Alternative Reading Frame (ARF) overexpression in LN229 glioma cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Abdessamad Zerrouqi
PROVIDER: E-MEXP-3476 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:U2OS cells were stably transfected with an ecotropic receptor expression plasmid. These cells were infected with retroviruses expressing MIZ-1 or MYC and subsequently superinfected with retroviruses expressing p14ARF. Selection was carried out 48h following superinfection and selected cells were harvested within 1 - 2 passages. For each condition around 2.5x10<superscript6> cells were pooled.<br>Using the two color Quick-Amp labelling kit (Agilent, 5190-0444) 100ng of total RNA were used for cDNA synthesis, aRNA amplification and labelling according to manufacturer's instructions.<br>Transcriptional profiling was done on a whole human genome oligo microarray (Agilent, G4112F, 014850) in a 4x44k slide format.
2009-11-01 | E-MEXP-2310 | biostudies-arrayexpress
Project description:Initiation of mineralisation during endochondral ossification is a multistep process and was assumed to correlate with specific interactions of annexins and collagens. Annexins A5 and A6 are postulated to represent the essential annexins promoting cartilage mineralisation. However, skeletal development appears to be normal in annexin A5 or A6 deficient mice. The highly conserved structures of annexins led to the assumption that annexins A5 and A6 may fulfill redundant functions. We now generated mice deficient for both proteins, annexins A5 and A6. Mice were viable, fertile and showed no obvious abnormalities. Assessment of skeletal elements using histological, ultrastructural and peripheral quantitative computed tomography methods revealed that mineralisation and development of the skeleton was not significantly affected in mutant mice. In respect of the lack of an obvious phenotype we now applied microarray analysis to the growth plate to define changes in the transcriptome of juvenile murine growth plates from mutant mice. Global gene expression analysis revealed subtle phenotypes at the transcriptome level of genes involved in cell growth and intermediate metabolism in mutant mice. These data demonstrate that both annexins are dispensable for proper cartilage mineralisation but may affect cell proliferation processes at the transcriptomic level.
2009-02-17 | E-MEXP-1718 | biostudies-arrayexpress
Project description:BackgroundThe survival of glioma patients with the current treatments is poor. Early clinical trails with replicating adenoviruses demonstrated the feasibility and safety of the use of adenoviruses as oncolytic agents. Antitumor efficacy has been moderate due to inefficient virus replication and spread. Previous studies have shown that truncation of the adenovirus i-leader open reading frame enhanced cytopathic activity of HAdV-5 in several tumor cell lines. Here we report the effect of an i-leader mutation on the cytopathic activity in glioma cell lines and in primary high-grade glioma cell cultures.ResultsA mutation truncating the i-leader open reading frame was created in a molecular clone of replication-competent wild-type HAdV-5 by site-directed mutagenesis. We analyzed the cytopathic activity of this RL-07 mutant virus. A cell-viability assay showed increased cytopathic activity of the RL-07 mutant virus on U251 and SNB19 glioma cell lines. The plaque sizes of RL-07 on U251 monolayers were seven times larger than those of isogenic control viruses. Similarly, the cytopathic activity of the RL-07 viruses was strongly increased in six primary high-grade glioma cell cultures. In glioma cell lines the RL-07 virus was found to be released earlier into the culture medium. This was not due to enhanced viral protein synthesis, as was evident from equivalent E1A, Fiber and Adenovirus Death Protein amounts, nor to higher virus yields.ConclusionThe cytopathic activity of replicating adenovirus in glioblastoma cells is increased by truncating the i-leader open reading frame. Such mutations may help enhancing the antitumor cytopathic efficacy of oncolytic adenoviruses in the treatment of glioblastoma.
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Project description:Increasing evidence has suggested that gliomas can supply blood through vasculogenic mimicry. In this study, the expression and function of ZNRD1-AS1-144aa-uORF (144aa-uORF) and some non-coding RNAs in gliomas were assessed. Real-time quantitative PCR or Western blot was used to discover the expression of 144aa-uORF, ZNRD1-AS1, miR-499a-5p, ELF1 and EMI1 in gliomas. In addition, RIP and RNA pull-down assays were applied to explore the interrelationship between 144aa-uORF and ZNRD1-AS1. The role of the 144aa-uORF\ZNRD1-AS1\miR-499a-5p\ELF1\EMI1 axis in vasculogenic mimicry formation of gliomas was analysed. This study illustrates the reduced expression of the 144aa-uORF in glioma tissues and cells. Up-regulation of 144aa-uORF inhibits proliferation, migration, invasion and vasculogenic mimicry formation within glioma cells. The up-regulated 144aa-uORF can increase the degradation of ZNRD1-AS1 through the nonsense-mediated RNA decay (NMD) pathway. Knockdown of ZNRD1-AS1 inhibits vasculogenic mimicry in glioma cells by modulating miR-499a-5p. At the same time, miR-499a-5p is down-regulated and has a tumour-suppressive effect in gliomas. In addition, ZNRD1-AS1 serves as a competitive endogenous RNA (ceRNA) and regulates the expression of ELF1 by binding to miR-499a-5p. Notably, ELF1 binds to the promoter region of EMI1 and up-regulates EMI1 expression, while simultaneously promoting vasculogenic mimicry in glioma cells. This study suggests that the 144aa-uORF\ZNRD1-AS1\miR-499a-5p\ELF1\EMI1 axis takes key part in regulating the formation of vasculogenic mimicry in gliomas and may provide a potential target for glioma treatment.
