BRCA1 depletion effect on HeLa cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE22259 | GEO | 2010/06/09
SECONDARY ACCESSION(S): PRJNA128731
REPOSITORIES: GEO
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Project description:Analysis of HeLa cells following depletion of BRCA1 tumor supressor using RNAi against BRCA1. Results provide insight into the molecular mechanisms underlying loss of the BRCA1 function. Six samples (three control samples and three BRCA1 depleted samples) have been analysed. For the control, the samples derived from the HeLa cells treated with RNAi against GFP were used.
2010-06-23 | E-GEOD-22259 | biostudies-arrayexpress
Project description:LncRNAs represent a major transcriptional output of the human genome, but the function of many of these elements is unknown. In this experiment, we have used the ‘CUT&RUN’ technique to quantify the changes in histone mark enrichment across the genome upon depletion of the lncRNA LINC00899 in HeLa cells. LINC00899 is of interest as its depletion results in mitotic delay, suggesting a role in mitotic progression. The CUT&RUN procedure uses antibodies to target a nuclease to the relevant protein binding site, cleaving the surrounding DNA for sequencing and yielding output equivalent to that of ChIP-seq. This experiment contains 2 replicate batches where each batch contains a sample with LINC00899 knocked down by RNA interference (RNAi); a RNAi negative control; a sample with LINC00899 knocked down with locked nucleic acid antisense oligonucleotides (LNA); and a LNA negative control. This was performed using antibodies against H3K4me3, H3K27ac, H3K36me3 and H3K27me3, as well as an IgG (goat-derived anti-rabbit) control. All samples in each batch were generated at the same time. Within each batch, all CUT&RUN experiments with the same knockdown were performed on nuclei obtained from the same cell culture. Independent cell cultures were used for experiments with different knockdown or in different batches.
2019-03-29 | E-MTAB-7419 | biostudies-arrayexpress
Project description:Using RNAi technology, Cyclin F, E2F7+8, or the combination of all proteins in were knocked down HeLa cells. The goal was to study which gene expression programmes are altered by cyclin F depletion in G2/M cells. Furthermore, we had performed experiments suggesting that cyclin F mediates degradation of the atypical E2F repressor proteins E2F7 and E2F8. Therefore we investigated using combinatorial knockdown if additional depletion of E2F7/8 rescues gene expression changes caused by cyclin F. Our resuilts show that cyclin F depletion downregulates expression hundreds of E2F target genes, which could be prevented by additional E2F7/8 depletion.
2019-08-29 | GSE133416 | GEO
Project description:Effect of PHRF1 depletion on gene expression in HeLa cells
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Project description:BRCA1 (breast cancer 1, early onset) mutations confer a high breast and ovarian cancer risk. Most of BRCA1 cancer-predisposing mutations originate truncated proteins, but missense mutations have also been detected in familial breast and ovarian cancer patients. These variants are rare and their role in cancer predisposition is often difficult to ascertain. Our purpose in the present work was to study the molecular mechanisms affected in human cells by two BRCA1 missense variants both located in the second BRCA1 BRCT domain, M1775R and A1789T. These variants were isolated from familial breast cancer patients and their role in the pathogenesis of breast cancer was also investigated by a study previously performed by our group in yeast cells. Here we present a microarray study to compare the expression profiles of HeLa cells transfected with these two variants and HeLa cells transfected with BRCA1 wild type. Data analysis was performed by evaluating three comparisons: M1775R versus wild-type (M1775RvsWT-contrast), A1789T versus wild-type (A1789TvsWT-contrast) and the mutated BRCT domain versus wild-type (MutvsWT-contrast), obtained by considering the two variants as a unique BRCT mutation. We found 173 differentially expressed genes in MutvsWT-contrast, 201 in M1775RvsWT-contrast and 313 in A1789TvsWT-contrast. Our results showed that the considered BRCA1 variants had an impact on cell processes often deregulated in cancerogenesis, such as cell cycle progression and DNA damage response and repair. Thus, our study further supports the putative role in the pathogenesis of cancer of the M1775R and A1789T BRCA1 variants from a molecular point of view.
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Project description:Caveolae-associated protein 3 (cavin3), a putative tumor suppressor protein, is inactivated in most cancers. The molecular basis for its actions remains poorly understood. We characterized the effects on the proteome of cavin3 loss by utilizing genome-edited cells together with label-free quantitative proteomics. These studies revealed a prominent role for cavin3 in DNA repair pathways with downregulation of BRCA1 and the BRCA1 A-complex components. Using cellular and cell-free expression assays, we show a direct interaction between BRCA1 and cavin3. Association of BRCA1 and cavin3 occurs when cavin3 is released from disassembling caveolae by multiple stressors such as UV and mechanical stress. Cavin3-deficient cells were sensitised to PARP inhibition and showed a loss of components of the BRCA1 A-complex associated with UV DNA damage foci. Overexpression and RNAi-depletion strategies in several cancer cell lines revealed that cavin3 sensitized a variety of cancer cells to UV-induced apoptosis. We conclude that cavin3 functions together with BRCA1 in multiple pathways that contribute to tumorigenesis.
2021-06-15 | PXD026724 | Pride
Project description:Long noncoding RNAs (lncRNAs) are a major transcriptional output of the mammalian genome, yet their functions are poorly characterized. In this experiment, we used RNA interference (RNAi) and locked nucleic acid antisense oligonucleotides (LNAs) to deplete the lncRNAs LINC00899 and C1QTNF1-AS1 (C1) in HeLa cells. Both of these lncRNAs are of interest as their depletion results in mitotic delay, suggesting a role in mitotic progression. After depletion of each lncRNA with RNAi or LNAs, we performed high-throughput RNA sequencing and tested for differential expression compared to negative control samples (using control siRNAs or negative control LNAs) to identify downstream regulatory targets of each lncRNA. We generated 3-4 replicates for each condition, spread across multiple batches and experiments. Samples with the same batch number were treated at roughly the same time (within the same month), while the experiment number is nested within batch and refers to cells treated on the same day. Samples were pooled and sequenced across multiple lanes, yielding 8-9 technical replicates per sample.
2019-03-01 | E-MTAB-7432 | biostudies-arrayexpress
Project description:Effect of LINC00899 depletion on histone mark enrichment in HeLa cells
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