Molecular Regulation Research Articles

LSD1 Demethylates and Destabilizes Autophagy Protein LC3B in Ovarian Cancer

Autophagy is a complex cellular process that can either promote or inhibit cancer progression and development, depending on the context and molecular regulation involved. This study investigates how LSD1 regulates autophagy in ovarian cancer by interacting with the autophagy protein LC3B. Utilizing the bioinformatic analysis of TCGA, CPTAC, and GEO datasets, as well as immunohistochemistry in ovarian cancer patients, we explored the expression association between LSD1 and LC3B. Molecular mechanisms were further analyzed using Western blotting, immunoprecipitation, and GST pull-down assays. Our findings reveal that LSD1 binds to LC3B via its SWIRM domain, and high levels of LSD1 are closely associated with aggressive ovarian cancer and poor patient outcomes. Mechanistically, LSD1 demethylates LC3B, leading to decreased LC3B stability. The observed inverse correlation between LSD1 expression and LC3B protein levels in clinical samples underscores the need for further investigation to elucidate how reduced LC3B protein levels induced by LSD1 demethylation may contribute to ovarian cancer.

Impact of Hypoxia and the Levels of Transcription Factor HIF-1α and JMJD1A on Epithelial-Mesenchymal Transition in Head and Neck Squamous Cell Carcinoma Cell Lines.

This study aimed to assess the impact of hypoxia on epithelial-mesenchymal transition (EMT) in head and neck squamous cell carcinoma (HNSCC), focusing on the involvement of transcription factors hypoxia inducible factor 1 (HIF-1α) and Jumonji Domain-Containing Protein 1A (JMJD1A). FaDu and Cal33 cell lines were subjected to hypoxic and normoxic conditions. Cell proliferation was quantified electronically, while PCR and western blot analyses were used to measure mRNA and protein levels of HIF-1α, JMJD1A, and EMT markers. EMT was further characterized through immunofluorescence, migration, and invasion assays. Hypoxic conditions significantly reduced cell proliferation after 48 hours in both cell lines. HIF-1α mRNA levels increased initially during short-term hypoxia but declined thereafter, while JMJD1A mRNA levels showed a sustained increase with prolonged hypoxia. Western blot analysis revealed contrasting trends in protein levels. EMT marker expression varied markedly over time at both the mRNA and protein levels, suggesting EMT induction in hypoxia within 24 hours. Immunofluorescence, migration, and invasion assays supported these findings. The study provides evidence of hypoxia-induced EMT in HNSCC, although conflicting results suggest a complex interplay among molecular regulators involved in this process.

Three-Dimensional Organotypic Systems for Modelling and Understanding Molecular Regulation of Oral Dentogingival Tissues

Three-dimensional organotypic models benefit from the ability to mimic physiological cell–cell or cell–matrix interactions and therefore offer superior models for studying pathological or physiological conditions compared to 2D cultures. Organotypic models consisting of keratinocytes supported by fibroblasts embedded in collagen matrices have been utilised for the study of oral conditions. However, the provision of a suitable model for investigating the pathogenesis of periodontitis has been more challenging. Part of the complexity relates to the different regional epithelial specificities and connective tissue phenotypes. Recently, it was confirmed, using 3D organotypic models, that distinct fibroblast populations were implicated in the provision of specific inductive and directive influences on the overlying epithelia. This paper presents the organotypic model of the dentogingival junction (DGJ) constructed to demonstrate the differential fibroblast influences on the maintenance of regionally specific epithelial phenotypes. Therefore, the review aims are (1) to provide the biological basis underlying 3D organotypic cultures and (2) to comprehensively detail the experimental protocol for the construction of the organotypic cultures and the unique setup for the DGJ model. The latter is the first organotypic culture model used for the reconstruction of the DGJ and is recommended as a useful tool for future periodontal research.

Human amniotic membrane scaffold enhances adipose mesenchymal stromal cell mitochondrial bioenergetics promoting their regenerative capacities.

