The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region −2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [−357 (G > A), −447 (C > G), and −663 (A > G)] in the 5′ regulatory region and one in the 3′ non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5′ regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens.
We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection. Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering, revealed different aspects of the protein-mRNA relationship. Violin plot analysis showed that some genes exhibited similar distribution patterns for proteins and mRNAs. We also demonstrate that cells can be separated into subpopulations based on their protein-mRNA expression profiles, and that different subpopulations have distinct correlation coefficient values. Our results demonstrated that integrated investigations of mRNA and protein levels in single cells allows comprehensive analysis not attainable at bulk levels.
Stochastic and deterministic allele specific gene expression (ASE) might influence single cell phenotype, but the extent and nature of the phenomenon at the onset of early mouse development is unknown. Here we performed single cell RNA-Seq analysis of single blastomeres of mouse embryos, which revealed significant changes in the transcriptome. Importantly, over half of the transcripts with detectable genetic polymorphisms exhibit ASE, most notably, individual blastomeres from the same two-cell embryo show similar pattern of ASE. However, about 6% of them exhibit stochastic expression, indicated by altered expression ratio between the two alleles. Thus, we demonstrate that ASE is both deterministic and stochastic in early blastomeres. Furthermore, we also found that 1,718 genes express two isoforms with different lengths of 3′UTRs, with the shorter one on average 5–6 times more abundant in early blastomeres compared to the transcripts in epiblast cells, suggesting that microRNA mediated regulation of gene expression acquires increasing importance as development progresses.
Multiple myeloma (MM) is an incurable disease. This study focused on the expression of circular RNA circ_0069767 in MM and its influence on prognosis, in order to provide a potential target.Totally 66 MM patients participated in this research. Using RT-PCR method to determine the expression level of circ_0069767 in 66 sorted samples from multiple myeloma patients and 21 normal control bone marrow samples, Kaplan-Meier was applied for survival analysis. We constructed stable over-expressing circ_0069767 and silenced circ_0069767 cell lines and used MTS experiment to detect cell viability, transwell experiment to detect cell migration and invasion ability and flow cytometry to detect cell apoptosis. Dual luciferase experiment, qRT-PCR experiment and Western blot were used to explore miRNA and downstream genes.The expression of circ_0069767 in MM was significantly higher than that of the normal control group. Patients with high expression of circ_0069767 had longer PFS and OS. Cell function experiments showed that overexpression of circ_0069767 in MM cells led to decreased proliferation, migration and invasion, but increased apoptosis; meanwhile, knockdown of circ_0069767 caused opposite biological behaviors. Circ_0069767 by sponging miR-636 in MM cells regulates the expression of K-RAS while the K-RAS gene remained unmutated.Circ_0069767 plays an antitumor role and its expression can be used as a reliable prognostic indicator for MM patients.
Abstract Background PCBP1 (or alpha CP1 or hnRNP E1), a member of the PCBP family, is widely expressed in many human tissues and involved in regulation of transcription, transportation process, and function of RNA molecules. However, the role of PCBP1 in CD44 variants splicing still remains elusive. Results We found that enforced PCBP1 expression inhibited CD44 variants expression including v3, v5, v6, v8, and v10 in HepG2 cells, and knockdown of endogenous PCBP1 induced these variants splicing. Invasion assay suggested that PCBP1 played a negative role in tumor invasion and re-expression of v6 partly reversed the inhibition effect by PCBP1. A correlation of PCBP1 down-regulation and v6 up-regulation was detected in primary HCC tissues. Conclusions We first characterized PCBP1 as a negative regulator of CD44 variants splicing in HepG2 cells, and loss of PCBP1 in human hepatic tumor contributes to the formation of a metastatic phenotype.
To study the adaptive response induced by hydroquinone(HQ) on eukaryocyte and its possible mechanism.After hydroquinone treatment, AlamarBlue reduce rate, LDH release rate were observed to determine the cell proliferation and death. Annexin V/propidium iodide (PI) staining was performed for each treatment to distinguish viable, early, and late apoptosis or dead cells. The total cellular proteins were separated using two- dimensional gel electrophoresis and visualized by sliver staining. Digital images were analyzed using ImageMaster 2D platinum 5.0 software. The differentially expressed protein spots were picked and digested in gel then identified by tandem mass spectrum.The results of AlamarBlue reduce rate, LDH leakage and Annexin V-FITC/PI staining showed that no effect on cell viability was observed at a concentration of 10 micromol/L HQ while 250 micromol/L HQ significantly decreased cell viability. Cells pretreated with 10 micromol/L HQ for 12h show increasing survival to the following expose to 250 micromol/L HQ. In control MRC-5 cells 1429 +/- 369 protein spots were detected and, 1453 +/- 307 in low HQ group, 1191 +/- 393 in high HQ group, and 1107 +/- 247 in adaptive group by two dimensional gel electrophoresis. Twenty-four protein spots showed significant change after HQ stimulation and 22 protein spots were identified by tandems mass spectra. These identified proteins involved in energy metabolism, translation and RNA processing, protein folding, redox regulation, cell structure and cell signaling.Adaptive response can be induced by low concentration of HQ on MRC-5 cells and cellular adaptation is a complex process involving in a modulation of diverse cellular functions.
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