Transcript Levels Research Articles

Antrodia cinnamomea triterpenoids attenuate cardiac hypertrophy via the SNW1/RXR/ALDH2 axis.

Aldehyde dehydrogenase 2 (ALDH2), a pivotal enzyme in the metabolism of toxic aldehydes produced by oxidative stress, has been demonstrated to play a cardioprotective role in cardiovascular diseases. Antrodia cinnamomea triterpenoids (ACT) is a medicinal mushroom with anti-inflammatory and antioxidant properties, and our previous study found that ACT can exert anti-fatty liver effects by regulating ALDH2. This study aimed to elucidate the impact of ACT and its monomer on cardiac hypertrophy and investigate the relationship between its pharmacological mechanism and ALDH2. Through examining cardiac morphology and expression levels of hypertrophic biomarkers, ACT significantly reduced myocardial hypertrophy induced by angiotensin II (Ang II) and transverse aortic constriction (TAC)surgery in wild-type mice, but not in ALDH2 knockout mice. In vitro, ACT and its monomeric dehydrosulphurenic acid (DSA) inhibited the hypertrophic phenotype of Ang II-stimulated neonatal cardiac myocytes (NRCMs) in an ALDH2-dependent manner. Regarding the pharmacological mechanism, it was observed that ACT and DSA restored ALDH2 expression and activity in myocardial tissues of WT-Ang II/TAC mice and Ang II-induced NRCMs. Furthermore, it inhibited oxidative stress and improved mitochondrial quality control (MQC) homeostasis in an ALDH2-dependent manner. We screened SNW1, a transcriptional coactivator, as a DSA-binding protein by "target fishing" and cellular enthusiasm transfer assay techniques and validated that SNW1 promoted ALDH2 transcription and translation levels through synergistic interaction with the transcription factor RXR. In conclusion, the findings demonstrate that ACT/DSA upregulates ALDH2 expression via regulating SNW1/RXR, thereby inhibiting oxidative stress and maintaining MQC homeostasis, and then protects against cardiac hypertrophy.

Caseinolytic protease P (ClpP) is a c-di-GMP effector protein modulating motility, biofilm and virulence in Stenotrophomonas maltophilia

Cyclic di-GMP (c-di-GMP) is a crucial secondary messenger in bacterial cells, profoundly impacting various physiological and biochemical processes. Numerous studies showed that c-di-GMP regulates specific bacterial pathways by interacting with related effectors, and modulating their functions at the transcriptional or post-transcriptional levels. How c-di-GMP regulates bacterial global metabolism remains to be explored. In this study, we employed c-di-GMP pull-down assays in Stenotrophomonas maltophilia. We identified one target protein as caseinolytic protease P (ClpP), a highly conserved protease in both eukaryotic and prokaryotic cells, playing an essential role in global cellular metabolism regulation. We examined the binding site of c-di-GMP with ClpP and demonstrated that c-di-GMP enhances the peptidase activity of ClpP. Furthermore, ClpP is shown to play a vital regulatory role in bacterial motility and can activate bacterial motility in the presence of high c-di-GMP level. This research demonstrates that c-di-GMP mediates global regulation at the metabolic level via protein homeostasis. Additionally, it offers critical insights into the functional role of ClpP, which may inform the development of novel antimicrobial strategies.

C-repeat binding factor (CBF) identification and expression pattern to abiotic stress response in Casuarina equisetifolia and overexpression of CeCBF4 increase stress tolerance in Arabidopsis

