ChIP-Seq hnRNP E1, Cervical cancer SiHa cells
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ABSTRACT:
PROVIDER: PRJNA838137 | ENA |
REPOSITORIES: ENA
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Project description:Based on the specificity with which the unique KH structural domains of hnRNP E1 bind with RNA/DNA, considering that HPV16 provides RNA/DNA binding sites, we hypothesized that hnRNP E1 may be crucial to HPV16 oncogenes expression and cervical carcinogenesis. Based on the main purpose of this study was to explore the role of hnRNP E1 on the regulation of HPV16 oncogene expression in cervical cancerization, we conducted ChIP-seq in the untreated SiHa cell line.
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Project description:Regulation of gene expression at the post-transcriptional level plays an indispensable role during TGFbeta-induced EMT and metastasis. This regulation involves a transcript-selective translational regulatory pathway in which a ribonucleoprotein (mRNP) complex, consisting of heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) and eukaryotic elongation factor 1A1 (eEF1A1), binds to a 3M-bM-^@M-^Y-UTR regulatory BAT (TGFM-NM-2 activated translation) element and silences translation of Dab2 and ILEI mRNAs, two transcripts which are involved in mediating EMT. TGFbeta activates a kinase cascade terminating in the phosphorylation of hnRNP E1, by isoform-specific stimulation of protein kinase B/Akt2, inducing the release of the mRNP complex from the 3M-bM-^@M-^Y-UTR element, resulting in the reversal of translational silencing and increased expression of Dab2 and ILEI transcripts. We adopted a combinatorial approach involving polysome profiling and RIP-Chip analyses using hnRNP E1 and filtered the array data based on the regulatory mechanism of Dab2 and ILEI. This led to the identification and validation of a cohort of target mRNAs that follow the same pattern of regulation as Dab2 and ILEI. To identify potential target mRNA transcripts that are translationally regulated by hnRNP E1 in a TGF-beta-dependent manner, we adopted a combinatorial approach involving expression profiling analyses and RNA immunoprecipitation analysis (RIP-Chip). We performed a screen using: 1) total mRNA and 2) RNA isolated from monosomal (non-translating) versus polysomal (translating) fractions from TGF-beta-treated (24 h) and non-treated NMuMG cells and from the hnRNP E1 knockdown derivative (E1KD), that undergo constitutive EMT even in the absence of TGF-beta. In addition, we screened for transcripts that selectively interact with hnRNP E1 in NMuMG cells under unstimulated conditions and subsequently lose their temporal association following TGF-beta stimulation. The samples were individually hybridized to Affymetrix GeneChipM-BM-. Mouse Genome 430 2.0 arrays.
2012-08-30 | E-GEOD-40466 | biostudies-arrayexpress
Project description:Regulation of gene expression at the post-transcriptional level plays an indispensable role during TGFbeta-induced EMT and metastasis. This regulation involves a transcript-selective translational regulatory pathway in which a ribonucleoprotein (mRNP) complex, consisting of heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) and eukaryotic elongation factor 1A1 (eEF1A1), binds to a 3’-UTR regulatory BAT (TGFβ activated translation) element and silences translation of Dab2 and ILEI mRNAs, two transcripts which are involved in mediating EMT. TGFbeta activates a kinase cascade terminating in the phosphorylation of hnRNP E1, by isoform-specific stimulation of protein kinase B/Akt2, inducing the release of the mRNP complex from the 3’-UTR element, resulting in the reversal of translational silencing and increased expression of Dab2 and ILEI transcripts. We adopted a combinatorial approach involving polysome profiling and RIP-Chip analyses using hnRNP E1 and filtered the array data based on the regulatory mechanism of Dab2 and ILEI. This led to the identification and validation of a cohort of target mRNAs that follow the same pattern of regulation as Dab2 and ILEI.
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Project description:This study assessed the transcriptional profile of SiHa cells. SiHa is a cervical cancer cell line with integrated HPV16, and was used as a model to study human gene expression in the context of integrated virus. Gene expression in SiHa, calculated by Cufflinks, was scored in windows around the locations of known viral integrations in patients or cell lines to determine if there was an association between gene expression and viral integration. We found that SiHa gene expression was higher near loci of integration for HPV18 vs. HPV16, cervical tissues vs. head and neck cancers, and cervical cancers vs. in vitro integrations. This study provides insight into the factors that may influence where viruses integrate in the human genome.
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Project description:The objective was to identify how cervical cancer cells respond to treatment with the investigational new agent, Sulfur Heteroartoinoid A2 (SHetA2, NSC 726189) by identify proteins that are detected at significantly different levels in SHetA2-treated compared to untreated control cultures. Triplicate cultures of SiHa and C-33 A human cervical cancer cell lines were treated with 10 micromolar SHetA2 or the same volume of dimethylsulfoxide solvent (untreated controls) for 24 hours. Proteins were extracted from the cultures using M-PER (ThermoFisher).
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Project description:Human immortal cervical cell line H8, human cervical cancer cell line SiHa and SiHa transfected with Wnt11-overexpression vector were included in the study. We identified circRNAs differentially expressed between H8 and SiHa or between SiHa and SiHa transfected with OV-Wnt11.
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Project description:circCDKN2B-AS1 is significantly upregulated circRNA in HPV16 positive cervical cancer tissues comprared with both HPV16 positive and HPV16 negative normal cervical tissues.So we chose it for further study.To explore the mRNA expression profiles following circCDKN2B-AS1 knockdown, we performed RNA sequencing analysis in SiHa cells with or without circCDKN2B-AS1 knockdown.We performed RNA sequencing in two pairs of RNA samples of SiHa cells with or without circCDKN2B-AS1 knockdown.
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Project description:The Galectin-7 gene has been found subregulated in several cervical cancer cell lines and in clinical samples. To study the changes in the cell system after the ectopic expression of Galectin-7, we used microarrays to analyze transcriptome of HeLa and SiHa cancer cell line. Cells were transfected with a viral vector with the Galectin-7 gene and negative controls in 3 biological replicates and analyzed to study gene expression changes. Array data from the same study has also been deposited at ArrayExpress under accession number E-MTAB-3307 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3307/) and E-MTAB-3308 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3308/)
2016-03-01 | E-MTAB-3306 | biostudies-arrayexpress