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SUMMARY: The utilization of rice heterosis is essential for ensuring global food security; however, its molecular mechanism remains unclear. In this study, comprehensive analyses of accessible chromatin regions (ACRs), DNA methylation, and gene expression in inter‐subspecific hybrid and its parents were performed to determine the potential role of chromatin accessibility in rice heterosis. The hybrid exhibited abundant ACRs, in which the gene ACRs and proximal ACRs were directly related to transcriptional activation rather than the distal ACRs. Regarding the dynamic accessibility contribution of the parents, paternal ZHF1015 transmitted a greater number of ACRs to the hybrid. Accessible genotype‐specific target genes were enriched with overrepresented transcription factors, indicating a unique regulatory network of genes in the hybrid. Compared with its parents, the differentially accessible chromatin regions with upregulated chromatin accessibility were much greater than those with downregulated chromatin accessibility, reflecting a stronger regulation in the hybrid. Furthermore, DNA methylation levels were negatively correlated with ACR intensity, and genes were strongly affected by CHH methylation in the hybrid. Chromatin accessibility positively regulated the overall expression level of each genotype. ACR‐related genes with maternal Z04A‐bias allele‐specific expression tended to be enriched during carotenoid biosynthesis, whereas paternal ZHF1015‐bias genes were more active in carbohydrate metabolism. Our findings provide a new perspective on the mechanism of heterosis based on chromatin accessibility in inter‐subspecific hybrid rice. Significance Statement: The utilization of rice heterosis is an essential avenue to overcome the yield bottleneck; however, the underlying molecular mechanism remains unclear. We characterized the more actively accessible chromatin state in the inter‐subspecific hybrid compared to that in its parents, revealing the regulation of chromatin accessibility and DNA methylation. This study offers a novel perspective on ACR as an embodiment of the regulation of hybrid rice. [ABSTRACT FROM AUTHOR]

Machine learning methods have been used in identifying omics markers for a variety of phenotypes. We aimed to examine whether a supervised machine learning algorithm can improve identification of alcohol-associated transcriptomic markers. In this study, we analysed array-based, whole-blood derived expression data for 17 873 gene transcripts in 5508 Framingham Heart Study participants. By using the Boruta algorithm, a supervised random forest (RF)-based feature selection method, we selected twenty-five alcohol-associated transcripts. In a testing set (30 % of entire study participants), AUC (area under the receiver operating characteristics curve) of these twenty-five transcripts were 0·73, 0·69 and 0·66 for non-drinkers v. moderate drinkers, non-drinkers v. heavy drinkers and moderate drinkers v. heavy drinkers, respectively. The AUC of the selected transcripts by the Boruta method were comparable to those identified using conventional linear regression models, for example, AUC of 1958 transcripts identified by conventional linear regression models (false discovery rate < 0·2) were 0·74, 0·66 and 0·65, respectively. With Bonferroni correction for the twenty-five Boruta method-selected transcripts and three CVD risk factors (i.e. at P < 6·7e-4), we observed thirteen transcripts were associated with obesity, three transcripts with type 2 diabetes and one transcript with hypertension. For example, we observed that alcohol consumption was inversely associated with the expression of DOCK4 , IL4R , and SORT1 , and DOCK4 and SORT1 were positively associated with obesity, and IL4R was inversely associated with hypertension. In conclusion, using a supervised machine learning method, the RF-based Boruta algorithm, we identified novel alcohol-associated gene transcripts. [ABSTRACT FROM AUTHOR]

The basic leucine zipper (bZIP) transcription factors constitute the most widely distributed and conserved eukaryotic family. They play crucial roles in plant growth, development, and responses to both biotic and abiotic stresses, exerting strong regulatory control over the expression of downstream genes. In this study, a genome-wide characterization of the CebZIP transcription factor family was conducted using bioinformatic analysis. Various aspects, including physicochemical properties, phylogenetics, conserved structural domains, gene structures, chromosomal distribution, gene covariance relationships, promoter cis-acting elements, and gene expression patterns, were thoroughly analyzed. A total of 70 CebZIP genes were identified from the C. ensifolium genome, and they were randomly distributed across 18 chromosomes. The phylogenetic tree clustered them into 11 subfamilies, each exhibiting complex gene structures and conserved motifs arranged in a specific order. Nineteen pairs of duplicated genes were identified among the 70 CebZIP genes, with sixteen pairs affected by purifying selection. Cis-acting elements analysis revealed a plethora of regulatory elements associated with stress response, plant hormones, and plant growth and development. Transcriptome and qRT-PCR results demonstrated that the expression of CebZIP genes was universally up-regulated under low temperature conditions. However, the expression patterns varied among different members. This study provides theoretical references for identifying key bZIP genes in C. ensifolium that confer resistance to low-temperature stress, and lays the groundwork for further research into their broader biological functions. [ABSTRACT FROM AUTHOR]