Casuarina equisetifolia stands out as a highly valuable tree species crucial for industries and ecological restoration projects in tropical and subtropical regions, owing to its exceptional salt resistance. However, its growth is hampered in cold and drought-prone areas. Understanding the genetic basis for abiotic stress tolerance is imperative for enhancing stress-resistant breeding efforts of C. equisetifolia. However, the CBF genes are renowned for their pivotal roles in cold response and broad resilience to other adverse environments, such as drought, and high salinity. In this study, five CeCBFs were identified from the genome of C. equisetifolia. CeCBF1 and CeCBF3 belong to Clade I group, which diverged early from DREBIII members, while CeCBF2, CeCBF4, and CeCBF5 are classified into Clade II, a group innovated from Clade I. These genes lack introns in their sequences. The proteins encoded by CeCBFs feature classic AP2 domains and CBF signature sequences, localize in the nucleus and exhibit transactivation activity. Additionally, stress-related, abscisic acid, and jasmonic acid responsive elements are present on the CeCBFs promoters. Expression analysis revealed that CeCBFs were prodominantly induced by cold, drought, and salinity treatments, except for CeCBF1, which showed repression specifically under low temperature. Moreover, CeCBF1, CeCBF4, and CeCBF5 were inhibited by abscisic acid, while CeCBF1 showed reduced transcript levels in response to methyl jasmonate treatment. Furthermore, overexpression of CeCBF4 enhanced tolerance to low temperature, depriving of water, and salt by up-regulating stress-responsive genes expression and promoting proline accumulation, albeit with a trade-off in growth and productivity. Hence, CeCBFs emerge as potential regulators contributing significantly to stress tolerance mechanisms in C. equisetifolia.

Impact of hexafluoropropylene oxide trimer acid (HFPO-TA) on sex differentiation after exposures during different development stages of zebrafish (Danio rerio)

Hexafluoropropylene oxide trimer acid (HFPO-TA), a novel alternative to perfluorooctanoic acid (PFOA), has been widely used and ubiquitously detected in aquatic environments. However, its potential effects on sex differentiation of aquatic organisms are not well known. Therefore, in this study, zebrafish were exposed to HFPO-TA at different development stages (0-21, 21-42, and 42-63 dpf) to investigate the effects on sex differentiation and its underlying mechanisms. All three exposures to HFPO-TA resulted in the feminization of zebrafish, and the impact of Stage II was most significant. The transcription levels of key genes related to female differentiation (bpm15, cyp19a1a, esr1, vtg1, and sox9b) were up-regulated, while those of key genes related to male differentiation (dmrt1, gata4, amh, and sox9a) were down-regulated, which could lead to the feminization. In addition, it was found that the dysregulations of these genes were prolonged in adult zebrafish even through a long recovery, which could cause sex imbalance in populations. Therefore, HFPO-TA might not be a safe alternative to PFOA, and more evidences from multi- and transgenerational toxicology are warranted.

Oleoylethanolamide mitigates cardiometabolic disruption secondary to obesity induced by high-fat diet in mice

Chronic lipid overnutrition has been demonstrated to promote cardiac dysfunction resulting from metabolic derangement, inflammation, and fibrosis. Oleoylethanolamide (OEA), an endogenous peroxisome proliferator activating receptor (PPAR)-α agonist, has been extensively studied for its metabolic properties.The aim of this study was to determine if OEA has beneficial effects on high-fat diet (HFD)-induced cardiac disruption in obese mice, focusing on the underlying pathological mechanisms.OEA treatment restores the metabolic pattern, improving serum glycaemic and lipid profile. OEA also reduces heart weight and serum creatine kinase-myocardial band (CK-MB), a marker of cardiac damage. Accordingly, OEA modulates cardiac metabolism, increasing insulin signaling and reducing lipid accumulation. OEA increases AMPK and AKT phosphorylation, converging in the rise of AS160 activation and glucose transporter (GLUT)4 protein level. Moreover, OEA reduces the transcription of the cardiac fatty acid transporter CD36 and fatty acid synthase and increases PPAR-α mRNA levels. Adiponectin and meteorite-like protein transcription levels were significantly reduced by OEA in HFD mice, as well as those of inflammatory cytokines and pro-fibrotic markers. An increased autophagic process was also shown, contributing to OEA's cardioprotective effects. Metabolomic analyses of cardiac tissue revealed the modulation of different lipids, including triglycerides, glycerophospholipids and sphingomyelins by OEA treatment. In vitro experiments on HL-1 cardiomyocytes showed OEA's capability in reducing inflammation and fibrosis following palmitate challenge, demonstrating a direct activity of OEA on cardiac cells, mainly mediated by PPAR-α activation.Our results indicate OEA as a potential therapeutic to restrain cardiac damage associated with metabolic disorders.

DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements

Gene transcription is an essential process involved in all aspects of cellular functions with significant impact on biological traits and diseases. This process is tightly regulated by multiple elements that co-operate to jointly modulate the transcription levels of target genes. To decipher the complicated regulatory network, we present a novel multi-view attention-based deep neural network that models the relationship between genetic, epigenetic, and transcriptional patterns and identifies co-operative regulatory elements (COREs). We applied this new method, named DeepCORE, to predict transcriptomes in various tissues and cell lines, which outperformed the state-of-the-art algorithms. Furthermore, DeepCORE contains an interpreter that extracts the attention values embedded in the deep neural network, maps the attended regions to putative regulatory elements, and infers COREs based on correlated attentions. The identified COREs are significantly enriched with known promoters and enhancers. Novel regulatory elements discovered by DeepCORE showed epigenetic signatures consistent with the status of histone modification marks.

AhGSNOR1 negatively regulates Al-induced programmed cell death by regulating intracellular NO and redox levels

The toxicity of aluminum (Al) in acidic soil inhibits plant development and reduces crop yields. Programmed cell death (PCD) is one of the important mechanisms in the plant response to Al toxicity. However, it is yet unknown if S-nitrosoglutathione reductase (GSNOR) provides Al-PCD. Here, transcription and protein expression of AhGSNOR1 were both induced by Al stress. AhGSNOR1-overexpressing transgenic tobacco plants reduced Al-induced nitric oxide (NO) and S-nitrosothiol accumulation, the inhibitory effect of Al stress on root elongation and the degree of cell death, and enhanced antioxidant enzyme activity to effectively remove hydrogen peroxide. In addition, AhGSNOR1 directly interacted with AhTRXh in vivo. Expression of Trxh3 in AhGSNOR1-overexpressing transgenic plants was significantly upregulated, indicating that AhGSNOR1 positively regulated the transcriptional level of Trxh3. Together, these results suggested that AhGSNOR1 was a negative regulatory factor of Al-induced PCD and improved plant Al-tolerance by modulating intracellular NO and redox homeostasis.

Phosphatidylethanolamine exerts anti-inflammatory action by regulating mitochondrial function in macrophages of large yellow croaker (Larimichthys crocea).

Phosphatidylethanolamine (PE) is a ubiquitous bioactive lipid in cells, which participates in regulating many metabolic processes. Exogenous PE has been reported to play a positive regulatory role in macrophage inflammatory responses. However, the molecular mechanisms of PE in regulating macrophage inflammation are not completely understood. In the present study, transcriptomic analysis of PE-stimulated macrophages of large yellow croaker revealed that differentially expressed genes were mainly active in cellular components of the mitochondrial respiratory chain, which corresponded to the significant enrichment of the oxidative phosphorylation pathway. Consistent with this result, PE significantly increased ATP content and protein expression of NDUFB3 (mitochondrial respiratory chain complex I subunit) in macrophages. Meanwhile, transcriptomic data showed that PE treatment downregulated the transcript levels of nlrp3 and upregulated the transcript levels of suppressor of cytokine signaling 3 (socs3), suggesting that PE may alleviate macrophage inflammation by interfering with the activation of NLRP3 inflammasome. Further analysis showed that PE significantly attenuated dietary PA-mediated macrophage inflammation via NLRP3-Caspase-1 invitro and invivo. Given that PE abundance is strongly correlated with mitochondrial function, the present study hypothesized that PE-mediated inflammatory modulation may be attributed to the positive effects on mitochondrial function. As expected, PE significantly ameliorated PA-induced mitochondrial dysfunction and reduced intracellular reactive oxygen species production and malondialdehyde content in macrophages, indicating that the improvement of mitochondrial function is an important mechanism involved in the positive effect of PE on PA-induced inflammation. In conclusion, this study elucidates the critical role of mitochondrial function in PE-mediated regulation of inflammation in macrophages, which expands the understanding of the regulatory mechanisms of phospholipid metabolism on dietary fatty acid-induced inflammation. This study may provide new intervention targets and nutritional regulation strategies for improving chronic inflammatory diseases.

Bacteria Engineered to Produce Serotonin Modulate Host Intestinal Physiology.

