Activation Of Gene Expression Research Articles

Selective BET inhibitor RVX-208 ameliorates periodontal inflammation and bone loss.

To determine the effects of RVX-208, a selective bromodomain and extra-terminal domain (BET) inhibitor targeting bromodomain 2 (BD2), on periodontal inflammation and bone loss. Macrophage-like cells (RAW264.7) and human gingival epithelial cells were challenged by Porphyromonas gingivalis (Pg) with or without RVX-208. Inflammatory gene expression and cytokine production were measured by reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay, respectively. RAW264.7 cells were induced to osteoclast differentiation. After RVX-208 treatment, osteoclast differentiation was evaluated by histology, tartrate-resistant-acid-phosphatase (TRAP) activity and the expression of osteoclast-specific genes. The effect of RVX-208 on osteoclast transcriptome was studied by RNA sequencing. Periodontitis was induced in rats by ligature and local RVX-208 treatment was administered every other day. Alveolar bone loss was measured by micro-computed tomography. RVX-208 inhibited inflammatory gene expression and cytokine production in Pg-infected cells. Osteoclast differentiation was inhibited by RVX-208, as evidenced by reduced osteoclast number, TRAP activity and osteoclast-specific gene expression. RVX-208 displayed a more selective and less profound suppressive impact on transcriptome compared with pan-BET inhibitor, JQ1. RVX-208 administration prevented the alveolar bone loss in vivo. RVX-208 regulated both upstream (inflammatory cytokine production) and downstream (osteoclast differentiation) events that lead to periodontal tissue destruction, suggesting that it may be a promising 'epi-drug' for the prevention of periodontitis.

Mechanism of Fluoride Ion Encapsulation by Magnesium Ions in a Bacterial Riboswitch.

Riboswitches sense various ions in bacteria and activate gene expression to synthesize proteins that help maintain ion homeostasis. The crystal structure of the aptamer domain (AD) of the fluoride riboswitch shows that the F- ion is encapsulated by three Mg2+ ions bound to the ligand-binding domain (LBD) located at the core of the AD. The assembly mechanism of this intricate structure is unknown. To this end, we performed computer simulations using coarse-grained and all-atom RNA models to bridge multiple time scales involved in riboswitch folding and ion binding. We show that F- encapsulation by the Mg2+ ions bound to the riboswitch involves multiple sequential steps. Broadly, two Mg2+ ions initially interact with the phosphate groups of the LBD using water-mediated outer-shell coordination and transition to a direct inner-shell interaction through dehydration to strengthen their interaction with the LBD. We propose that the efficient binding mode of the third Mg2+ and F- is that they form a water-mediated ion pair and bind to the LBD simultaneously to minimize the electrostatic repulsion between three Mg2+ bound to the LBD. The tertiary stacking interactions among the LBD nucleobases alone are insufficient to stabilize the alignment of the phosphate groups to facilitate Mg2+ binding. We show that the stability of the whole assembly is an intricate balance of the interactions among the five phosphate groups, three Mg2+, and the encapsulated F- ion aided by the Mg2+ solvated water. These insights are helpful in the rational design of RNA-based ion sensors and fast-switching logic gates.

Genetic dissection of regulation by a repressing and novel activating corrinoid riboswitch enables engineering of synthetic riboswitches.

In addition to proteins, microbes can use structured RNAs such as riboswitches for the important task of regulating gene expression. Riboswitches control gene expression by changing their structure in response to binding a small molecule and are widespread among bacteria. Here we determine the mechanism of regulation in a riboswitch that responds to corrinoids-a family of coenzymes related to vitamin B12. We report the alternative RNA secondary structures that couple corrinoid sensing with response in a repressing and novel activating corrinoid riboswitch. We then applied this knowledge to flipping the regulatory sign by constructing synthetic riboswitches that activate expression to a higher level than the natural one. In the process, we observed patterns in which sequence, in addition to structure, impacts function in paired RNA regions. The synthetic riboswitches we describe here have potential applications as biosensors.

