Contrerascoyne1165

Keratin 18 (KRT18), one of the most abundant keratins in epithelial and endothelial cells, has been reported to be aberrantly expressed in many malignancies and extensively regarded as a biomarker and important regulator in multiple cancers, including gastric cancer (GC). But the molecular regulatory mechanisms of KRT18 in GC patients and cells are largely unknown. In the present study, we analyzed the expression level of KRT18 in 450 stomach adenocarcinoma tissue samples from TCGA database and found a significantly higher expression level in tumor tissues. We then explored the potential functions of KRT18 in AGS cells (human gastric adenocarcinoma cell line) by KRT18 knockdown using siRNA and whole transcriptome RNA-seq analysis. Notably, KRT18 selectively regulates expression of cell proliferation and apoptotic genes. Beyond this, KRT18 affects the alternative splicing of genes enriched in apoptosis, cell cycle, and other cancer-related pathways, which were then validated by reverse transcription-quantitative polymerase chain reaction approach. We validated KRT18-KD promoted apoptosis and inhibited proliferation in AGS cells. We then used RNA-seq data of GC samples to further demonstrate the modulation of KRT18 on alternative splicing regulation. These results together support the conclusion that KRT18 extensively modulates diverse alternative splicing events of genes enriched in proliferation and apoptosis processes. And the dysregulated splicing factors at transcriptional or posttranscriptional level by KRT18 may contribute to the alternative splicing change of many genes, which expands the functional importance of keratins in apoptotic and cell cycle pathways at the posttranscriptional level in GC.Systemic sclerosis (SSc) is an immune-mediated connective tissue disease characterized by fibrosis of multi-organs, and SSc-related interstitial lung disease (SSc-ILD) is a leading cause of morbidity and mortality. To explore molecular biological mechanisms of SSc-ILD, we constructed a competing endogenous RNA (ceRNA) network for prediction. Expression profiling data were obtained from the Gene Expression Omnibus (GEO) database, and differential expressed mRNAs and miRNAs analysis was further conducted between normal lung tissue and SSc lung tissue. Also, the interactions of miRNA-lncRNA, miRNA-mRNA, and lncRNA-mRNA were predicted by online databases including starBase, LncBase, miRTarBase, and LncACTdb. The ceRNA network containing 11 lncRNAs, 7 miRNAs, and 20 mRNAs were constructed. Based on hub genes and miRNAs identified by weighted correlation network analysis (WGCNA) method, three core sub-networks-SNHG16, LIN01128, RP11-834C11.4(LINC02381)/hsa-let-7f-5p/IL6, LINC01128/has-miR-21-5p/PTX3, and LINC00665/hsa-miR-155-5p/PLS1-were obtained. Combined with previous studies and enrichment analyses, the lncRNA-mediated network affected LPS-induced inflammatory and immune processes, fibrosis development, and tumor microenvironment variations. The ceRNA network, especially three core sub-networks, may be served as early biomarkers and potential targets for SSc, which also provides further insights into the occurrence, progression, and accurate treatment of SSc at the molecular level.Halogeton glomeratus is a succulent annual herbaceous halophyte belonging to the Chenopodiaceae family, has attracted wide attention as a promising candidate for phytoremediation and as an oilseed crop and noodle-improver. More importantly, H. glomeratus has important medicinal value in traditional Chinese medicine. However, there are few comprehensive studies on the nutrients, particularly secondary metabolites. Here, we adopted untargeted metabolomics to compare the differences in metabolites of different tissues (root, stem, leaf, and seed) and identify the compounds related to pharmacological effects and response to abiotic stress in H. glomeratus. A total of 2,152 metabolites were identified, and the metabolic profiles of root, stem, leaf, and seed samples were clearly separated. More than 50% of the metabolites showed significant differences among root, stem, leaf, and seed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differential metabolites suggested an extensive alteration in the metabolome among the different organs. Furthermore, the identified metabolites related to pharmacological effects and response to abiotic stress included flavones, flavonols, flavandiols, glucosinolates, isoquinolines, pyridines, indoles, amino acids, lipids, carbohydrates, and ATP-binding cassette transporters. These metabolites have application in treating human cardiovascular diseases, cancers, diabetes, and heart disease, induce sleeping and have nutritive value. In plants, they are related to osmotic adjustment, alleviating cell damage, adjusting membrane lipid action and avoiding toxins. To the best of our knowledge, this is the first metabolomics-based report to overview the metabolite compounds in H. glomeratus and provide a reference for future development and utilization of H. glomeratus.In polyploids, whole genome duplication (WGD) played a significant role in genome expansion, evolution and diversification. Many gene families are expanded following polyploidization, with the duplicated genes functionally diversified by neofunctionalization or subfunctionalization. These mechanisms may support adaptation and have likely contributed plant survival during evolution. Flowering time is an important trait in plants, which affects critical features, such as crop yields. The flowering-time gene family is one of the largest expanded gene families in plants, with its members playing various roles in plant development. Here, we performed genome-wide identification and comparative analysis of flowering-time genes in three palnt families i.e., Malvaceae, Brassicaceae, and