Bacteria in the gastrointestinal tract play a crucial role in intestinal motility, homeostasis, and dysfunction. Unraveling the mechanisms by which microbes impact the host poses many challenges due to the extensive array of metabolites produced or metabolized by bacteria in the gut. Here, we describe the engineering of a gut commensal bacterium, Escherichia coli Nissle 1917, to biosynthesize the human metabolite serotonin for examining the effects of microbially produced biogenic amines on host physiology. Upon oral administration to mice, our engineered bacteria reach the large intestine, where they produce serotonin. Mice treated with serotonin-producing bacteria exhibited biological changes in the gut at transcriptional and physiological levels. This work establishes a novel framework employing engineered bacteria to modulate luminal serotonin levels and suggests potential clinical applications of modified microbial therapeutics to address gut disorders in humans.

Mechanism of Action of Tongjiang Mixture for Treating Reflux Esophagitis: A Study Using Serum Pharmacochemistry and Network Pharmacology.

Tongjiang Mixture (TJM) is a traditional Chinese formula for treating reflux esophagitis (RE). Nevertheless, its active ingredients and potential pharmacological mechanisms are not yet clearly elucidated. This study will identify the active ingredients of TJM using serum pharmacochemistry and to elucidate the mechanism on RE through network pharmacology. The blood-borne ingredients of TJM are identified by the Ultra-performance liquid chromatography-quadrupole-time of flight-mass spectrometer. Subsequently, a "compound-target-disease" network is established and obtained core targets associated with TJM and RE. Then, the potential signaling pathways are forecasted through the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Finally, the rat model of RE is established to verify the results predicted by network pharmacology through animal experiments. Fifteen blood-borne ingredients of TJM are identified, with eight active ingredients-namely Tangeretin, Tricin, Palmati, Berberine, Limonin, Evodiamine, Tetrahydropalmatine and Rutecarpine - making significant contributions to its efficacy. Moreover, TJM is predicted to act on 193 targets related to RE, involving AKT1, HSP90AA1, PIK3CA, and other targets, which enriches mainly in PI3K/AKT /NF-κB signaling. Additionally, TJM can alleviate inflammation of the esophageal mucosa, reduce pathological damage, and increase gastric pH. It can downregulate PI3K, AKT, and NF-κB mRNA transcription levels and reduce the protein expression of PI3K, AKT, and NF-κB. Furthermore, it can inhibit the overproduction of IL-6, TNF-α and IL-17. TJM can alleviate immune-inflammatory responses and ameliorate RE by restraining the PI3K/AKT pathway and its downstream NF-κB.

ZFP36 Regulates Vascular Smooth Muscle Contraction and Maintains Blood Pressure.

Hypertension remains a major risk factor for cardiovascular diseases, but the underlying mechanisms are not well understood. Zinc finger protein 36 (ZFP36) is an RNA-binding protein that regulates mRNA stability by binding to adenylate-uridylate-rich elements in the mRNA 3'-untranslated region. This study reveals that ZFP36 expression is highly elevated in the arteries of hypertensive patients and rodents. In cultured vascular smooth muscle cell (VSMC), angiotensin II (AngII) activates poly (ADP-ribose) polymerases1 (PARP1) to stimulate Zfp36 expression at the transcriptional level. VSMC-specific ZFP36 deletion reduces vessel contractility and blood pressure levels in mice. Mechanistically, ZFP36 regulates G protein-coupled receptors (GPCRs)-mediated increases in intracellular calcium levels through impairing the mRNA stability of regulator of G protein signaling 2 (RGS2). Moreover, the VSMC-specific ZFP36 deficiency attenuates AngII-induced hypertension and vascular remodeling in mice. AAV-mediated ZFP36 knockdown ameliorates spontaneous hypertension in rats. These findings elucidate that ZFP36 plays an important role in the regulation of smooth muscle contraction and blood pressure through modulating RGS2 expression. ZFP36 inhibition may represent a new therapeutic strategy for the treatment of hypertension.

Characterisation of cytochrome c oxidase-coding genes from mung bean and their response to cadmium stress based on genome-wide identification and transcriptome analysis.