SAT635 Role Of The Human Prolactin Receptor I-tail In The Pathogenesis Of Breast Cancer

Abstract Disclosure: C.V. Clevenger: None. S. Shen: None. Evidence from epidemiological, cellular, and genetic analyses indicate that the hormone prolactin (PRL) and its receptor (hPRLr) in humans are significantly involved in breast cancer pathogenesis. The intermediate form of hPRLr (hPRLrI) induces significant increases in proliferation and anchorage-independent growth of normal mammary epithelia in vitro when co-expressed with the long form hPRLr (hPRLrL). However, the exact mechanism of how the hPRLrI transforms mammary epithelium is not well understood. The hPRLrI is produced by alternative splicing that induces a frameshift, resulting in a premature stop codon and a novel 13 amino acid tail ("I-Tail") gain. The ubiquitin-like protein neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) was found to be associated with the I-tail by yeast two-hybrid analysis. Treatment with a selective NEDD8 inhibitor resulted in the altered stability of the hPRLrL and the death of breast cancer cells. Given this, we hypothesized that the hPRLrI I-tail contributes to mammary transformation. hPRLrL, hPRLrI, hPRLrIΔ13 (I-tail removed mutant due to loss of 13 C-terminal amino acid resides) were delivered to MCF10AT cells by lentivirus transduction and subsequently analyzed. Anchorage-independent cell growth was determined by soft agar assay, cell proliferation was determined with a Incucyte analysis, and cell motility was examined by wound healing assay. In addition, signaling pathway and differential gene expression alterations mediated by the I-tail were determined by RNA-seq and signaling analysis. Successful expression of the hPRLrL+hPRLrIΔ13 in the MCF10AT transfectant resulted in significant reductions or alterations of anchorage-independent growth, cell proliferation, ERK1/2 activation, and PRL-induced different gene expression. These findings demonstrate that the hPRLrI I-tail contributes to the transformation of normal mammary epithelia cells. Presentation: Saturday, June 17, 2023

A member of NF-Y family, OsNF-YC5 negatively regulates salt tolerance in rice

NF-Y, a critical transcription factor, binds to the CCAAT-box in target gene promoters, playing a pivotal role in plant development and abiotic stress response. OsNF-YC5, encodes a putative subunit of the NF-Y transcription factor in rice, had an undetermined function. Our research revealed that OsNF-YC5 is induced by high salinity and exogenous abscisic acid (ABA). Subcellular localization studies showed that OsNF-YC5 is nuclear- and cytoplasm-localized. Using CRISPR-Cas9 to disrupt OsNF-YC5, we observed significantly enhanced rice salinity tolerance and ABA-hypersensitivity. Compared to the wild-type, osnf-yc5 mutants exhibited reduced H2O2 and malondialdehyde (MDA) levels, increased catalase (CAT) activity, and elevated OsCATA transcripts under salt stress. Moreover, ABA-dependent (OsABI2 and OsLEA3) and ABA-independent (OsDREB1A, OsDREB1B, and OsDREB2A) marker genes were upregulated in mutant lines in response to salinity. These results indicate that disrupting OsNF-YC5 enhances rice salinity tolerance, potentially by boosting CAT enzyme activity and modulating gene expression in both ABA-dependent and ABA-independent pathways. Therefore, this study provides a valuable theoretical foundation and genetic resources for developing novel salt-tolerant rice varieties.

Bacteria- and fungus-derived PAMPs induce innate immune memory via similar functional, metabolic, and transcriptional adaptations.

Exposure to pathogen-associated molecular patterns (PAMPs) induces an augmented, broad-spectrum antimicrobial response to subsequent infection, a phenomenon termed innate immune memory. This study examined the effects of treatment with β-glucan, a fungus-derived dectin-1 ligand, or monophosphoryl lipid A (MPLA), a bacteria-derived Toll-like receptor 4 ligand, on innate immune memory with a focus on identifying common cellular and molecular pathways activated by these diverse PAMPs. Treatment with either PAMP prepared the innate immune system to respond more robustly to Pseudomonas aeruginosa infection in vivo by facilitating mobilization of innate leukocytes into blood, recruitment of leukocytes to the site of infection, augmentation of microbial clearance, and attenuation of cytokine production. Examination of macrophages ex vivo showed amplification of metabolism, phagocytosis, and respiratory burst after treatment with either agent, although MPLA more robustly augmented these activities and more effectively facilitated killing of bacteria. Both agents activated gene expression pathways in macrophages that control inflammation, antimicrobial functions, and protein synthesis and suppressed pathways regulating cell division. β-glucan treatment minimally altered macrophage differential gene expression in response to lipopolysaccharide (LPS) challenge, whereas MPLA attenuated the magnitude of the LPS-induced transcriptional response, especially cytokine gene expression. These results show that β-glucan and MPLA similarly augment the innate response to infection in vivo. Yet, MPLA more potently induces alterations in macrophage metabolism, antimicrobial functions, gene transcription and the response to LPS.

