and serves as an exceptional domestic turfgrass in China. However, the changes in chromatin accessibility during drought in zoysiagrass are not well understood. We conducted a preliminary evaluation of the phenotypic changes in drought tolerance for six zoysiagrass cultivars, taking into account their growth characteristics and physiological traits under drought conditions. Additionally, we utilized an integrated multi-omics strategy, encompassing RNA sequencing (RNA-seq), Assay for Transposase Accessible Chromatin using high-throughput sequencing (ATAC-seq), and reverse transcription quantitative PCR (RT-qPCR) verification experiments, to gain deeper understanding of the chromatin accessibility patterns linked to gene expression in response to drought stress in zoysiagrass. Preliminary analysis of the trends in relative water content and proline content suggested that the variety 'X4' exhibited superior drought tolerance compared to the other five accessions. The KEGG pathway enrichment analysis revealed that zoysiagrass responded to environmental stress by regulating stress response and antioxidant defense pathways. Notably, the expression levels of genes Zja03G031540 and Zja11G000860 were significantly increased in the 'X4' zoysiagrass genotype, which exhibited improved drought tolerance, compared to the 'X1' zoysiagrass genotype with reduced drought tolerance. This study suggested that 63 high-confidence genes are related to drought stress, including Zja03G031540 and Zja11G000860. Additionally, six motifs regulating drought responses were unearthed. Furthermore, the heterologous expression of Zja11G000860 in yeast enhanced tolerance to drought stress. The study discovered a positive correlation between ATAC-seq peak intensity and gene expression levels. The expression of high-confidence genes was linked to zoysiagrass resistance evaluation and phenotypic traits, implying that these genes are involved in responding to external drought stress. This study combined ATAC-seq and RNA-seq technologies for the first time to identify drought-related gene expression in zoysiagrass, elucidating the grass adaptation to environmental stress and the regulatory mechanisms underlying stress responses, and laying the groundwork for zoysiagrass improvement and breeding.

A KNOTTED1-LIKE HOMEOBOX PROTEIN1-interacting transcription factor SlGATA6 maintains the auxin-response gradient to inhibit abscission

The KNOTTED1-LIKE HOMEOBOX PROTEIN1 (SlKD1) is a master abscission regulator in tomato (Solanum lycopersicum). Here, we identified an SlKD1-interacting transcription factor GATA transcription factor 6 (SlGATA6), which is required for maintaining the auxin-response gradient and preventing abscission. SlGATA6 up-regulates the expression of SlLAX2 and SlIAA3. The AUXIN RESISTANT/LIKE AUXIN RESISTANT (AUX/LAX) proteins SlLAX2-dependent asymmetric auxin distribution causes differential accumulation of Auxin/Indole-3-Acetic Acid 3 (SlIAA3) and its homolog SlIAA32 across different abscission zone cells. It is also required for SUMOylation of AUXIN RESPONSE FACTOR 2a (SlARF2a), a key suppressor of auxin signaling and abscission initiator. Moreover, SlIAA3 and SlIAA32 depress SUMOylated SlARF2a, thus suppressing SlARF2a function. The interaction between SlKD1 and SlGATA6 suppresses SlGATA6 binding to the promoters of SlLAX2 and SlIAA3, thereby disrupting the auxin-response gradient and triggering abscission. This regulatory mechanism is conserved under low light-induced abscission in diverse Solanaceae plants. Our findings reveal a critical role of SlKD1 in modulating the auxin-response gradient and abscission initiation.