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Project description:Upon initiation at an AUG start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. Although some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known how the ribosome normally prevents spontaneous frameshift errors. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3’ end of 18S rRNA to scan the AUG-like codons after the decoding process. The internal mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a post-decoding mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like “sticky” codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes codon “stickiness”. Further supporting the role of “sticky” sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes by minimizing the appearance of AUG-like codons in the frame 2. These results suggest an important layer of information embedded within the protein coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.
2016-04-12 | GSE80156 | GEO
Project description:POLGARF is an upstream Alternative Reading Frame in POLG gene partially overlapping POLG sequence. To obtain POLGARF peptide reference spectra POLGARF was overexpressed in HEK293T and HEK293F cells .
2021-09-08 | PXD016007 | Pride
Project description:CARF, a collaborator of ARF (alternative reading frame protein), was cloned as a novel ARF-binding protein from a yeast-interaction screen. It potentiated ARF-mediated p53 function, and also caused a moderate increase in p53 activity in the absence of ARF. We herein report the molecular mechanism of ARF-independent function of CARF. By employing a variety of approaches, including overexpression of CARF, its suppression by small interfering RNA and use of protease inhibitors, we demonstrate that: (i) CARF directly interacts with wild-type p53, causing its stabilization and functional activation; and (ii) CARF and p53 levels show an inverse relationship that is instigated by a negative-feedback control via a proteasome-mediated degradation pathway.
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Project description:Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus.
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Project description:Human astrovirus (HAstV) strains exhibit high levels of genetic diversity, and many recombinant strains with different recombination patterns have been reported. The aims of the present study were to investigate the emergence of HAstV recombinant strains and to characterize the recombination patterns of the strains detected in pediatric patients admitted to the hospital with acute gastroenteritis in Chiang Mai, Thailand. A total of 92 archival HAstV strains detected in 2011 to 2020 were characterized regarding their open reading frame 1a (ORF1a) genotypes in comparison with their ORF1b genotypes to identify recombinant strains. The recombination breakpoints of the putative recombinant strains were determined by whole-genome sequencing and were analyzed by SimPlot and RDP software. Three HAstV strains (CMH-N178-12, CMH-S059-15, and CMH-S062-15) were found to be recombinant strains of three different HAstV genotypes, i.e., HAstV5, HAstV8, and HAstV1 within the ORF1a, ORF1b, and ORF2 regions, respectively. The CMH-N178-12 strain displayed recombination breakpoints at nucleotide positions 2681 and 4357 of ORF1a and ORF1b, respectively, whereas the other two recombinant strains, CMH-S059-15 and CMH-S062-15, displayed recombination breakpoints at nucleotide positions 2612 and 4357 of ORF1a and ORF1b, respectively. This is the first study to reveal nearly full-length genome sequences of HAstV recombinant strains with a novel recombination pattern of ORF1a-ORF1b-ORF2 genotypes. This finding may be useful as a guideline for identifying other recombinant HAstV strains in other geographical regions and may provide a better understanding of their genetic diversity, as well as basic knowledge regarding virus evolution. IMPORTANCE Recombination is one of the mechanisms that plays a crucial role in the genetic diversity and evolution of HAstV. We wished to investigate the emergence of HAstV recombinant strains and to analyze the whole-genome sequences of the putative HAstV recombinant strains detected in pediatric patients with acute gastroenteritis in 2011 to 2020. We reported 3 novel intergenotype recombinant strains of HAstV5-HAstV8-HAstV1 at the ORF1a-ORF1b-ORF2 regions of the HAstV genome. The hot spots of recombination occur frequently near the ORF1a-ORF1b and ORF1b-ORF2 junctions of the HAstV genome. The findings indicate that intergenotype recombination of HAstV occurs frequently in nature. The emergence of a novel recombinant strain allows the new virus to adapt and successfully escape from the host immune system, eventually emerging as the predominant genotype to infect human populations that lack herd immunity against novel recombinant strains. The virus may cause an outbreak and needs to be monitored continually.
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