Background: Lysosomal cathepsin D (CTSD) can degrade internalized advanced glycation end products (AGEs) in dermal fibroblasts. CTSD expression is decreased in photoaged fibroblasts, which contributes to intracellular AGEs deposition and further plays a role in AGEs accumulation of photoaged skin. The mechanism under downregulated CTSD expression is unclear. Objective: To explore possible mechanism of regulating CTSD expression in photoaged fibroblasts. Methods: Dermal fibroblasts were induced into photoaging with repetitive ultraviolet A (UVA) irradiation. The competing endogenous RNA (ceRNA) networks were constructed to predict candidate circRNAs or miRNAs related with CTSD expression. AGEs‐BSA degradation by fibroblasts was studied with flow cytometry, ELISA, and confocal microscopy. Effects of overexpressing circRNA‐406918 via lentiviral transduction on CTSD expression, autophagy, AGE‐BSA degradation were analyzed in photoaged fibroblasts. The correlation between circRNA‐406918 and CTSD expression or AGEs accumulation in sun‐exposed and sun‐protected skin was studied. Results: CTSD expression, autophagy, and AGEs‐BSA degradation were significantly decreased in photoaged fibroblasts. CircRNA‐406918 was identified to regulate CTSD expression, autophagy, and senescence in photoaged fibroblasts. Overexpressing circRNA‐406918 potently decreased senescence and increased CTSD expression, autophagic flux, and AGEs‐BSA degradation in photoaged fibroblasts. Moreover, circRNA‐406918 level was positively correlated with CTSD mRNA expression and negatively associated with AGEs accumulation in photodamaged skin. Further, circRNA‐406918 was predicted to mediate CTSD expression through sponging eight miRNAs. Conclusion: These findings suggest that circRNA‐406918 regulates CTSD expression and AGEs degradation in UVA‐induced photoaged fibroblasts and might exert a role in AGEs accumulation in photoaged skin. [ABSTRACT FROM AUTHOR]

Although overexpression of genes encoding detoxification enzymes is a well-known mechanism of pesticide resistance of mites, the regulators involved in this process are still illiterate. Previous studies in our laboratory demonstrated that the overexpression of six P450 genes contributes to fenpropathrin resistance in T. cinnabarinus . In this study, six transcription factor genes that likely regulate the expression of P450 genes were identified and characterized. Quantitative PCR (qPCR) analysis showed that three transcription factor genes were highly expressed in a fenpropathrin-resistant (FeR) strain of T. cinnabarinus . The cap ‘n’ collar isoform C (CncC) and muscle aponeurosis fibromatosis (Maf) family transcription factors were identified as the key regulator of P450 genes by RNA interference (RNAi). Furthermore, research on the promoters of these P450 genes using reporter assays identified that CncC and Maf influence the susceptibility of T. cinnabarinus to fenpropathrin through regulating the expression of P450 genes. This study increases our understanding of the molecular mechanisms underlying the regulation of P450 genes involved in detoxification of acaricides in T. cinnabarinus . [ABSTRACT FROM AUTHOR]