The human amniotic membrane (hAM) has been applied as a scaffold in tissue engineering to sustain stem cells and enhance their regenerative capacities. We investigated the molecular and biochemical regulations of mesenchymal stromal cells (MSCs) cultured on hAM scaffold in a three-dimensional (3D) setting. Culture of adipose-MSCs (AMSCs) on decellularized hAM showed significant improvement in their viability, proliferative capacity, resistance to apoptosis, and enhanced MSC markers expression. These cultured MSCs displayed altered expression of markers associated with pro-angiogenesis and inflammation and demonstrated increased potential for differentiation into adipogenic and osteogenic lineages. The hAM scaffold modulated cellular respiration by upregulating glycolysis in MSCs as evidenced by increased glucose consumption, cellular pyruvate and lactate production, and upregulation of glycolysis markers. These metabolic changes modulated mitochondrial oxidative phosphorylation (OXPHOS) and altered the production of reactive oxygen species (ROS), expression of OXPHOS markers, and total antioxidant capacity. They also significantly boosted the urea cycle and altered the mitochondrial ultrastructure. Similar findings were observed in bone marrow-derived MSCs (BMSCs). Live cell imaging of BMSCs cultured in the same 3D environment revealed dynamic changes in cellular activity and interactions with its niche. These findings provide evidence for the favorable properties of hAM as a biomimetic scaffold for enhancing the in vitro functionality of MSCs and supporting their potential usefulness in clinical applications.

Covalent Organic Framework Stabilized Single CoN4Cl2 Site Boosts Photocatalytic CO2 Reduction into Tunable Syngas

AbstractSolar carbon dioxide (CO2) reduction provides an attractive alternative to producing sustainable chemicals and fuel. However, the construction of a highly active photocatalyst was challenging because of the rapid charge recombination and sluggish surface CO2 reduction. Herein, a unique Co−N4Cl2 single site was fabricated by loading Co species into the 2,2′‐bipyridine and triazine‐containing covalent organic framework (COF) for CO2 conversion into syngas under visible light irradiation. The resulting champion catalyst TPy‐COF‐Co enabled a record‐high CO production rate of 426 mmol g−1 h−1, associated with the unprecedented turnover number (TON) and turnover frequency (TOF) of 2095 and 1607 h−1, respectively. The catalyst also exhibited favorable recycling performance and widely adjustable syngas production (CO/H2 ratio: 1.8 : 1–1 : 16). A systematical investigation including operando synchrotron X‐ray absorption fine structure (XAFS) spectroscopy, in situ attenuated total reflection surface‐enhanced infrared absorption spectroscopy (ATR‐SEIRAS), and theoretical calculation indicated that the triazine‐based COF framework promoted the charge transfer towards the single Co−N4Cl2 sites that greatly promoted the CO2 activation by lowering the energy barrier of *COOH generation, facilitating the CO2 transformation. This work highlights the great potential of the molecular regulation of COF‐derived single‐atom catalysts to boost CO2 photoreduction efficiency.

The role of high mobility group proteins in cellular senescence mechanisms

Aging is a universal physiological phenomenon, and chronic age-related diseases have become one of the leading causes of human mortality, accounting for nearly half of all deaths. Studies have shown that reducing the incidence of these diseases can not only extend lifespan but also promote healthy aging. In recent years, the potential role of non-histone high-mobility group proteins (HMGs) in the regulation of aging and lifespan has attracted widespread attention. HMGs play critical roles in cellular senescence and associated diseases through various pathways, encompassing multi-layered mechanisms involving protein interactions, molecular regulation, and chromatin dynamics. This review provides a comprehensive analysis of the interactions between HMG family proteins and senescence-associated secretory phenotype (SASP), chromatin structure, and histone modifications, offering a deeper exploration of the pivotal functions and impacts of HMGs in the aging process. Furthermore, we summarize recent findings on the contributions of HMG proteins to aging and age-related diseases. HMG proteins not only regulate senescence-associated inflammation through modulating the SASP but also influence genomic stability and cell fate decisions via interactions with chromatin and histones. Targeting HMG proteins holds great potential in delaying the progression of aging and its associated diseases. This review aims to provide a systematic overview of HMG proteins’ roles in aging and to lay a solid foundation for future anti-aging drug development and therapeutic strategies. With the advancing understanding of the mechanisms by which HMGs regulate aging, developing therapeutic interventions targeting HMGs may emerge as a promising approach to extending lifespan and enhancing healthspan.

Reconstructing Molecular Networks by Causal Diffusion Do-Calculus Analysis with Deep Learning.