Cytochrome c oxidase (COX) is a crucial mitochondrial enzyme in the electron transport chain of plants, implicated in energy production and stress responses. Despite its importance, the function of COX in leguminous plants, especially under heavy metal stress like cadmium (Cd), remains understudied. In this study, COX genes (COX s) were identified based on the genome annotation file in mung bean (Vigna radiata (Linn.) R. Wilczek), and the gene structure, physicochemical properties and systematic relationships of the relevant amino acid sequences were analyzed by using bioinformatics method. The effects of Cd on the transcription levels and activities of COX in mung bean roots, stems, and leaves were detected to understand the mechanism of COX in mung bean in response to cadmium (Cd) stress. Transcriptome sequencing revealed tissue-specific expression with roots showed the highest levels. Cd stress significantly altered the expression and activity of VrCOXs, particularly in roots and stems, with varied responses among different genes. The differential response of VrCOX s to Cd stress indicates a role in the plant stress tolerance mechanism. The study provides insights into the function of COXs in legumes and a foundation for further research into Cd tolerance mechanisms, which could be vital for enhancing legume production and ensuring food safety in contaminated environments.

The role of fibromodulin in myocardial fibrosis in a diabetic cardiomyopathy rat model.

Diabetic cardiomyopathy (DCM) is pathologically characterized by excessive deposition of extracellular matrix proteins, leading to myocardial fibrosis. Fibromodulin (Fmod) plays a crucial role in the pathogenesis of fibrotic diseases. However, the role and mechanism of Fmod in DCM-related myocardial fibrosis remain unclear. In the present study, we established a DCM rat model and an in vitro model of rat primary cardiac fibroblasts (RPCFs) exposed to high glucose. We assessed mRNA and protein expression levels of Col1a1, Col3a1, α-SMA and Fmod in both models. Fmod-overexpressing (ov-Fmod) and Fmod-knockdown (si-Fmod) rat cardiac fibroblasts (RCFs) were generated. Subsequently, whole RNA sequencing was conducted on ov-Fmod RCFs. The gene Col15a1 was evaluated in the DCM rat and all cell models. The correlation between plasma levels of Fmod and Col15a1 in DCM rat models was assessed. Transcription and protein levels of Fmod, Col1a1, Col3a1 and α-SMA were significantly elevated in DCM rat hearts and RPCFs. In ov-Fmod RCFs, fibrosis markers were similarly increased, except for Col3a1, which decreased. The Col1a1/Col3a1 ratio was elevated. Conversely, knocking down Fmod yielded opposite results. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that Fmod participates in multiple fibrosis-related pathways, affecting Col15a1. Expression of Col15a1 was significantly decreased in all models, compared to controls, except in si-Fmod RCFs. Importantly, Col15a1 and Fmod in plasma exhibited an inverse relationship in DCM. In summary, Fmod is implicated in DCM, with Fmod overexpression downregulating Col15a1 and increasing the Col1a1/Col3a1 ratio. This mechanism may influence diastolic heart failure in DCM by modulating myocardial stiffness and elasticity.

Accumulation of Anthocyanin in the Aleurone of Barley Grains by Targeted Restoration of the MYC2 Gene

Blue barley grain pigmentation results from anthocyanin accumulation in the aleurone layer. Anthocyanins are known for their beneficial effects on human health. The gene encoding the MYELOCYTOMATOSIS 2 (MYC2) transcription factor is potentially responsible for the blue coloration of the aleurone. In non-pigmented barley, a single nucleotide insertion in this gene causes a frameshift mutation with a premature stop codon. It was hypothesized that restoring the MYC2 reading frame could activate anthocyanin accumulation in the aleurone. Using a targeted mutagenesis approach in the present study, the reading frame of MYC2 was restored in the non-pigmented cultivar Golden Promise. Genetic constructs harboring cas9 and gRNA expression units were developed, pre-validated in protoplasts, and then functional MYC2 alleles were generated at the plant level via Agrobacterium-mediated transformation. Anthocyanin accumulation in the aleurone layer of grains from these mutants was confirmed through microscopy and chemical analysis. The expression of anthocyanin biosynthesis genes was analyzed, revealing that the restoration of MYC2 led to increased transcript levels of F3H and ANS genes. These results confirm the critical role of the MYC2 transcription factor in the blue aleurone trait and provide a biotechnological solution for enriching barley grain with anthocyanins.

