Comprehensive analysis of Clade A PP2C family in poplar unveils PtrPP2C-9 as a negative regulator of osmotic stress tolerance through ABF3/GBF3 network.

Integrated CUT&Tag-seq and RNA-seq analysis reveals the transcriptional regulatory network of Gshdz4 under alkaline and heavy metal stress.

Multi-omics analysis of gibberellin-induced internode elongation in Apocynum pictum Schrenk and preliminary investigation into the potential role of WRKY40.

A review of transcriptional control and adaptive functions in terpenoid biosynthesis: Focus on MYB regulatory networks.

Engineering lignin pathway, plant cell wall modification, and genome editing for advanced renewable bioenergy and material applications.

R2R3-MYB transcription factor FaesMYB15 controls floral shape and color via regulating ABC-class MADS-box genes in Long-homostyle common buckwheat.

Pharmacological inhibition of histone Lactylation enhances immunotherapy efficacy in gastrointestinal cancers.

Molecular actions of sepantronium bromide (YM155) on survivin-dependent cell death in cancer and beyond.

Mixed-gas ARTP mutagenesis Decodes the Argon-, Air-, and hybrid Plasma-Specific regulation of Biomass-Lipid-Carbon trade-offs in Chlorella sorokiniana.

Beyond similarity: Unveiling the distinctive transcriptional regulatory roles of ARA1 in plant biomass utilization by Myceliophthora thermophila and related fungi.

Bifidobacterium animalis RH exopolysaccharide bidirectionally modulates inflammatory bone metabolism disorders.

ATAC-seq revealing chromatin accessibility and novel motifs linked to corneal fibrosis.

ZoERF60 enhances antioxidant defense and osmotic homeostasis for heat and humidity resilience in ginger.

HaGATAe regulates chitin synthase 2 and insect intestinal mucin expression with ecdysone responsive transcription factors in Helicoverpa armigera.

Single-cell chromatin accessibility analysis enables high-resolution dissection of regulatory elements and gene regulatory mechanisms. However, standardized and comprehensive analysis workflows remain limited. In this study, we present a streamlined pipeline for analyzing single-cell chromatin accessibility data. The workflow begins with data preprocessing using single-cell assay for transposase-accessible chromatin (scATAC)-pro or Cell Ranger ATAC, followed by peak calling with MACS2 and differential accessibility analysis to detect open chromatin regions and perform differential accessibility analysis to highlight regulatory differences among cell populations. Transcription factor activity is then inferred using chromVAR, incorporating motif enrichment and footprinting analysis. Finally, SCENIC+ is applied to reconstruct transcriptional regulatory networks, enabling in-depth exploration of epigenetic mechanisms at the single-cell level. This integrative approach offers a robust framework for decoding the regulatory landscape and understanding cellular heterogeneity in complex biological systems.

Enhancing cereal grain quality while maintaining yield stability represents a pressing global challenge for sustainable agricultural development. Optimizing grain quality in cereal crops, which account for more than 60% of global dietary energy, relies heavily on managing nitrogen dynamics during the heading and grain-filling stages. Late-stage nitrogen application (from heading to early grain-filling stages) optimizes the temporal dynamics of nitrogen supply and exhibits substantial regulatory potential in mediating the yield–quality trade-off. Nitrogen availability can profoundly influence source–sink dynamics, carbon–nitrogen metabolic coordination, and the biosynthesis of storage reserves. This systematic review consolidates current understanding of the molecular and physiological mechanisms by which late-stage nitrogen application affects grain development and final quality in cereals, with a particular focus on major cereal crops including wheat, rice, and malting barley, which represent contrasting quality objectives and nitrogen management requirements. At the physiological level, late-stage nitrogen application delays functional leaf senescence, sustains photosynthetic carbon assimilation capacity, facilitates assimilate transport and partition to developing grains, and optimizes the accumulation dynamics and compositional profiles of starch and protein. At the molecular level, this review elucidates the sequential regulatory cascades governing nitrogen signal perception and transduction, the coordinated transcriptional networks underlying carbon–nitrogen metabolic crosstalk, and the expression dynamics of genes encoding starch biosynthetic enzymes and storage proteins. Integrating those recent research advances, this review also highlights several critical challenges currently facing the field. To address these challenges, we delineate promising avenues for future research including constructing time-series multi-omics frameworks, employing genome-editing technologies to functionally validate key regulatory genes and integrating artificial intelligence and big data analytics. The goal of this review is to establish a theoretical basis for precision nitrogen management strategies designed to optimize cereal crop production, targeting high yield, superior quality, and improved nitrogen use efficiency concurrently.

Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of respiratory variants.

In Arabidopsis (Arabidopsis thaliana), a family of five receptors mediates ethylene responses in roots, with Ethylene Response 1 (ETR1) controlling increases in root hair proliferation and decreases in lateral root formation. To define the ETR1-dependent gene regulatory network (GRN) controlling root development, we profiled the root transcriptome from Col-0 and the etr1-3 gain-of-function and etr1-7 loss-of-function mutants in the presence and absence of ethylene or the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). We identified 4,522 differentially expressed (DE) transcripts in Col-0 roots that displayed altered abundance in response to ethylene and/or ACC treatment, with larger-magnitude changes induced by ethylene. These included 553 DE transcripts that were ETR1 dependent, defined by a lack of response to treatment with ethylene and/or ACC in ethylene-insensitive etr1-3 and constitutive alteration response in etr1-7 in the presence or absence of treatment relative to time-0 Col-0. Among these ETR1-dependent transcripts were transcripts from genes associated with ethylene biosynthesis and those encoding transcription factors. Reporter fusions driven by promoters from ACC OXIDASE 2 (ACO2) and ACO3, which convert ACC to ethylene, were regulated by ACC in root tissues in appropriate locations to control root development, with pACO5-driven GFP detected in root hairs. We examined the abundance of ETR1-dependent transcripts predicted to encode transcription factors and ACOs in Col-0 and an ein3 eil1 mutant, with and without ACC treatment. Our results suggested that the ETR1 and Ethylene Insensitive 3 (EIN3)/EIN3-like 1 (EIL1) canonical ethylene signaling pathway regulates some, but not all, of these transcriptional responses. Together, these findings reveal features of an ETR1-dependent GRN that controls both ethylene biosynthesis and root growth and development.

Retinoic acid signaling, mediated through its receptors (RARs and RXRs), plays a fundamental role in regulating cell differentiation, proliferation, and apoptosis. While well established in hematologic malignancies, particularly acute promyelocytic leukemia, its therapeutic potential in breast cancer remains underexplored. Emerging evidence has identified aberrant epigenetic regulation of retinoic acid receptors as a central mechanism of resistance to retinoic acid. This review integrates recent advances in epigenetic control, receptor biology, and translational studies to re-evaluate the therapeutic potential of retinoic acid in breast cancer. Among the many factors that influence retinoic acid signaling are reduced receptor expression and altered intracellular delivery of retinoic acid. Promoter hypermethylation and histone deacetylation silence RARβ2 and disrupt canonical retinoic acid transcriptional networks, while imbalanced intracellular routing via CRABP2 and FABP5 and subtype-specific expression of RAR isoforms further determine therapeutic outcomes. Luminal tumors with preserved RARα and CRABP2 expression display strong retinoic acid sensitivity, in contrast to HER2-enriched and triple-negative subtypes, where MYC-driven CRABP2 suppression and DNA hypermethylation confer retinoid resistance. Epigenetic therapies using DNMT or HDAC inhibitors can restore RARβ2 expression and resensitize tumors. Combination regimens such as retinoic acid with entinostat and doxorubicin achieve potent antitumor synergy in preclinical models. Retinoic acid also remodels the tumor microenvironment by modulating angiogenesis, fibroblast activation, and immune responses, although stromal RARβ signaling can paradoxically promote tumor progression. Early clinical trials lacked biomarker stratification and were limited by unfavorable pharmacokinetics, likely obscuring therapeutic benefit. Future clinical development should focus on biomarker-driven patient stratification, pharmacological optimization, and rational combination strategies that integrate retinoids with targeted or immune-based therapies. Notably, emerging methylation-based classifiers that identify retinoid-responsive triple-negative breast cancer subsets, together with the paradoxical pro-tumorigenic effects of stromal RARβ, underscore the novelty and translational significance of integrating tumor-intrinsic and microenvironmental determinants of retinoid sensitivity. Together, these approaches may help re-establish functional retinoid signaling and realize the therapeutic potential of retinoic acid in breast cancer.

The Histone-Modified Landscape: Core Mechanisms of Osimertinib Resistance in EGFR-Mutant Lung Cancer.