Gene expression profile of B55a/PPP2R2A knocked-down Parkin-expressing HeLa cells
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PROVIDER: PRJNA1314588 | ENA |
REPOSITORIES: ENA
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Project description:Or study identified the PP2A-B55a/PPP2R2A Ser-Thr phosphatase as a regulator of Parkin-dependent mitophagy and mitochondrial biogenesis. HeLa cells expressing Parkin and knocked-down for B55a/PPP2R2A induce a lysosome- and mitochondria-related transcriptional programmes down-stream TFEB and PGC-1a transcription factor activation.
2025-09-07 | GSE307113 | GEO
Project description:Transcriptional elongation factor Elongin A exhibits an activity to repress the temporary pause of RNA polymerase II (RNAPII) on the DNA template, resulting in increase of mRNA synthesis in vitro. However, actual elongation ability of Elongin A in mammalian cells has not been determined yet. To elucidate the practical transcriptional role of mammalian Elongin A in vivo, we carried out whole genome expression analysis using Elongin A knocked-down HeLa cells. Gene expression in Elongin A knocked-down HeLa cells was measured at 2 hours after doxorubicin treatment (1microM).
2013-09-03 | E-GEOD-30432 | biostudies-arrayexpress
Project description:Transcriptional elongation factor Elongin A exhibits an activity to repress the temporary pause of RNA polymerase II (RNAPII) on the DNA template, resulting in increase of mRNA synthesis in vitro. However, actual elongation ability of Elongin A in mammalian cells has not been determined yet. To elucidate the practical transcriptional role of mammalian Elongin A in vivo, we carried out whole genome expression analysis using Elongin A knocked-down HeLa cells.
2013-09-03 | GSE30432 | GEO
Project description:Transcriptome analysis of HeLa cells knocked down for EXT1 or FBXW7 gene expression
| PRJNA574199 | ENA
Project description:Exostosin-1 (EXT1) is an ER-resident glycosyltransferase known to polymerize heparan sulfate chain by sequential addition of glucuronic acid and N-acetylglucosamine molecules. This reaction results in heavily glycosylated proteoglycans (PG) at the plasma membrane, which form cell-type specific complexes and play vital roles in cell-cell and cell-pathogens interactions, cell growth, plasticity and proliferation in the local tissue environment. Different evolutionary forces drive the structure and function of protein glycosylation between the inside and outside of the plasma membrane, and an understanding of how the proteome composition of internal cell membranes is regulated remains a fundamental question in biology. In addition, potential interplays between whole cell proteome and membrane composition are completely unknown. We performed EXT1 knockdown in HeLa cells using shRNA, isolated ER microsomes, performed label-free mass spectrometry, and processed the data with byonic 3.5 software to identify glycoproteins. We identified a total of 1080 proteins, 226 with altered expression, 51 phosphoproteins, 25 O-glycosylated and 97 N-glycosylated membrane proteins. We also performed stable isotope labeling amino acids in cell culture comparing proteomes from HeLa knocked down for EXT1 and control cells. We identified a total 5215 proteins, with 3713 proteins having a SILAC ratio and 396 proteins out of total with a significant p-value (p-value <0.05). Our study demonstrate that the glycosyltransferase enzyme contributes to the heterogeneity of intracellular membrane proteins, particularly proteins controlling ER membrane morphologies in response to different cell types and states.
2021-05-10 | PXD015660 | Pride
Project description:Purpose: The E3 ubiquitin ligase Parkin is a well-characterized regulator of mitochondrial autophagy (mitophagy); however, it is becoming increasingly appreciated to perform additional roles in various compartments of the cell. Our laboratory confirmed the presence of Parkin in the nucleus of various tissues (biochemical fractionations) and cell types (immunofluorescent imaging). Hypoxia-induced nuclear translocation of Parkin occured independent of the mitophagy regulator PINK1, and Parkinson's disease-associated mutants were restricted from the nuclueus. Accordingly, we inserted a nuclear localization sequence (NLS) at the n-terminus of Parkin and overexpressed both NLS Parkin and the wild-type protein in HeLa cells cultured at normoxia and hypoxia. Next-generation RNA-sequencing (RNA-seq) was used to determine the effect of nuclear Parkin on cellular transcription. Methods: mCherry-tagged NLS and wild-type Parkin were overexpressed in HeLa cells. Differential expression analyses were performed on Parkin vs. mCherry control cells and NLS Parkin vs. mCherry control cells at normoxia and following 12hr of hypoxia (n=3/group/condition). Paired-end sequencing was performed using the HiSeq4000. FastQC v0.11.3 was used for quality control, Trimmomatic v0.36 was used to trim reads which were aligned to the human genome (GRCh37.p13) using the STAR aligner v2.5.3a. Read quantification was performed with RSEM v 1.3.0 and the Gencode release 19. The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis. Results: During normoxia, Parkin had no effect on basal transcription; however, overexpression of NLS Parkin was associated with 168 differentially expressed genes (DEGs: fold-change </= 1.5, FDR < 0.05) relative to mCherry control cells. Following hypoxia, the transcriptome associated with the overexpression of wild-type Parkin more closely resembled that of NLS Parkin. Along these lines, Parkin overexpression during hypoxia coincided with a total of 158 DEGs, 37% of which were shared with NLS Parkin. Overlapping and shared DEGs among Parkin and NLS Parkin were implicated in cellular metabolism, HIF1 signaling and survival. Our follow up co-immunoprecipitation and real-time quantitative PCR studies demonstrated that Parkin interacts with the Estrogen Related Receptor Alpha (ERRa) to promote the induction of its downstream target genes. Conclusions: Nuclear translocation of Parkin is a novel means by which this cytoprotective protein contributes to cellular homeostasis and especially critical during hypoxia.
2019-11-06 | GSE139989 | GEO
Project description:RNA-seq analysis about MuERVL knocked down samples
| PRJNA449389 | ENA
Project description:Epigenome analysis of ALKBH5 knocked down HCT116 cell
| PRJNA786900 | ENA
Project description:Gene expression by TRPS1 knocked down in T47D
| PRJNA408130 | ENA
Project description:Epigenome analysis of HDAC1 stably knocked down HCT116 cells and HCT116 cells stably expressing UHRF1 mutant
| PRJNA637512 | ENA