Genome-wide analysis of the effects of the rs4919510C>G genotypes on the miRNA-608 target genes expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Li Wei
PROVIDER: E-GEOD-46372 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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.
2013-05-15 | GSE46372 | GEO
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
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. U937 cells transfected by has-miR-608 inhibitor lentiviral vectors or negative control virus were analyzed. There are three samples in each group.
2015-12-12 | E-GEOD-75911 | biostudies-arrayexpress
Project description:Genome-wide analysis of the effects of the rs4919510C>G genotypes on the miRNA-608 target genes expression
| PRJNA198858 | ENA
Project description:Analysis of photodynamic therapy with hypericin of nasopharyngeal carcinoma cells CNE-2 in different time-points at gene expression level. The hypothesis tested in the present study was that HY-PDT could induce apoptosis on CNE-2 cells via intrinsic pathways. Results provide important information of the response of apoptosis, such as specific oxidative stress genes, mitochondrial related genes, cell cycle related genes, etc.
2011-01-28 | GSE20134 | GEO
Project description:Analysis of photodynamic therapy with hypericin of nasopharyngeal carcinoma cells CNE-2 in different time-points at gene expression level. The hypothesis tested in the present study was that HY-PDT could induce apoptosis on CNE-2 cells via intrinsic pathways. Results provide important information of the response of apoptosis, such as specific oxidative stress genes, mitochondrial related genes, cell cycle related genes, etc. Total RNAs were isolated from the cultured cells treatment with 20 μg/ml HY and irradiation then cultured in dark for 0, 2, 6, 12, 20 h respectively compared to cells treatment with 20 μg/ml HY only then cultured in dark for 20 h.
2011-01-28 | E-GEOD-20134 | biostudies-arrayexpress
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
Project description:Schmitz2014 - RNA triplex formation
The model is parameterized using the
parameters for gene CCDC3 from Supplementary Table S1. The two
miRNAs which form the triplex together with CCDC3 are miR-551b and
miR-138.
This model is described in the article:
Cooperative gene regulation
by microRNA pairs and their identification using a
computational workflow.
Schmitz U, Lai X, Winter F,
Wolkenhauer O, Vera J, Gupta SK.
Nucleic Acids Res. 2014 Jul; 42(12):
7539-7552
Abstract:
MicroRNAs (miRNAs) are an integral part of gene regulation
at the post-transcriptional level. Recently, it has been shown
that pairs of miRNAs can repress the translation of a target
mRNA in a cooperative manner, which leads to an enhanced
effectiveness and specificity in target repression. However, it
remains unclear which miRNA pairs can synergize and which genes
are target of cooperative miRNA regulation. In this paper, we
present a computational workflow for the prediction and
analysis of cooperating miRNAs and their mutual target genes,
which we refer to as RNA triplexes. The workflow integrates
methods of miRNA target prediction; triplex structure analysis;
molecular dynamics simulations and mathematical modeling for a
reliable prediction of functional RNA triplexes and target
repression efficiency. In a case study we analyzed the human
genome and identified several thousand targets of cooperative
gene regulation. Our results suggest that miRNA cooperativity
is a frequent mechanism for an enhanced target repression by
pairs of miRNAs facilitating distinctive and fine-tuned target
gene expression patterns. Human RNA triplexes predicted and
characterized in this study are organized in a web resource at
www.sbi.uni-rostock.de/triplexrna/.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000530.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000530 | BioModels
Project description:Target resequencing of neurodevelopmental-related genes
| PRJDB4619 | ENA
Project description:From the results of microarray, 7616 miRNAs with significantly different expression ratios were selected when CNE-2-S-18/SP cells were treated with DC120. Among these, 80 miRNAs were up-regulated and 78 were down-regulated. We then chose 20 miRNAs through the qRT M-bM-^@M-^S PCR, and our results showed that 9 miRNAs were up-regulated after treatment with DC120, which was consistent with the results of the microarray. Among these, miR-30a were significantly up-regulated. These results indicated that miR 30a expression was up-regulated by DC120. We then investigated the role of miR 30a in DC120-treated cells, we explored its potential targets using a bioinformatics approach of complementary base pairing. The relative luciferase activity of the reporter that contained the wild type 3' UTR was significantly suppressed when miR 30a was contransfected. In contrast, the luciferase activity of the mutant reporter was unaffected by the contransfection of miR 30a, indicating that miR 30a suppressed Sox2 gene expression using the miR 30a binding sequence at the 3' UTR of the Sox2 gene. Additionally, the ectopic expression of miR 30a caused a decrease in Sox2 protein expression and mRNA levels in CNE-2-S-18 cells. These data demonstrate that miR 30a may directly target the Sox2 gene via seed matches on both 3' UTR. Taken together, our results demonstrate that DC120 regulates Sox2 via up-regulation of miR 30a. In this study, two samples were used to acquire the miRNA expression profiling. We analyzed the differences in miRNA profiles between control (DMSO solution) and DC120 treatment in CNE-2-S-18/SP cells from miRNA microarrays. The CNE-2-S-18/SP cells were separately cultured with a DMSO solution or 10M-NM-<mol/L DC120 for 15h, and total RNA from all of the cells was extracted. Then we chose 20 up-regulated miRNAs through the qRT M-bM-^@M-^S PCR, and our results showed that 9 miRNAs were up-regulated after treatment with DC120. Among these, miR-30a were significantly up-regulated. Then we investigated the role of miR 30a in DC120-treated cells by bioinformatic methods and Dual luciferase reporter system, the function of miR-30a was analyzed through ectopic expression of miR 30a. Taken together, our results demonstrate that DC120 regulates Sox2 via up-regulation of miR 30a.
2014-07-18 | E-GEOD-59503 | biostudies-arrayexpress