The MYC Gene RrbHLH105 Contributes to Salt Stress-Induced Geraniol in Rose by Regulating Trehalose-6-Phosphate Signalling

Rose (Rosa rugosa) is an important perfume plant, but its cultivation is significantly constrained by salt stress. Terpenes represent the most abundant volatile aromatic compounds in roses, yet little is known about how terpene metabolism responds to salt stress. In this study, salt-treated rose petals presented significant accumulation of monoterpenes, including geraniol, due to the disruption of jasmonic acid (JA) biosynthesis and signalling. Overexpression and silencing analyses revealed a MYC transcription factor involved in JA signalling (RrbHLH105) as a repressor of geraniol biosynthesis. RrbHLH105 was shown to activate the trehalose-6-phosphate synthase genes RrTPS5 and RrTPS8 by binding to the E-box (5'-CANNTG-3'). The increased trehalose-6-phosphate content and decreased geraniol content in rose petals overexpressing TPS5 or RrTPS8, along with the high accumulation of geraniol in petals where both RrbHLH105 and TPSs were cosilenced, indicate that trehalose signalling plays a role in the negative regulation of geraniol accumulation via the RrbHLH105-TPS module. In summary, the suppression of RrbHLH105 by salt stress leads to excessive geraniol accumulation through the inhibition of both RrbHLH105-mediated JA signalling and RrTPS-mediated trehalose signalling in rose petals. Additionally, this study highlights the emerging role of RrbHLH105 as a critical integrator of JA and trehalose signalling crosstalk.

Two antagonistic gene regulatory networks drive Arabidopsis root hair growth at low temperature linked to a low-nutrient environment

Root hair (RH) cells can elongate to several hundred times their initial size, and are an ideal model system for investigating cell size control. Their development is influenced by both endogenous and external signals, which are combined to form an integrative response. Surprisingly, a low-temperature condition of 10°C causes increased RH growth in Arabidopsis and in several monocots, even when the development of the rest of the plant is halted. Previously, we demonstrated a strong correlation between RH growth response and a significant decrease in nutrient availability in the growth medium under low-temperature conditions. However, the molecular basis responsible for receiving and transmitting signals related to the availability of nutrients in the soil, and their relation to plant development, remain largely unknown. We have discovered two antagonic gene regulatory networks (GRNs) controlling RH early transcriptome responses to low temperature. One GNR enhances RH growth and it is commanded by the transcription factors (TFs) ROOT HAIR DEFECTIVE 6 (RHD6), HAIR DEFECTIVE 6-LIKE 2 and 4 (RSL2-RSL4) and a member of the homeodomain leucine zipper (HD-Zip I) group I 16 (AtHB16). On the other hand, a second GRN was identified as a negative regulator of RH growth at low temperature and it is composed by the trihelix TF GT2-LIKE1 (GTL1) and the associated DF1, a previously unidentified MYB-like TF (AT2G01060) and several members of HD-Zip I group (AtHB3, AtHB13, AtHB20, AtHB23). Functional analysis of both GRNs highlights a complex regulation of RH growth response to low temperature, and more importantly, these discoveries enhance our comprehension of how plants synchronize RH growth in response to variations in temperature at the cellular level.

Arabidopsis research in 2030: Translating the computable plant

Plants are essential for human survival. Over the past three decades, work with the reference plant Arabidopsis thaliana has significantly advanced plant biology research. One key event was the sequencing of its genome 25 years ago, which fostered many subsequent research technologies and datasets. Arabidopsis has been instrumental in elucidating plant-specific aspects of biology, developing research tools, and translating findings to crop improvement. It not only serves as a model for understanding plant biology and but also biology in other fields, with discoveries in Arabidopsis also having led to applications in human health, including insights into immunity, protein degradation, and circadian rhythms. Arabidopsis research has also fostered the development of tools useful for the wider biological research community, such as optogenetic systems and auxin-based degrons. This 4th Multinational Arabidopsis Steering Committee Roadmap outlines future directions, with emphasis on computational approaches, research support, translation to crops, conference accessibility, coordinated research efforts, climate change mitigation, sustainable production, and fundamental research. Arabidopsis will remain a nexus for discovery, innovation, and application, driving advances in both plant and human biology to the year 2030, and beyond.