Solanaceae, which indicate these genes were expanded following the event/s of polyploidization. Duplicated genes have been retained during evolution, although genome reorganization occurred in their flanking regions. Further investigation of sequence conservation and similarity network analyses provide evidence for functional diversification of duplicated genes during evolution. These functionally diversified genes play important roles in plant development and provide advantages to plants for adaptation and survival in response to environmental changes encountered during evolution. Collectively, we show that flowering-time genes were expanded following polyploidization and retained as large gene family by providing advantages from functional diversification during evolution.N 6-methyladenosine (m6A) modification is a dynamically regulated RNA modification that impacts many cellular processes and pathways. BTK signaling inhibitors This epitranscriptomic methylation relies on the participation of RNA methyltransferases (referred to as "writers") and demethylases (referred to as "erasers"), respectively. We previously demonstrated that the Arabidopsis thaliana protein atALKBH9B showed m6A-demethylase activity and interacted with the coat protein (CP) of alfalfa mosaic virus (AMV), causing a profound impact on the viral infection cycle. To dissect the functional activity of atALKBH9B in AMV infection, we performed a protein-mapping analysis to identify the putative domains required for regulating this process. In this context, the mutational analysis of the protein revealed that the residues between 427 and 467 positions are critical for in vitro binding to the AMV RNA. The atALKBH9B amino acid sequence showed intrinsically disordered regions (IDRs) located at the N-terminal part delimiting the internal AlkB-like domain and at the C-terminal part. We identified an RNA binding domain containing an RGxxxRGG motif that overlaps with the C-terminal IDR. Moreover, bimolecular fluorescent experiments allowed us to determine that residues located between 387 and 427 are critical for the interaction with the AMV CP, which should be critical for modulating the viral infection process. Finally, we observed that atALKBH9B deletions of either N-terminal 20 residues or the C-terminal's last 40 amino acids impede their accumulation in siRNA bodies. The involvement of the regions responsible for RNA and viral CP binding and those required for its localization in stress granules in the viral cycle is discussed.A subset of eukaryotic transcription factors (TFs) possess the ability to reprogram one cell type into another. Genes important for cellular reprograming are typically located in closed chromatin, which is covered by nucleosomes. Pioneer factors are a special class of TFs that can initially engage their target sites in closed chromatin prior to the engagement with, opening of, or modification of the sites by other factors. Although many pioneer factors are known in animals, a few have been characterized in plants. The TF LEAFY (LFY) acts as a pioneer factor specifying floral fate in Arabidopsis. In response to endogenous and environmental cues, plants produce appropriate floral inducers (florigens). During the vegetative phase, LFY is repressed by the TERMINAL FLOWER 1 (TFL1)-FD complex, which functions as a floral inhibitor, or anti-florigen. The florigen FLOWERING LOCUS T (FT) competes with TFL1 to prevent the binding of the FD TF to the LFY locus. The resulting FT-FD complex functions as a transient stimulus to activate its targets. Once LFY has been transcribed in the appropriate spatiotemporal manner, LFY binds to nucleosomes in closed chromatin regions. Subsequently, LFY opens the chromatin by displacing H1 linker histones and recruiting the SWI/SNF chromatin-remodeling complex. Such local changes permit the binding of other TFs, leading to the expression of the floral meristem identity gene APETALA1. This mini-review describes the latest advances in our understanding of the pioneer TF LFY, providing insight into the establishment of gene expression competence through the shaping of the plant epigenetic landscape.Perceiving incoming environmental information is critical for optimizing plant growth and development. Multiple B-box proteins (BBXs) play essential roles in light-dependent developmental processes in plants. However, whether BBXs function as a signal integrator between light and temperature in tomato plants remains elusive. In this study, 31 SlBBX genes were identified from the newly released tomato (Solanum lycopersicum) genome sequences and were clustered into five subgroups. Gene structure and protein motif analyses showed relatively high conservation of closely clustered SlBBX genes within each subgroup; however, genome mapping analysis indicated the uneven distribution of the SlBBX genes on tomato chromosomes. Promoter cis-regulatory elements prediction and gene expression indicated that SlBBX genes were highly responsive to light, hormones, and stress conditions. Reverse genetic approaches revealed that disruption of SlBBX7, SlBBX9, and SlBBX20 largely suppressed the cold tolerance of tomato plants. Furthermore, the impairment of SlBBX7, SlBBX9, and SlBBX20 suppressed the photosynthetic response immediately after cold stress. Due to the impairment of non-photochemical quenching (NPQ), the excess photon energy and electron flow excited by low temperature were not consumed in SlBBX7-, SlBBX9-, and SlBBX20- silenced plants, leading to the over reduction of electron carriers and damage of the photosystem. Our study emphasized the positive roles of light signaling transcription factors SlBBXs in cold tolerance in tomato plants, which may improve the current understanding of how plants integrate light and temperature signals to adapt to adverse environments.