Quantifying molecular regulations between genes/molecules causally from observed data is crucial for elucidating the molecular mechanisms underlying biological processes at the network level. Presently, most methods for inferring gene regulatory and biological networks rely on association studies or observational causal-analysis approaches. This study introduces a novel approach that combines intervention operations and diffusion models within a do-calculus framework by deep learning, i.e., Causal Diffusion Do-calculus (CDD) analysis, to infer causal networks between molecules. CDD can extract causal relations from observed data owing to its intervention operations, thereby significantly enhancing the accuracy and generalizability of causal network inference. Computationally, CDD has been applied to both simulated data and real omics data, which demonstrates that CDD outperforms existing methods in accurately inferring gene regulatory networks and identifying causal links from genes to disease phenotypes. Especially, compared with the Mendelian randomization algorithm and other existing methods, the CDD can reliably identify the disease genes or molecules for complex diseases with better performances. In addition, the causal analysis between various diseases and the potential factors in different populations from the UK Biobank database is also conducted, which further validated the effectiveness of CDD.

AMBRA1 controls the translation of immune-specific genes in T lymphocytes

T cell receptor (TCR) engagement causes a global cellular response that entrains signaling pathways, cell cycle regulation, and cell death. The molecular regulation of mRNA translation in these processes is poorly understood. Using a whole-genome CRISPR screen for regulators of CD95 (FAS/APO-1)-mediated T cell death, we identified AMBRA1, a protein previously studied for its roles in autophagy, E3 ubiquitin ligase activity, and cyclin regulation. T cells lacking AMBRA1 resisted FAS-mediated cell death by down-regulating FAS expression at the translational level. We show that AMBRA1 is a vital regulator of ribosome protein biosynthesis and ribosome loading on select mRNAs, whereby it plays a key role in balancing TCR signaling with cell cycle regulation pathways. We also found that AMBRA1 itself is translationally controlled by TCR stimulation via the CD28-PI3K-mTORC1-EIF4F pathway. Together, these findings shed light on the molecular control of translation after T cell activation and implicate AMBRA1 as a translational regulator governing TCR signaling, cell cycle progression, and T cell death.

Transcriptome Analysis Deciphers the Underlying Molecular Mechanism of Peanut Lateral Branch Angle Formation Using Erect Branching Mutant.

Background The growth habit (GH), also named the branching habit, is an important agronomic trait of peanut and mainly determined by the lateral branch angle (LBA). The branching habit is closely related to peanut mechanized farming, pegging, yield, and disease management. Objectives However, the molecular basis underlying peanut LBA needs to be uncovered. Methods In the present study, an erect branching peanut mutant, eg06g, was obtained via 60Co γ-ray-radiating mutagenesis of a spreading-type peanut cultivar, Georgia-06G (G06G). RNA-seq was performed to compare the transcriptome variation of the upper sides and lower sides of the lateral branch of eg06g and G06G. Results In total, 4908 differentially expressed genes (DEGs) and 5833 DEGs were identified between eg06g and G06G from the lower sides and upper sides of the lateral branch, respectively. GO, KEGG, and clustering enrichment analysis indicated that the carbohydrate metabolic process, cell wall organization or biogenesis, and plant hormone signal transduction were mainly enriched in eg06g. Conclusions Further analysis showed that the genes involved in starch biosynthesis were upregulated in eg06g, which contributed to amyloplast sedimentation and gravity perception. Auxin homeostasis and transport-related genes were found to be upregulated in eg06g, which altered the redistribution of auxin in eg06g and in turn triggered apoplastic acidification and activated cell wall modification-related enzymes, leading to tiller angle establishment through the promotion of cell elongation at the lower side of the lateral branch. In addition, cytokinin and GA also demonstrated synergistic action to finely regulate the formation of peanut lateral branch angles. Collectively, our findings provide new insights into the molecular regulation of peanut LBA and present genetic materials for breeding peanut cultivars with ideotypes.