LG1 promotes preligule band formation through directly activating ZmPIN1 genes in maize

Increasing plant density is an effective strategy for enhancing crop yield per unit land area. A key architectural trait for crops adapting to high planting density is a smaller leaf angle (LA). Previous studies have demonstrated that LG1, a SQUAMOSA BINDING PROTEIN (SBP) transcription factor, plays a critical role in LA establishment. However, the molecular mechanisms underlying the regulation of LG1 on LA formation remain largely unclear. In this study, we conduct comparative RNA-seq analysis of the preligule band (PLB) region of wild type and lg1 mutant leaves. Gene Ontology (GO) term enrichment analysis reveals enrichment of phytohormone pathways and transcription factors, including three auxin transporter genes ZmPIN1a, ZmPIN1b, and ZmPIN1c. Further molecular experiments demonstrate that LG1 can directly bind to the promoter region of these auxin transporter genes and activate their transcription. We also show that double and triple mutants of these ZmPINs genes exhibit varying degrees of auricle size reduction and thus decreased LA. On the contrary, overexpression of ZmPIN1a causes larger auricle and LA. Taken together, our findings establish a functional link between LG1 and auxin transport in regulating PLB formation and provide valuable targets for genetic improvement of LA for breeding high-density tolerant maize cultivars.

A comprehensive analytical method 'Regulatome' revealed a novel pathway for aerenchyma formation under waterlogging in wheat

Waterlogging is a major abiotic stress restricting crop yield globally, and aerenchyma formation is one of the most important adaptive strategies in waterlogging-tolerant plants. However, the conservation of this process remains poorly understood, and additional pathways are yet to be identified. Here, physiological, anatomical, transcriptomic, and metabolomic analyses were conducted on wheat seedlings under normal and waterlogging conditions. Waterlogging caused growth inhibition and physiological damage, as well as induced aerenchyma formation in roots. A total of 10,346 differentially expressed genes and 3,419 differential metabolites were identified in roots. In addition to the AP2/ERF (APETALA2/ETHYLENE RESPONSIVE FACTOR) gene family, integrating analyses also revealed the role of LOB/AS2 (LATERAL ORGAN BOUNDARIES/ASYMMETRIC LEAVES2) in aerenchyma formation under waterlogging. It was revealed that the classical pathway of aerenchyma formation mediated by ethylene response, as well as synergy of calcium ion and reactive oxygen species, was deeply conserved in both monocots and eudicots during 160 million years of evolution through gene co-expression networks of cross-species. The newly introduced concept 'Regulatome' supported the classical pathway of aerenchyma formation, with a proposed model of the jasmonic acid signalling pathway involved in waterlogging, suggesting its usefulness in gene identification and function exploration. These findings provide a novel insight into the regulatory mechanisms of aerenchyma formation and breeding approaches for developing wheat cultivars with high waterlogging tolerance.

Epigenetic regulation and beyond in grapevine-pathogen interactions: a biotechnological perspective

As one of the most important crop plants worldwide, understanding the mechanisms underlying grapevine response to pathogen attacks is key to achieving a productive and sustainable viticulture. Recently, epigenetic regulation in plant immunity has gained significant traction in the scientific community, not only for its role in gene expression regulation but also for its heritability, giving it enormous biotechnological potential. Epigenetic marks have been shown to be dynamically modulated in key genomic regions upon infection, with some being maintained after such, being responsible for priming defense genes. In grapevine, however, knowledge of epigenetic mechanisms is still limited, especially regarding biotic stress responses, representing a glaring gap in knowledge in this important crop plant. Here, we report and integrate current knowledge on grapevine epigenetic regulation as well as non-epigenetic non-coding RNAs in the response to biotic stress. We also explore how epigenetic marks may be useful in grapevine breeding for resistance, considering different approaches, from uncovering and exploiting natural variation to inducing it through different means.

Antagonizing cis-regulatory elements of a conserved flowering gene mediate developmental robustness