Inhibition of RtTg neurons reverses methamphetamine-induced attention deficits

Chronic methamphetamine (METH) use, a prevalent psychostimulant, is known to impair attention, yet the cellular mechanisms driving these deficits remain poorly understood. Here, we employed a rat model of repeated passive METH injections and evaluated attentional performance using the 5-choice serial reaction time task (5-CSRTT). Using single-nucleus RNA sequencing, immunofluorescence and in situ hybridization, we characterized the response of neurons in the reticulotegmental nucleus (RtTg) to METH exposure. Our results indicate that METH exposure disrupts RtTg neurons at the transcriptional level and results in an increased activation ratio of RtTg under 5-CSRTT conditions. Crucially, chemogenetic inactivation of these neurons or RtTg lesion attenuated METH-induced attention deficits, whereas their activation reproduced the deficits. These findings underscore the critical role of RtTg neurons in mediating METH-induced attention deficits, positioning RtTg as a promising therapeutic target for the treatment of attention deficits linked to chronic METH use.

The ABC transporter SmABCG1 mediates tanshinones export from the peridermic cells of Salvia miltiorrhiza root.

Plants have mechanisms to transport secondary metabolites from where they are biosynthesized to the sites where they function, or to sites such as the vacuole for detoxification. However, current research has mainly focused on metabolite biosynthesis and regulation, and little is known about their transport. Tanshinone, a class diterpenoid with medicinal properties, is biosynthesized in the periderm of Salvia miltiorrhiza roots. Here, we discovered that tanshinone can be transported out of peridermal cells and secreted into the soil environment and that the ABC transporter SmABCG1 is involved in the efflux of tanshinone ⅡA and tanshinone Ⅰ. The SmABCG1 gene is adjacent to the diterpene biosynthesis gene cluster in the S. miltiorrhiza genome. The temporal-spatial expression pattern of SmABCG1 is consistent with tanshinone accumulation profiles. SmABCG1 is located on the plasma membrane and preferentially accumulates in the peridermal cells of S. miltiorrhiza roots. Heterologous expression in Xenopus laevis oocytes demonstrated that SmABCG1 can export tanshinone ⅡA and tanshinone Ⅰ. CRISPR/Cas9-mediated mutagenesis of SmABCG1 in S. miltiorrhiza hairy roots resulted in a significant decrease in tanshinone contents in both hairy roots and the culture medium, whereas overexpression of this gene resulted in increased tanshinone contents. CYP76AH3 transcript levels increased in hairy roots overexpressing SmABCG1 and decreased in knockout lines, suggesting that SmABCG1 may affect the expression of CYP76AH3, indirectly regulating tanshinone biosynthesis. Finally, tanshinone ⅡA showed cytotoxicity to Arabidopsis roots. These findings offer new perspectives on plant diterpenoid transport and provide a new genetic tool for metabolic engineering and synthetic biology research.

Expression analysis of defense signaling marker genes in Capsicum annuum in response to phytohormones elicitation.

To tolerate biotic stress, plants employ phytohormones such as jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) to regulate the immune response against different pathogens. Phytohormone-responsive genes, known as "Defense signaling marker genes," are used to evaluate plant disease resistance during pathogen infection. Most information on these marker genes derives from studies on the model plant Arabidopsis thaliana. The present study was aimed analyze the effect of hormonal elicitation at different concentrations at 24h pos-treatment in the transcript level of 8 traditional genes selected for molecular studies plant-pathogen interactions in Capsicum. Chemical treatment was achieved by spraying leaves of in vitro seedlings C. annuum L. with 0.1mM, 1mM or 2.5mM ET; 1mM, 2.5mM, or 5mM SA; 2.5mM BABA; or 0.150mM MeJA. Twenty-four hours after treatments were applied molecular analyses were carried out using qPCR to investigate the expression. Results revealed that 1mM of ET or 0.15mM of MeJA activated the expression CaPR1 (18--11.64-fold change), CaLOX2 (13.80-fold), CaAP2/ERF06 (22- 5.3- fold change), and CaPDF1.2 (2.3-1.5- fold). While, 5mM of SA present effect of negative regulation on the expression in most of these genes. Our results show that the expression profile induced by phytohormones in CaPR1 are particular in C. annuum, because were significantly induced for ET/MeJA, and dow-regulation with SA Contrary to Arabidopsis. Although, on both plants it is observed the cross talk between JA/ET and SA mediated signal pathways for the regulation of this gene.