H Antigen expression modulates epidermal Keratinocyte Integrity and differentiation

BackgroundABO blood group antigens (ABH antigens) are carbohydrate chains glycosylated on epithelial and red blood cells. Recent findings suggest reduced ABH expression in psoriasis and atopic dermatitis, a chronic inflammatory skin disease with retained scale. H antigen, a precursor for A and B antigens, is synthesized by fucosyltransferase 1 (FUT1). Desmosomes, critical for skin integrity, are known to require N-glycosylation for stability. We investigate the impact of H antigens, a specific type of glycosylation, on desmosomes in keratinocytes.MethodPrimary human keratinocytes were transfected with FUT1 siRNA or recombinant adenovirus for FUT1 overexpression. Cell adhesion and desmosome characteristics and their underlying mechanisms were analyzed.ResultThe knockdown of FUT1, responsible for H2 antigen expression in the skin, increased cell-cell adhesive strength and desmosome size in primary cultured keratinocytes without altering the overall desmosome structure. Desmosomal proteins, including desmogleins or plakophilin, were upregulated, suggesting enhanced desmosome assembly. Reduced H2 antigen expression via FUT1 knockdown led to increased keratinocyte differentiation, evidenced by elevated expression of differentiation markers. Epidermal growth factor receptor (EGFR) has been described to be associated with FUT1 and promotes cell migration and differentiation. The effects of FUT1 knockdown were recapitulated by an EGFR inhibitor concerning desmosomal proteins and cellular differentiation. Further investigation demonstrated that the FUT1 knockdown reduced EGFR signaling by lowering the levels of EGF ligands rather than directly regulating EGFR activity. Moreover, FUT1 overexpression reversed the effects observed in FUT1 knockdown, resulting in the downregulation of desmosomal proteins and differentiation markers while increasing both mRNA and protein levels of EGFR ligands.ConclusionThe expression level of FUT1 in the epidermis appears to influence cell-cell adhesion and keratinocyte differentiation status, at least partly through regulation of H2 antigen and EGFR ligand expression. These observations imply that the fucosylation of the H2 antigen by FUT1 could play a significant role in maintaining the molecular composition and regulation of desmosomes and suggest a possible involvement of the altered H2 antigen expression in skin diseases, such as psoriasis and atopic dermatitis.

Post-transcriptional regulation of Dufour’s gland reproductive signals in bumble bees

Pheromone communication is a key mechanism by which the reproductive division of labor is maintained within insect communities. Understanding how pheromones evolved to regulate social behavior requires knowledge of the molecular regulation of their production. However, even in cases where pheromones were identified, our understanding of their biosynthesis and molecular regulation remains limited. Bumble bees provide a unique system to explore pheromone biosynthesis since workers produce ester sterility signals in their Dufour’s gland that differ from gyne-specific esters and are not produced by queens. These esters are hypothesized to be produced in the exocrine gland where they are stored, and indeed queens, gynes and workers differ significantly in the expression of Dufour’s gland genes coding to enzymes involved in the biosynthesis of esters. However, a previous transcriptome analysis revealed no gene expression differences in the Dufour’s gland of workers despite differences in both ester production and ovarian activation, suggesting that ester production may be regulated lower down. Proteomics of the Dufour’s gland of queens, gynes, and workers recovered over 2400 proteins and broadly matched the previous RNAseq data. However, more than 100 differentially expressed proteins were found between the worker groups, including key enzymes in fatty acid biosynthesis, indicating that the regulation of reproductive signal biosynthesis in workers is done post-transcription. Overall, our data provide evidence that pheromone biosynthesis in the Dufour’s gland is caste specific, that gynes and workers are likely using different enzymes to make their respective wax esters, and that the regulation on pheromone production in queens, gynes and workers is likely done at different regulatory levels, with workers signals being subjected to regulation at the protein level.

EQTL in diseased colon tissue identifies novel target genes associated with IBD.

Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14 , and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.

Effect control of novel Hirudinaria manillensis extract on the molecular regulation of EGFR gene and its protein expression in HeLa cells.

Most anticancer drugs possess the capacity to control precise molecular processes and gene-regulated protein expressions, which could enhance the efficacy of cancer treatments. Hirudinaria manillensis is prevalent in South Asia and has been employed for several decades in medical conditions based on its curative benefits. The present study aimed to explore the molecular regulation of the target EGFR gene, and the protein expression of EGFR on the HeLa cell line. To achieve our aim, quantitative real-time PCR and immunocytochemistry assays were conducted. Interestingly, qRT-PCR results confirmed the downregulation of the EGFR gene on the HeLa cells in comparison with the β- actin internal control gene. Furthermore, immunocytochemistry assay results confirmed the decreasing level of EGFR gene expression in the HeLa cells. Therefore, Hirudinaria manillensis could be a promising anticancer candidate for cervical cancer treatment.