Arginase is upregulated in healthy women infected by oncogenic HPV types

IntroductionThe implication of arginase enzyme in Human Papillomavirus (HPV) infections has not been clearly elucidated. The present study investigates whether HPV infection is correlated with changes in plasmatic arginase activity and cervical ARG1 and ARG2 mRNA expression among infected women negative for intraepithelial lesions (NIL).Materiel and methodsThe present study included 300 women. The plasmatic arginase activity was evaluated by a colorimetric assay. Cervical HPV was detected by real-time PCR. The circulating viral load and ARG1 and ARG2 mRNA expression quantification were performed by quantitative real-time PCR.ResultsA significant increase in plasma arginase activity and ARG1 and ARG2 mRNA expression levels in cervical cells was observed among HPV-positive women compared to the HPV-negative group. The highest levels were significantly associated with oncogenic HPV, and increased arginase activity was associated with a high HPV circulating viral load. Moreover, the highest levels of arginase activity were observed in oncogenic HPV-positive inflammatory smears.DiscussionThese data suggest that HPV could modulate arginase activity and expression, which may restrict arginine bioavailability and inhibit this amino acid’s antiviral properties.ConclusionOur findings revealed that arginase activity and isoform gene expression were upregulated in women with HPV infection, particularly the oncogenic HPV types.

Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs.

Long non-coding RNAs (lncRNAs) are involved in gene expression regulation in cis. Although enriched in the cell chromatin fraction, to what degree this defines their regulatory potential remains unclear. Furthermore, the factors underlying lncRNA chromatin tethering, as well as the molecular basis of efficient lncRNA chromatin dissociation and its impact on enhancer activity and target gene expression, remain to be resolved. Here, we developed chrTT-seq, which combines the pulse-chase metabolic labeling of nascent RNA with chromatin fractionation and transient transcriptome sequencing to follow nascent RNA transcripts from their transcription on chromatin to release and allows the quantification of dissociation dynamics. By incorporating genomic, transcriptomic, and epigenetic metrics, as well as RNA-binding protein propensities, in machine learning models, we identify features that define transcript groups of different chromatin dissociation dynamics. Notably, lncRNAs transcribed from enhancers display reduced chromatin retention, suggesting that, in addition to splicing, their chromatin dissociation may shape enhancer activity.

Pulling rank with RNA: RANKL promotes the association of PGC-1β/RNA complexes with NCoR/HDAC3 to activate gene expression in osteoclasts

In this issue, Abe etal1 report a novel mechanism by which RANKL stimulates osteoclast differentiation and bone resorption through non-coding RNAs that bind PGC-1β and convert the NCoR/HDAC3 co-repressor complex into a co-activator of AP-1- and NFκB-regulated genes.

147P Non-small cell lung cancer: Artificial intelligence enables the identification of survival signatures complementary to an Immunologically active gene expression signature involving previous therapies

147P Non-small cell lung cancer: Artificial intelligence enables the identification of survival signatures complementary to an Immunologically active gene expression signature involving previous therapies

Amentoflavone attenuates oxidative stress and neuroinflammation induced by cerebral ischemia/reperfusion in rats by targeting HMGB1-mediated TLR4/NF-κB signaling pathway

Surveys indicated that stroke classified among the leading cause of death as well as combined death and disability worldwide resulting in a great loss for the global economy. The present study aims to evaluate the neuroprotective potential of the biflavonoid amentoflavone (AMNT) in alleviating cerebral ischemia/reperfusion (IR) injury in rats, and to elucidate the possible underlying mechanism of an experimental condition with similar circumstances to stroke. Cerebral ischemia was achieved through left common carotid artery occlusion for 60 min, followed by blood flow restoration. Sham-operated control rats subjected to the same surgical process except for brain IR. Rats were orally administered AMNT/ or vehicle for three days’ prior surgical operation, and for another three days after left brain IR. Rats of all groups were assessed for neurological deficits 24 h following brain IR. Each group was divided into two subgroups one for the rotarod testing and biochemical assessment while the other subgroup to perform the activity cage testing, histopathological study, immunohistochemistry, and gene expression analysis. AMNT enhanced brain levels of GSH and CAT activities, suppressed neuroinflammation via reducing the inflammatory cytokines in the serum, and enhanced brain contents of TBK1 and IFNβ. AMNT downregulated TLR4-/NF-κB signaling pathway as a result of the HMGB1 suppression. Moreover, AMNT blocked apoptotic cell death by suppressing the NF-κB signaling pathway and reducing the activation of caspase-3. These findings revealed that AMNT attenuates I/R–induced cerebral injury possibly by regulating the HMGB1-mediated TLR4/NF-kB pathway. Thus, AMNT could provide potential preventive and therapeutic option for cerebral stroke.

