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Genome-wide analysis of the effects of the rs4919510C>G genotypes on the miRNA-608 target genes expression

ABSTRACT: Analysis of the effects of the rs4919510C>G SNP on miRNA-608 target gene expression. The hypothesis tested in the present study was that the rs4919510C>G SNP may influence the expression of miRNA-608 target genes. Results provide important information of the effects of the rs4919510C>G SNP on miRNA-608 target genes, including immunity and defense genes, DNA repair genes, cell growth-related genes, tumor invasion and metastasis-related genes, cancer stem cell-related genes, and cell death-related genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE46372 | GEO | 2013/05/15

SECONDARY ACCESSION(S): PRJNA198858

REPOSITORIES: GEO

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Genome-wide analysis of the effects of the rs4919510C>G genotypes on the miRNA-608 target genes expression

Project description:Analysis of the effects of the rs4919510C>G SNP on miRNA-608 target gene expression. The hypothesis tested in the present study was that the rs4919510C>G SNP may influence the expression of miRNA-608 target genes. Results provide important information of the effects of the rs4919510C>G SNP on miRNA-608 target genes, including immunity and defense genes, DNA repair genes, cell growth-related genes, tumor invasion and metastasis-related genes, cancer stem cell-related genes, and cell death-related genes. Total RNA was extracted from the cultured cells in both experimental (CNE-1-miRNA-608-C and CNE-1-miRNA-608-G) and control (CNE-1-empty vector) groups.

2013-05-15 | E-GEOD-46372 | biostudies-arrayexpress

Expression data from U937 cells infected by hsa-miR-608 inhibitor virus

Project description:The expression level of miR-608 was found to be down regulated in several types of cancer. In our previous study, a single SNP in miR-608 (rs4919510) was found to be strongly associated with a higher risk of developing sepsis and multiple organ dysfunctions in all 3 independent study cohorts. However, the clinicopathological impact and the exact roles of miR-608 and its underlying molecular mechanisms in inflammation remain to be identified. In order to identify the exact terget gene of miR-608 in monocytes, we constructed lentiviral vectors with has-miR-608 inhibitor sequences and transfected U937 cells.We used microarrays to identified distinct classes of up-regulated genes during this process and look for possible target genes.

2015-12-12 | GSE75911 | GEO

Expression data from U937 cells infected by hsa-miR-608 inhibitor virus

2015-12-12 | E-GEOD-75911 | biostudies-arrayexpress

Genome-wide analysis of miR-552-3p- and miR-608-mediated gene silencing in A549 lung cancer cells

Project description:Analysis of changes in gene expression after transfection with miR-552-3p or miR-608 mimic in A549 cells Total RNA was obtained from A549 cells transfected with miR-552-3p or miR-608 or negative control mimic, and gene expression was compared using microarrays.

2015-12-15 | E-GEOD-62723 | biostudies-arrayexpress

Genome-wide analysis of miR-552-3p- and miR-608-mediated gene silencing in A549 lung cancer cells

Project description:Analysis of changes in gene expression after transfection with miR-552-3p or miR-608 mimic in A549 cells

2015-12-15 | GSE62723 | GEO

Homo sapiens

Project description:Genome-wide analysis of the effects of the rs4919510C>G genotypes on the miRNA-608 target genes expression

| PRJNA198858 | ENA

Campylobacter fetus subsp. venerealis 97/608

Project description:Campylobacter fetus subsp. venerealis 97/608 Genome sequencing

| PRJNA73807 | ENA

Respones to treatment of H209 and H838 cell lines to treatment with the non-covalent inhibitor of TRXR1, DKFZ-608

Project description:DKFZ-608 induces oxidative stress in the cytoplasm of treated cancer cell lines. The molecular reason for this is the inhibition of the cytoplamic thioredoxin reductase TRXR1. The EC50 of cytotoxicity differes substantialy in SCLC (hypersensitive) and NSCLC (resistant). The experiment aims to identify stress response pathways induced by the compound which could explain the cytotoxic activity of the compound and its differential effect.

2019-12-02 | GSE123340 | GEO

The Interplay between K63-linked Polyubiquitinated DDX17 and m6A-modified miRNAs Regulates Hypoxia-induced Tumor Initiation

Project description:DEAD-box RNA-binding proteins (RBPs) play a significant role in RNA metabolism to achieve cellular homeostasis, including miRNA biogenesis and transcription. Hypoxia induces stemness cell-like characteristics in cancer cells and promotes malignant progression. Despite the fact that hypoxia can induce the changes in protein and RNA modification, thereby regulating downstream gene expressions, how modifications at different molecular layers interplay with each other are poorly understood. Here we show that hypoxia induces HectH9-mediated K63-linked polyubiquitination of the DEAD-box protein DDX17 as well as reduces N6-methyladenosine (m6A) marks in pri-miRNAs. While m6A potentiates DDX17 binding to pri-miRNAs, decreased m6A modifications of pri-miRNAs and increased polyubiquitination of DDX17 under hypoxia lead to decreased DDX17 binding to pri-miRNAs binding. These events enhance the association of DDX17 with the ubiquitin receptor p300 and lead to a decrease in miRNA biogenesis, especially for miRNAs regulating stemness and stemness-related genes. In addition, polyubiquitinated DDX17 together with p300 upregulates H3K56Ac levels on the stemness and stemness-related genes, resulting in enhancement of tumor initiating ability. Post-transcriptionally, decreased miRNA production, including those targeting stemness genes or stemness-related genes, also facilitates tumor initiation. Together, hypoxia triggers DDX17 poly-ubiquitination, which orchestrates dual mechanisms to increase tumor initiating ability and promote tumor progression.

2018-03-09 | PXD006059 | JPOST Repository

Integrative transcriptome and proteome revealed high-yielding mechanisms of epsilon-poly-L-lysine by Streptomyces albulus

Project description:ε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by S. albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering. Here, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18. Our results show that key genes in the glycolysis, glyoxylate, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. Furthermore, transcriptional and translational upregulation of genes involved in the tricarboxylic acid cycle, oxidative phosphorylation, and pentose phosphate pathway also increase the pools of available NADH, ATP, and NADPH. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure, thus further regulating the ε-PL biosynthesis. This study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing a theoretical foundation development of advanced Streptomycetaceae microbial cell factories.

2023-07-20 | PXD036099 | Pride

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