The molecular dynamics between reactive oxygen species (ROS), reactive nitrogen species (RNS) and phytohormones in plant's response to biotic stress.

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are critical for plant development as well as for its stress response. They can function as signaling molecules to orchestrate a well-defined response of plants to biotic stress. These responses are further fine-tuned by phytohormones, such as salicylic acid, jasmonic acid, and ethylene, to modulate immune response. In the past decades, the intricacies of redox and phytohormonal signaling have been uncovered during plant-pathogen interactions. This review explores the dynamic interplay of these components, elucidating their roles in perceiving biotic threats and shaping the plant's defense strategy. Molecular regulators and sites of oxidative burst have been explored during pathogen perception. Further, the interplay between various components of redox and phytohormonal signaling has been explored during bacterial, fungal, viral, and nematode infections as well as during insect pest infestation. Understanding these interactions highlights gaps in the current knowledge and provides insights into engineering crop varieties with enhanced resistance to pathogens and pests. This review also highlights potential applications of manipulating regulators of redox signaling to bolster plant immunity and ensure global food security. Future research should explore regulators of these signaling pathways as potential target to develop biotic stress-tolerant crops. Further insights are also needed into roles of endophytes and host microbiome modulating host ROS and RNS pool for exploiting them as biocontrol agents imparting resistance against pathogens in plants.

Identification and Targeting of Regulators of SARS-CoV-2-Host interactions in the Airway Epithelium.

Although the impact of SARS-CoV-2 in the lung has been extensively studied, the molecular regulators and targets of the host-cell programs hijacked by the virus in distinct human airway epithelial cell populations remain poorly understood. This is in part ascribed to the use of non-primary cell systems, overreliance on single-cell gene expression profiling that not ultimately reflect protein activity and bias toward the downstream effects rather than their mechanistic determinants. Here we address these issues by network-based analysis of single cell transcriptomic profiles of pathophysiologically relevant human adult basal, ciliated and secretory cells to identify master regulator (MR) protein modules controlling their SARS-CoV-2-mediated reprogramming. This uncovered chromatin remodeling, endosomal sorting, ubiquitin pathway as well as proviral factors identified by CRISPR analyses as components of the host response collectively or selectively activated in these cells. Large-scale perturbation assays, using a clinically-relevant drug library, identified 11 drugs able to invert the entire MR signature activated by SARS-CoV-2 in these cell types. Leveraging MR analysis and perturbational profiles of human primary cells, represents a novel mechanism-based approach and resource that can be directly generalized to interrogate signatures of other airway conditions for drug prioritization.

Innate players in Th2 and non-Th2 asthma - emerging roles for the epithelial cell, mast cell and monocyte/macrophage network.

Asthma is one of the most common chronic respiratory diseases and is characterized by airway inflammation, increased mucus production and structural changes in the airways. Recently, there is increasing evidence that the disease is much more heterogeneous than expected, with several distinct asthma endotypes. Based on the specificity of T cells as the best-known driving force in airway inflammation, bronchial asthma is categorized into T helper cell (Th)2 and non-Th2 asthma. The most studied effector cells in Th2 asthma include T cells and eosinophils. In contrast to Th2 asthma, much less is known about the pathophysiology of non-Th2 asthma, which is often associated with treatment resistance. Besides T cells, the interaction of myeloid cells such as monocytes/macrophages and mast cells with the airway epithelium significantly contributes to the pathogenesis of asthma. However, the underlying molecular regulation and particularly the specific relevance of this cellular network in certain asthma endotypes remains to be understood. In this review, we summarize recent findings on the regulation of and complex interplay between epithelial cells and the "non-classical" innate effector cells, mast cells and monocytes/macrophages, in Th2 and non-Th2 asthma with the ultimate goal to provide the rationale for future research into targeted therapy regimens.

Genetic and molecular regulation of fruit development in cucumber.

Fruit development can be generally classified into a set of biologically sequential stages including fruit initiation, growth, and ripening. Cucumber, a globally important vegetable crop, displays two important features during fruit development: parthenocarpy at fruit initiation and prematurity at harvest for consumption. Therefore, fruit growth plays essential role for cucumber yield and quality formation, and has become the research hot spot in cucumber fruit development. Here, we describe recent advances in molecular mechanisms underlying fruit growth in cucumber, include key players and regulatory networks controlling fruit length variation, fruit neck elongation, and locule development. We also provide insights into future directions for scientific research and breeding strategies in cucumber.