Insights into bacterial community metatranscriptome and metabolome in river water influenced by palm oil mill effluent final discharge.

This study aimed to investigate the effect of palm oil mill effluent (POME) final discharge on the active bacterial composition, gene expression, and metabolite profiles in the receiving rivers to establish a foundation for identifying potential biomarkers for monitoring POME pollution in rivers. The POME final discharge, upstream (unpolluted by POME), and downstream (effluent receiving point) parts of the rivers from two sites were physicochemically characterized. The taxonomic and gene profiles were then evaluated using de novo metatranscriptomics, while the metabolites were detected using qualitative metabolomics. A similar bacterial community structure in the POME final discharge samples from both sites was recorded, but their composition varied. Redundancy analysis showed that several families, particularly Comamonadaceae and Burkholderiaceae [Pr(>F) = 0.028], were positively correlated with biochemical oxygen demand (BOD5) and chemical oxygen demand (COD). The results also showed significant enrichment of genes regulating various metabolisms in the POME-receiving rivers, with methane, carbon fixation pathway, and amino acids among the predominant metabolisms identified (FDR<0.05, PostFC>4, and PPDE>0.95). This was further validated through qualitative metabolomics, whereby amino acids were detected as the predominant metabolites. The results suggest that genes regulating amino acid metabolism have significant potential for developing effective biomonitoring and bioremediation strategies in river water influenced by POME final discharge, fostering a sustainable palm oil industry.

HEXIM1 is an essential transcription regulator during human erythropoiesis

AbstractRegulation of RNA polymerase II (RNAPII) activity is an essential process that governs gene expression; however, its contribution to the fundamental process of erythropoiesis remains unclear. hexamethylene bis-acetamide inducible 1 (HEXIM1) regulates RNAPII activity by controlling the location and activity of positive transcription factor β. We identified a key role for HEXIM1 in controlling erythroid gene expression and function, with overexpression of HEXIM1 promoting erythroid proliferation and fetal globin expression. HEXIM1 regulated erythroid proliferation by enforcing RNAPII pausing at cell cycle check point genes and increasing RNAPII occupancy at genes that promote cycle progression. Genome-wide profiling of HEXIM1 revealed that it was increased at both repressed and activated genes. Surprisingly, there were also genome-wide changes in the distribution of GATA-binding factor 1 (GATA1) and RNAPII. The most dramatic changes occurred at the β-globin loci, where there was loss of RNAPII and GATA1 at β-globin and gain of these factors at γ-globin. This resulted in increased expression of fetal globin, and BGLT3, a long noncoding RNA in the β-globin locus that regulates fetal globin expression. GATA1 was a key determinant of the ability of HEXIM1 to repress or activate gene expression. Genes that gained both HEXIM1 and GATA1 had increased RNAPII and increased gene expression, whereas genes that gained HEXIM1 but lost GATA1 had an increase in RNAPII pausing and decreased expression. Together, our findings reveal a central role for universal transcription machinery in regulating key aspects of erythropoiesis, including cell cycle progression and fetal gene expression, which could be exploited for therapeutic benefit.

8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage

Riboswitches rely on structured aptamer domains to selectively sense their target ligands and regulate gene expression. However, some riboswitch aptamers in bacteria carry mutations in their otherwise strictly conserved binding pockets that change ligand specificities. The aptamer domain of a riboswitch class originally found to selectively sense guanine forms a three-stem junction that has since been observed to exploit numerous alterations in its ligand-binding pocket. These rare variants have modified their ligand specificities to sense other purines or purine derivatives, including adenine, 2'-deoxyguanosine (three classes), and xanthine. Herein, we report the characteristics of a rare variant that is narrowly distributed in the Paenibacillaceae family of bacteria. Known representatives are always associated with genes encoding 8-oxoguanine deaminase. As predicted from this gene association, these variant riboswitches tightly bind 8-oxoguanine (8-oxoG), strongly discriminate against other purine derivatives, and function as genetic "ON" switches. Following exposure of cells to certain oxidative stresses, a representative 8-oxoG riboswitch activates gene expression, likely caused by the accumulation of 8-oxoG due to oxidative damage to G nucleobases in DNA, RNA, and the nucleotide pool. Furthermore, an engineered version of the variant aptamer was prepared that exhibits specificity for 8-oxoadenine, further demonstrating that RNA aptamers can acquire mutations that expand their ability to detect and respond to oxidative damage.