Developmental transitions require precise temporal and spatial control of gene expression. In plants, such regulation is critical for flower formation, which involves the progressive maturation of stem cell populations within shoot meristems to floral meristems, followed by rapid sequential differentiation into floral organs. Across plant taxa, these transitions are orchestrated by the F-box transcriptional cofactor gene UNUSUAL FLORAL ORGANS (UFO). The conserved and pleiotropic functions of UFO offer a useful framework for investigating how evolutionary processes have shaped the intricate cis-regulation of key developmental genes. By pinpointing a conserved promoter sequence in an accessible chromatin region of the tomato ortholog of UFO, we engineered in vivo a series of cis-regulatory alleles that caused both loss- and gain-of-function floral defects. These mutant phenotypes were linked to disruptions in predicted transcription factor binding sites for known transcriptional activators and repressors. Allelic combinations revealed dosage-dependent interactions between opposing alleles, influencing the penetrance and expressivity of gain-of-function phenotypes. These phenotypic differences support that robustness in tomato flower development requires precise temporal control of UFO expression dosage. Bridging our analysis to Arabidopsis, we found that although homologous sequences to the tomato regulatory region are dispersed within the UFO promoter, they maintain similar control over floral development. However, phenotypes from disrupting these sequences differ due to the differing expression patterns of UFO. Our study underscores the complex cis-regulatory control of dynamic developmental genes and demonstrates that critical short stretches of regulatory sequences that recruit both activating and repressing machinery are conserved to maintain developmental robustness.

Transcription factors instruct DNA methylation patterns in plant reproductive tissues

DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to male or female reproductive tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. These findings not only reveal RIMs as the first sex-specific RdDM proteins but also establish a critical role for genetic information in targeting DNA methylation. This novel mode of targeting expands our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

ACT2.6: Global Gene Coexpression Network in Arabidopsis thaliana Using WGCNA

BACKGROUND/OBJECTIVES

Genes with similar expression patterns across multiple samples are considered coexpressed, and they may participate in similar biological processes or pathways. Gene coexpression networks depict the degree of similarity between the expression profiles of all genes in a set of samples. Gene coexpression tools allow for the prediction of functional gene partners or the assignment of roles to genes of unknown function. Weighted Gene Correlation Network Analysis (WGCNA) is an R package that provides a multitude of functions for constructing and analyzing a weighted or unweighted gene coexpression network.

METHODS

Previously preprocessed, high-quality gene expression data of 3500 samples of Affymetrix microarray technology from various tissues of the Arabidopsis thaliana plant model species were used to construct a weighted gene coexpression network, using WGCNA.

RESULTS

The gene dendrogram was used as the basis for the creation of a new Arabidopsis coexpression tool (ACT) version (ACT2.6). The dendrogram contains 21,273 leaves, each one corresponding to a single gene. Genes that are clustered in the same clade are coexpressed. WGCNA grouped the genes into 27 functional modules, all of which were positively or negatively correlated with specific tissues.

DISCUSSION

Genes known to be involved in common metabolic pathways were discovered in the same module. By comparing the current ACT version with the previous one, it was shown that the new version outperforms the old one in discovering the functional connections between gene partners. ACT2.6 is a major upgrade over the previous version and a significant addition to the collection of public gene coexpression tools.

Exogenous bacterial cellulose induces plant tissue regeneration through the regulation of cytokinin and defense networks

Regeneration is a unique feature of postembryonic development extensively observed in plants. The capacity to induce regeneration exogenously is limited and usually confined to meristematic-like tissues. We show that bacterial cellulose (BC), but not other structurally similar matrixes, induces postwounding regeneration in nonmeristematic plant tissues via a distinctive route to callus-mediated regenerative programs. The BC-specific program involves cytokinin operating concurrently with strongly activated plant biotic response genes to induce plant regeneration. A reactive oxygen species (ROS) burst, normally associated with defense responses, is sustained upon BC application, involving a network of tightly interconnected transcription factors, where WRKY8, known for regulating stress responses, shows a clustering and hierarchical prevalence. WRKY8 regulates BC-mediated plant regeneration and ROS homeostasis, including superoxide anion accumulation, to potentially promote cell proliferation after wounding. Collectively, our results demonstrate that the cytokinin- and ROS-associated defense responses can be targeted by BC application to promote plant wound regeneration through alternative regenerative programs.