OsPUKI, a PfkB protein, regulates seed germination in rice by influencing ABA synthesis

Rice seed germination is a crucial phase in rice growth and development, but its molecular mechanism has not been fully elucidated. In this study, we investigated the function of rice pfkB family gene OsPUKI in seed germination. Compared with WT (ZH11), ospuki mutants showed delayed seed germination and shorter shoot length. QRT-PCR results showed that OsPUKI was highly expressed in leaves and developing seeds of 21-day after pollination, and was highly expressed at the early stage of seed germination. GC-MS analysis demonstrated that content of abscisic acid (ABA) in ospuki-3 was higher than that in WT. QRT-PCR analysis revealed that ospuki mutants had higher transcription levels of ABA synthesis-related genes OsNCED2, OsNCED3, OsNCED4, and OsZEP1. Furthermore, it was shown that ospuki mutants were more sensitive to fluridone (Flu) during seed germination and seedling growth than WT according to exogenous Flu treatment experiments. In short, our findings suggest that OsPUKI may positively regulates rice seed germination by influencing ABA synthesis.

KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.

Gene regulation in most eukaryotes involves two fundamental physical processes -- alterations in the packaging of the genome by nucleosomes, with active cis-regulatory elements (CREs) generally characterized by an open-chromatin configuration, and the activation of transcription. Mapping these physical properties and biochemical activities genome-wide -- through profiling chromatin accessibility and active transcription -- are key tools used to understand the logic and mechanisms of transcription and its regulation. However, the relationship between these two states has until now not been accessible to simultaneous measurement. To address this, we developed KAS-ATAC, a combination of the KAS-seq (Kethoxal-Assisted SsDNA sequencing and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) methods for mapping single-stranded DNA (and thus active transcription) and chromatin accessibility, respectively, enabling the genome-wide identification of DNA fragments that are simultaneously accessible and contain ssDNA. We use KAS-ATAC to evaluate levels of active transcription over different classes of regulatory elements in the human genome, to estimate the absolute levels of transcribed accessible DNA over CREs, to map the nucleosomal configurations associated with RNA polymerase activities, and to assess transcription factor association with transcribed DNA through transcription factor binding site (TFBS) footprinting. We observe lower levels of transcription over distal enhancers compared to promoters and distinct nucleosomal configurations around transcription initiation sites associated with active transcription. Most TFs associate equally with transcribed and nontranscribed DNA but a few factors specifically do not exhibit footprints over ssDNA-containing fragments. We anticipate KAS-ATAC to continue to derive useful insights into chromatin organization and transcriptional regulation in other contexts in the future.

Constitutive HIF-1α expression in the epidermis fuels proliferation and is essential for effective barrier formation

Epidermis is one of the most rapidly proliferating tissues in the body with high demands for ATP and cellular building blocks. Here we show that, in order to meet these requirements, keratinocytes constitutively express hypoxia-inducible factor-1α (HIF-1α), even in the presence of oxygen levels sufficient for HIF-1α hydroxylation. We previously reported that mice with severe epidermal mitochondrial dysfunction actually showed a hyperproliferative epidermis, but rapidly died of systemic lactic acidosis and hypoglycemia, indicating excessive glycolysis. In the present work, we interrogated HIF-1α function in glycolysis by its epidermal ablation combined with mitochondrial dysfunction, which resulted in decreased proliferation but even earlier lethality due to a severe barrier defect. Our data demonstrate that HIF-1α is indispensable for maintaining a high aerobic glycolytic flux necessary for supplying energy, but also for synthetizing cellular building blocks like lipids, which are both essential for proliferation as well as barrier formation. HIF-1α is stabilized in keratinocytes in the presence of oxygen by high levels of HIF-1α transcripts, low levels of prolyl-4-hydroxylases (PHD2 and 3) and a low cellular α-ketoglutarate/lactate ratio, likely inhibiting PHD activity. Our data suggest a key role for constitutive HIF-1α expression allowing a Warburg-like metabolism in healthy, highly proliferative keratinocytes, similar to tumour cells.