Mei-Gin Formula Ameliorates Obesity through Lipolysis, Fatty Oxidation, and Thermogenesis in High-Fat Diet-Induced Obese Rats.

Obesity is a metabolic dysfunction characterized by excessive body fat deposition as a consequence of an energy imbalance. Novel therapeutic strategies have emerged that are safe and have comparatively low side effects for obesity treatment. Functional foods and nutraceuticals have recently received a great deal of attention because of their components with the properties of antimetabolic syndrome. Based on our previous in vitro and in vivo investigations on anti-adipogenesis activity and improved body fat accumulation in serials, the combination of three ingredients (including bainiku-ekisu, black garlic, and Mesona procumbens Hemsl), comprising the Mei-Gin formula (MGF), was eventually selected as a novel inhibitor that exhibited preventive effects against obesity. Herein, we verify the anti-obesity effects of MGF in obese rats induced by a high-fat diet and discuss the potential molecular mechanisms underlying obesity development. Oral administration of MGF significantly suppressed the final body weight, weight change, energy and water intake, subcutaneous and visceral fat mass, liver weight, hepatic total lipids and triglycerides (TG), and serum levels of TG, triglycerides (TC), low-density lipoprotein cholesterol (LDL-C), alanine transaminase (AST), uric acid, and ketone bodies and augmented fecal total lipids, TG, and cholesterol excretion in the high-dose MGF-supplemented groups. Furthermore, the corresponding lipid metabolic pathways revealed that MGF supplementation effectively increased lipolysis and fatty acid oxidation gene expression and attenuated fatty acid synthesis gene expression in the white adipose tissue (WAT) and liver and it also increased mitochondrial activation and thermogenic gene expression in the brown adipose tissue (BAT) of rats with obesity induced by a high-fat diet (HFD). These results demonstrate that the intake of MGF can be beneficial for the suppression of HFD-induced obesity in rats through the lipolysis, fatty oxidation, and thermogenesis pathway. In conclusion, these results demonstrate the anti-obesity efficacy of MGF in vivo and suggest that MGF may act as a potential therapeutic agent against obesity.

A small heat shock protein GmHSP18.5a improves the male fertility restorability of cytoplasmic male sterility-based restorer line under high temperature stress in soybean

Small heat shock protein (sHSP) is involved in high temperature (HT) stress response. However, the function of sHSPs in regulating male fertility of soybean under HT stress remains largely unknown. Here, we identified a sHSP gene, GmHSP18.5a, which was responded to HT stress during flowering in cytoplasmic male sterility (CMS)-based restorer line of soybean. Moreover, GmHSFA6b turned out to directly activated the expression of GmHSP18.5a by binding to the heat shock cis-element in its promoter. Overexpression of GmHSP18.5a increased male fertility in transgenic Arabidopsis, soybean CMS-based restorer line and its hybrid F1 with CMS line under HT stress. Reactive oxygen species (ROS) content detection revealed that GmHSP18.5a promoted the ROS scavenging ability of Arabidopsis inflorescence and soybean flower bud under HT stress. Enzyme activity assay and gene expression analysis indicated that GmHS18.5a mainly increased the activity of antioxidant enzymes and the expression level of ROS metabolism-related genes under HT stress. Our results indicated that GmHSP18.5a improved the male fertility restorability of CMS-based restorer line in soybean by regulating ROS metabolic pathway and reducing ROS accumulation. Our findings not only revealed the molecular mechanism of sHSP regulating the male fertility of soybean under HT stress, but also provided a theoretical basis for creating strong restorer line with thermotolerance.

Genome-Wide CRISPR Screens Identify Multiple Synthetic Lethal Targets That Enhance KRASG12C Inhibitor Efficacy.