Update on the structure and regulated biosynthesis of the apoplastic polymers cutin and suberin

The plant lipid polymers cutin and suberin play a critical role in many aspects of plant growth, development, and physiology. The mechanisms of cutin and suberin biosynthesis are relatively well understood thanks to just over 2 decades of work with primarily Arabidopsis (Arabidopsis thaliana) mutants. Recent advances in our understanding of cutin and suberin structure have arisen through the application of novel chemistries targeted at quantitative comprehension of intermolecular linkages, isolating intact suberins and cutins, and the application of advanced analytical techniques. The advent of high-throughput transcription factor binding assays and next-generation sequencing has facilitated the discovery of numerous cutin and suberin-regulating transcription factors and their gene promoter targets. Herein we provide an overview of aspects of cutin and suberin structure, biosynthesis, and transcriptional regulation of their synthesis highlighting recent developments in our understanding of these facets of cutin and suberin biology. We further identify outstanding questions in these respective areas and provide perspectives on how to advance the field to address these questions.

New solutions for antibiotic discovery: Prioritizing microbial biosynthetic space using ecology and machine learning

With the explosive increase in genome sequence data, perhaps the major challenge in natural-product-based drug discovery is the identification of gene clusters most likely to specify new chemistry and bioactivities. We discuss the challenges and state-of-the-art of antibiotic discovery based on ecological principles, genome mining and artificial intelligence.

Chromatin Topological Domains Associate With the Rapid Formation of Tandem Duplicates in Plants

In eukaryotes, chromatin is compacted within nuclei under the principle of compartmentalization. On top of that, condensin II establishes eukaryotic chromosome territories, while cohesin organizes the vertebrate genome by extruding chromatin loops and forming topologically associating domains (TADs). Thus far, the formation and roles of these chromatin structures in plants remain poorly understood. This study integrates Hi-C data from diverse plant species, demonstrating that nuclear DNA content influences large-scale chromosome conformation and affects the finer details of compartmental patterns. These contrasting compartmental patterns are distinguished by gene-to-gene loops and validated through cytological observations. Additionally, a novel chromatin domain type associated with tandem duplicate gene clusters is identified. These domains are independent of H3K27me3-mediated chromatin compartmentalization and exhibit evolutionary conservation across species. Gene pairs within TAD-like domains are younger and show higher levels of coexpression. These domains potentially promote the formation of tandem duplicates, a property appears unique to the Actinidia family. Overall, this study reveals functional chromatin domains in plants and provides evidence for the role of three-dimensional chromatin architecture in gene regulation and genome evolution.

A rare PRIMER cell state in plant immunity

Plants lack specialized and mobile immune cells. Consequently, any cell type that encounters pathogens must mount immune responses and communicate with surrounding cells for successful defence. However, the diversity, spatial organization and function of cellular immune states in pathogen-infected plants are poorly understood1. Here we infect Arabidopsis thaliana leaves with bacterial pathogens that trigger or supress immune responses and integrate time-resolved single-cell transcriptomic, epigenomic and spatial transcriptomic data to identify cell states. We describe cell-state-specific gene-regulatory logic that involves transcription factors, putative cis-regulatory elements and target genes associated with disease and immunity. We show that a rare cell population emerges at the nexus of immune-active hotspots, which we designate as primary immune responder (PRIMER) cells. PRIMER cells have non-canonical immune signatures, exemplified by the expression and genome accessibility of a previously uncharacterized transcription factor, GT-3A, which contributes to plant immunity against bacterial pathogens. PRIMER cells are surrounded by another cell state (bystander) that activates genes for long-distance cell-to-cell immune signalling. Together, our findings suggest that interactions between these cell states propagate immune responses across the leaf. Our molecularly defined single-cell spatiotemporal atlas provides functional and regulatory insights into immune cell states in plants.

A network-enabled pipeline for gene discovery and validation in non-model plant species

Identifying key regulators of important genes in non-model crop species is challenging due to limited multi-omics resources. To address this, we introduce the network-enabled gene discovery pipeline NEEDLE, a user-friendly tool that systematically generates coexpression gene network modules, measures gene connectivity, and establishes network hierarchy to pinpoint key transcriptional regulators from dynamic transcriptome datasets. After validating its accuracy with two independent datasets, we applied NEEDLE to identify transcription factors (TFs) regulating the expression of cellulose synthase-like F6 (CSLF6), a crucial cell wall biosynthetic gene, in Brachypodium and sorghum. Our analyses uncover regulators of CSLF6 and also shed light on the evolutionary conservation or divergence of gene regulatory elements among grass species. These results highlight NEEDLE's capability to provide biologically relevant TF predictions and demonstrate its value for non-model plant species with dynamic transcriptome datasets.

Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14

The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the regulatory function of AtWOX14, using the recently developed 5mC-incorporation strategy, this study performed SELEX and DAP-seq for AtWOX14 both in the presence and absence of cytosine methylation, systematically curated 65 motif models and identified 51,039 genomic binding sites for AtWOX14, and examined how 5mC affects DNA binding of AtWOX14 through bioinformatic analyses. Overall, 5mC represses the DNA binding of AtWOX14 monomers but facilitates the binding of its dimers, and the methylation effect on a cytosine's affinity to AtWOX14 is position-dependent. Notably, we found that the most preferred homodimeric configuration of AtWOX14 has changed from ER1 to ER0 upon methylation. This change has the potential to rewire the regulatory network downstream of AtWOX14, as suggested by the GO analyses and the strength changes in the DAP-seq peaks upon methylation. Therefore, this work comprehensively illustrates the specificity and targets of AtWOX14 and reports a previously unrecognized effect of DNA methylation on transcription factor binding.

The MAP kinase scaffold MORG1 shapes cell death in unresolved ER stress in Arabidopsis

Governed by the unfolded protein response (UPR), the ability to counteract endoplasmic reticulum (ER) stress is critical for maintaining cellular homeostasis under adverse conditions. Unresolved ER stress leads to cell death through mechanisms that are yet not completely known. To identify key UPR effectors involved in unresolved ER stress, we performed an ethyl methanesulfonate (EMS) suppressor screen on the Arabidopsis bzip28/60 mutant, which is impaired in activating cytoprotective UPR pathways. This screen identified MAP kinase organizer 1 (MORG1), a conserved MAP kinase scaffold protein, as a previously uncharacterized regulator of ER stress tolerance. The coffin1 mutant, which carries a mutation in MORG1 , exhibited enhanced resilience to ER stress by partially restoring UPR gene expression and promoting growth under stress conditions. Mechanistically, we found that MORG1 modulates MPK6-dependent phosphorylation of the stress-responsive transcription factor WRKY8. Loss of WRKY8 phenocopied the coffin1 mutant, highlighting WRKY8's role as a key repressor in the UPR. Together, these findings reveal a MORG1-MPK6-WRKY8 signaling axis that fine-tunes UPR gene expression, providing new insights into ER stress regulation and strategies for improving stress tolerance in multicellular eukaryotes.

An enhancer-promoter-transcription factor module orchestrates plant immune homeostasis by constraining camalexin biosynthesis

Effective plant defense against pathogens relies on highly coordinated regulation of immune gene expression. Enhancers, as cis-regulatory elements, are indispensable determinants of dynamic gene regulation, but the molecular functions in plant immunity are not well understood. In this study, we identified a novel enhancer, CORE PATTERN-INDUCED ENHANCER 35 (CPIE35), which is rapidly activated upon pathogenic elicitation and negatively regulates antifungal resistance through modulating WRKY15 expression. During immune activation, CPIE35 activates the transcription of WRKY15 by forming chromatin loops with the promoter of WRKY15 in a WRKY18/40/60-, WRKY33-, and MYC2-dependent manner. WRKY15 directly binds to the promoters of PAD3 and GSTU4, suppressing their expression and leading to reduced camalexin synthesis and resistance. Interestingly, CPIE35 region is evolutionarily conserved among Brassicaceae plants, and the CPIE35-WRKY15 module exerts similar functions in Brassica napus to negatively regulate antifungal resistance. Our work reveals the "enhancer-promoter-transcription factor" regulatory mechanism in maintenance of immune homeostasis, highlighting the importance and conserved role of enhancers in fine-tuning immune gene expression in plants.