Tigecycline and the newly Food and Drug Administration-approved tetracyclines, including eravacycline and omadacycline, are regarded as last-resort treatments for multidrug-resistant Enterobacterales. However, tigecycline resistance in Klebsiella pneumoniae has increased, especially the underlying mechanism of heteroresistance is unclear. This study aimed to elucidate the mechanisms underlying tigecycline resistance and heteroresistance in clinical K. pneumoniae isolates. A total of 153 clinical K. pneumoniae isolates were collected, and identified 15 tigecycline-resistant and three tigecycline-heteroresistant isolates using broth microdilution and population analysis profile methods, respectively. Total RNAs from K. pneumoniae ATCC13883 and the laboratory-induced tigecycline-resistant strain were extracted and sequenced on an Illumina platform. Differentially expressed genes and regulatory small RNAs (sRNAs) were analyzed and validated in clinical isolates of K. pneumoniae using quantitative real-time PCR. RNA sequencing results showed that mdtABC efflux pump genes were significantly upregulated in the tigecycline-resistant strains. Overexpression of mdtABC was observed in a clinical K. pneumoniae isolate, which increased tigecycline minimum inhibitory concentrations (MICs) and was involved in tigecycline heteroresistance. Sequencing analysis of sRNA demonstrated that candidate sRNA-120 directly interacted with the mdtABC operon and was downregulated in tigecycline-resistant strains. We generated an sRNA-120 deletion mutation strain and a complemented strain of K. pneumoniae. The sRNA-120 deletion strain displayed increased mRNA levels of mdtA, mdtB, and mdtC and an increase in MICs of tigecycline. The complemented strain of sRNA-120 restored the mRNA levels of these genes and the susceptibility to tigecycline. RNA antisense purification and parallel reaction monitoring mass spectrometry were performed to verify the interactions between sRNA-120 and mdtABC. Collectively, our study highlights that the post-transcriptional repression of mdtABC through sRNA-120 may provide an additional layer of efflux pump gene expression control, which is important for resistance and heteroresistance in clinical K. pneumoniae isolates. [ABSTRACT FROM AUTHOR]

Plants resist the invasion and establishment of pathogens through the existence of structural barriers and biochemical response mechanisms. In this regard, long non-coding RNAs (lncRNAs) have been found to play a role in various plant growth and developmental processes, as well as plant disease resistance. This study used high-throughput sequencing and bioinformatics to identify lncRNAs in kiwifruit and predict their function based on their inferred target genes. A total of 591 differentially expressed lncRNAs and 1819 mRNAs were identified in kiwifruit samples infected with P. expansum for 24 h. GO enrichment analysis indicated that the highest number of differentially expressed genes (DEGs) fell into the biological processes category of the three major ontology categories. KEGG pathway analysis indicated that most DEGs were annotated in the Plant-pathogen interaction and Plant hormone signal transduction pathways. LncRNAs in kiwifruit may be involved in the response to pathogen infections through salicylic acid (SA), gibberellin (GA), and abscisic acid (ABA) pathways. In this regard, genes, such as PP2C , GA20ox , and A-ARR , exhibited varying degrees of differential expression in kiwifruit in response to P. expansum infection. Our results provide insight into the molecular response of kiwifruit to invasion by P. expansum and provide a theoretical foundation for understanding and improving disease resistance. [Display omitted] • Identification of lncRNAs in tissues of kiwifruit. • Differential expression analysis of lncRNAs and mRNAs. • Studying the integrated relationship of lncRNAs and mRNAs. • Confirming the reliability of the differential expression genes by RT-qPCR. [ABSTRACT FROM AUTHOR]

Zexie Tang (ZXT), only two consists with Alismatis Rhizoma (AR) and Atractylodes macrocephala Rhizoma (AM), a classical Chinese medicine formula from Synopsis of the Golden Chamber with a history of 2000 years. Clinical observation in recent years has found that ZXT has excellent lipid-lowering effect. Aim of the study : To explore the potential mechanism of ZXT ameliorates hyperlipidemia based on FKBP38/mTOR/SREBPs pathway. WD-induced hyperlipidemia mice and oleic acid induced cell lipid accumulation model were used to investigate pharmacodynamic. The effect of ZXT on the transcriptional activity of SREBPs was detected by reporter gene assay. Proteins and downstream genes of mTOR/SREBPs pathway were detected in vivo and in vitro. Combined with network pharmacology and HPLC-Q-TOF/MS, the active ingredients were screened and identified. The interaction between active compounds of ZXT and FKBP38 protein were analyzed by docking analysis. ZXT decreased TC, TG and LDL-c levels in blood of WD-induced hyperlipidemia mouse model, and improved insulin resistance in vivo. ZXT also reduced TC, TG and lipid accumulation in cells line, and inhibited SREBPs luciferase activity, protein and its target genes expression such as FASN , HMGCR , etc. Meanwhile, ZXT inhibited protein expression levels of p-mTOR, p-S6K, etc in vitro and in vivo. Combined with network pharmacology and HPLC-Q-TOF/MS, 16 active ingredients were screened and identified. Docking results showed that active compounds of ZXT binding to FKBP38 and formed hydrogen bond. Our findings highlighted that ZXT ameliorates hyperlipidemia, in which FKBP/mTOR/SREBPs pathway might be the potential regulatory mechanism. [Display omitted] [ABSTRACT FROM AUTHOR]