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Homo sapiens

ABSTRACT: Episomal S/MAR-based replicons do not alter expression profile of host genome

PROVIDER: PRJNA382731 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5445378.fastq.gz	Fastqsanger.gz
	SRR5445379.fastq.gz	Fastqsanger.gz

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Similar Datasets

Homo sapiens

Project description:Episomal S/MAR-based replicons do not alter expression profile of host genome

| PRJNA383105 | ENA

Episomal S/MAR-based replicons do not alter expression profile of host genome

Project description:Methods: mRNA profiles of untransfected HeLa cells (wild-type; wt) were compared with mRNA profiles of HeLa cells stably maintaining an S/MAR-based episome. Results: We here report for the first time that episomally maintained S/MAR-based vectors do not alter gene expression profile of the host cell's genome. No global changes in gene expression in episome maintaining cells, compared to non-transfected cells could be observed. To identify differentially expressed genes, false discovery rate (FDR; q-value) cut off was set to 0.01. Significantly differentially expressed genes with q<0.01 and an absolute fold-change of 2 were not detected. For verification, we chose five genes with high fold-change and low q-values (q<0.05) and compared expression levels between untransfected HeLa and HeLa stably maintaining an S/MAR-based within three replicates in qPCR. Conclusions: S/MAR-based replicons used in this study do not code for viral proteins but tend to co-localise with promoter sequences and transcription start sites. Recent observations that cooperatively transcribed promoters can influence each other raise concerns that S/MAR-based replicons have the potential to alter endogenous gene expression. Therefore, we compared the transcriptome of untransfected HeLa cells with HeLa cells stably maintaining an S/MAR-based episome. Setting the FDR to <0.01, we found no significantly differentially expressed genes. This finding is of utmost importance for potential gene therapeutic application of S/MAR-based replicons.

2017-09-18 | GSE97725 | GEO

Episomal S/MAR-based replicons do not alter expression profile of host genome

Project description:Methods: Autonomously replicating vectors represent a simple and versatile model system for genetic modifications, but their localisation in the nucleus is largely unknown. Using circular chromosome conformation capture we mapped genomic contact sites of S/MAR-based replicons in HeLa cells. The influence of cis-active sequences on genomic localisation was assessed using replicons containing either an insulator sequence or an intron Results: While the original and the insulator-containing replicons displayed distinct contact sites, the intron-containing replicon showed a rather broad genomic contact pattern. Our results indicate a preference for certain chromatin structures and a rather non-dynamic behaviour during mitosis. Independent of inserted cis-active elements established vector molecules reside preferentially within actively transcribed regions, especially within promoter sequences and transcription start sites. Conclusions: S/MAR-based episomal replicons have a limited number of preferential contact sites and seem to be fairly non-dynamic during mitosis. We show that cis-acting elements do have an impact on the chormosomal localisation of episomal replicons, even though the epigenetic signatue of these contact sites are similar. Independently of the inserted cis-acting element, these contact sites are preferentially located within actively transcribed regions, especially promoter sites. Knowledge of preferred contact sites of exogenous DNA, e.g. viral or non-viral episomes, contribute to our understanding of episome behaviour in the nucleus and can be used for vector improvement and guiding of DNA sequences to specific subnuclear sites.

2017-09-18 | GSE97858 | GEO

Analysis of gene expression of hESCs upon genetic modification with EBNA and S/MAR episomal vectors

Project description:Analysis of the episomal backbone's influence on gene expression. The first hypothesis tested in the present study is that the episomal EBNA vectors, which rely on the EBNA-1 oncoprotein for episomal maintenance, have a greater influence on the cells' expression profiles than S/MAR vectors. The second hypothesis tested was that when bacterial sequences are removed from the episomal vector backbone, the gene disturbance is minimal.

2021-12-05 | GSE142299 | GEO

Homo sapiens whole blood.

Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.

2019-07-31 | GSE114179 | GEO

Homo sapiens immortalized MSCs: 3A6

Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.

2010-09-25 | GSE24338 | GEO

Crystal structure of Homo sapiens kynureninase.

Project description: Not available

| S-EPMC2531291 | biostudies-literature

The evolution of Homo sapiens denisova and Homo sapiens neanderthalensis miRNA targeting genes in the prenatal and postnatal brain.

Project description: Not available

| S-EPMC4686780 | biostudies-literature

Selection of Phototransduction Genes in Homo sapiens.

Project description: Not available

| S-EPMC3743458 | biostudies-literature

Homo sapiens MSCs: Normoxia vs. Hypoxia

Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression.

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