Identification of synthetic lethal genes with KRASG12C using genome-wide CRISPR/Cas9 screening and credentialing of the ability of TEAD inhibition to enhance KRASG12C efficacy provides a roadmap for combination strategies. See related commentary by Johnson and Haigis, p. 4005.

Anti-inflammatory and immunomodulating effects of rilpivirine: Relevance for the therapeutics of chronic liver disease

Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease (CLD) worldwide and inflammation is key to its progression/resolution. As we have previously described that rilpivirine (RPV) is hepatoprotective in murine models of CLD, here we determine the molecular mechanisms involved, focusing on its anti-inflammatory and immunomodulating properties. They were evaluated in vitro (human hepatic cell lines of the major hepatic cell types), in vivo (liver samples from a murine nutritional model of NAFLD) and ex vivo (peripheral blood mononuclear cells -PBMC- from patients with CLD). Transcriptomic analysis of liver samples from NAFLD mice showed RPV down-regulated biological processes associated with the inflammatory response (NF-κB/IκB signaling and mitogen-activated protein kinase -MAPK- activity) and leukocyte chemotaxis and migration. We observed a decrease in Adgre1 and Ccr2 expression and in the number of CCR2 + cells in the periportal areas of RPV-treated NAFLD mice. This RPV-induced effect on the CCL2/CCR2 axis was confirmed in vitro. A similar result was also obtained with CXCL10/IP10, one of the main chemokines in the liver. RPV also diminished activation of MAP kinases p38 and JNK. In addition, RPV inhibited the NLRP3 inflammasome pathway in vitro, decreasing NLRP3 protein expression, caspase-1 activation and IL-1β gene expression. RPV was also proven anti-inflammatory in PBMC from patients with CLD treated ex vivo. In conclusion, beyond its well-described role in antiretroviral therapy, RPV manifests anti-inflammatory and immunoregulatory effects, a finding that could be of great relevance for the search of novel targets or repositioning strategies for CLD.

Eugenol Effectively Inhibits Trichophyton rubrum Growth via Affecting Ergosterol Synthesis, Keratinase Activity, and SUB3 Gene Expression

Eugenol Effectively Inhibits Trichophyton rubrum Growth via Affecting Ergosterol Synthesis, Keratinase Activity, and SUB3 Gene Expression

Temporal Changes in Flavonoid Components, Free Radical Scavenging Activities and Metabolism-Related Gene Expressions during Fruit Development in Chinese Dwarf Cherry (Prunus humilis)

Temporal changes in total flavonoid content (TFC), composition, free radical scavenging activity and metabolism-related gene expression of three Prunus humilis cultivars with distinctively different fruit colors were investigated in this study. The highest fruit TFCs of all three cultivars were observed at the initial sampling stage (young-fruit stage, YFS), which then declined gradually until fruit ripening. The dark-red-fruited cultivar ‘Jinou 1’ had the highest TFC, followed by the yellow-red-fruited cultivar ‘Nongda 3’ and the yellow-fruited cultivar ‘Nongda 5’. Thirteen flavonoid compounds were found in the three cultivars by using high-performance liquid chromatography (HPLC), and the content of most flavonoid compounds gradually decreased throughout the fruit-ripening process, with the exception of cyanidin-3-O-glucoside (C3G). C3G, as the main anthocyanin in P. humilis fruits, increased drastically during the fruit-coloring process of cultivars ‘Jinou 1’ and ‘Nongda 3’, while it was not detected in the developing fruits of cultivar ‘Nongda 5’. The antioxidant activity assay (DPPH, FRAP and ABTS) revealed that fruits of all three cultivars at YFS also had the highest antioxidant activities, and cultivar ‘Jinou 1’ had the highest antioxidant activities. Correlation analysis revealed that the antioxidant activities were significantly positively correlated with the TFCs and contents of the main compounds such as catechin, proanthocyanidin B1 and phloretin-2′,4-O-diglucoside (p &lt; 0.01). Moreover, gene expression analysis showed that the flavonoid biosynthetic genes had different expression patterns in the three cultivars. The expression levels of ChCHS, ChCHI, ChF3H, ChDFR, ChLDOX and ChUFGT increased gradually with fruit ripening in cultivar ‘Jinou 1’, while all flavonoid-related genes in cultivar ‘Nongda 5’ decreased gradually during fruit development. The results from our study could significantly contribute to the deeper understanding of flavonoid accumulation mechanisms in P. humilis fruits and also help facilitate the targeted cultivar development and the utilization as a functional food of this fruit species.