Bcwf regulates the white petal color in pak choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis]

Flower color is important in determining the ornamental value of Brassica species. However, our knowledge about the regulation of flower color in pak choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis] is limited. In this study, we investigated the molecular mechanism underlying white flower traits in pak choi by analyzing a genetic population with white and yellow flowers. Our genetic analysis revealed that the white trait is controlled by a single recessive gene called Bcwf. Through BSA-Seq and fine mapping, we identified a candidate gene, BraC02g039450.1, which is similar to Arabidopsis AtPES2 involved in carotenoid ester synthesis. Sequence analysis showed some mutations in the promoter region of Bcwf in white flowers. Tobacco transient assay confirmed that these mutations reduce the promoter's activity, leading to downregulation of Bcwf expression in white flowers. Furthermore, the silencing of Bcwf in pak choi resulted in lighter petal color and reduced carotenoid content. These findings provide new insights into the molecular regulation of white flower traits in pak choi and highlight the importance of Bcwf in petal coloring and carotenoid accumulation.

Unveiling the Molecular Mechanisms Regulating Muscle Elasticity in the Large Yellow Croaker: Insights from Transcriptomics and Metabolomics.

The large yellow croaker (Larimichthys crocea) is an important economic fish in China. However, intensive farming practices, such as high stocking densities, suboptimal water quality, and imbalanced nutrition, have led to a decline in muscle quality. Muscle elasticity is a key texture property influencing muscle quality. Herein, transcriptomic and metabolomic analyses were performed on four groups: male high muscle elasticity (MEHM), female high muscle elasticity (MEHF), male low muscle elasticity (MELM), and female low muscle elasticity (MELF), to explore the molecular regulation underlying muscle elasticity in the large yellow croaker. Transcriptomics identified 2594 differentially expressed genes (DEGs) across the four groups, while metabolomics revealed 969 differentially expressed metabolites (DEMs). Association analysis indicated that the valine, leucine, and isoleucine biosynthesis pathways were significantly enriched between the MELF and MEHF groups; 2-Oxoisovalerate and L-Valine were DEMs; and the gene encoding L-threonine ammonia-lyase was a DEG. In the MELM and MEHM groups, pathways such as arginine biosynthesis; arginine and proline metabolism; and valine, leucine, and isoleucine degradation were significantly enriched. 4-guanidinobutanoate, L-aspartate, N-acetylornithine, and L-leucine were among the DEMs, while the DEGs included glul, gls, srm, hmgcs, and aacs. These findings provide insights into the molecular mechanisms controlling muscle elasticity, representing a theoretical foundation to breed high-quality large yellow croakers.

Exploiting Brassica rapa L. subsp. pekinensis Genome Research

Chinese cabbage, Brassica rapa L. subsp. pekinensis is a crucial and extensively consumed vegetable in the world, especially Eastern Asia. The market demand for this leafy vegetable increases year by year, resulting in multiple challenges for agricultural researchers worldwide. Multi-omic approaches and the integration of functional genomics helps us understand the relationships between Chinese cabbage genomes and phenotypes under specific physiological and environmental conditions. However, challenges exist in integrating multi-omics for the functional analysis of genes and for developing potential traits for Chinese cabbage improvement. However, the panomics platform allows for the integration of complex omics, enhancing our understanding of molecular regulator networks in Chinese cabbage agricultural traits. In addition, the agronomic features of Chinese cabbage are significantly impacted by the environment. The expression of these agricultural features is tightly regulated by a combination of signals from both the internal regulatory network and the external growth environment. To comprehend the molecular process of these characteristics, it is necessary to have a prior understanding of molecular breeding for the objective of enhancing quality. While the use of various approaches in Chinese cabbage is still in its early stages, recent research has shown that it has the potential to uncover new regulators both rapidly and effectively, leading to updated regulatory networks. In addition, the utilization of the efficient transformation technique in conjunction with gene editing using CRISPR/Cas9 will result in a reduction in time requirements and facilitate a more precise understanding of the role of the regulators. Numerous studies about Chinese cabbage have been conducted in the past two decades, but a comprehensive review about its genome still limited. This review provides a concise summary of the latest discoveries in genomic research related to Brassica and explores the potential future developments for this species.