Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA287548 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2071651.fastq.gz | Fastqsanger.gz | |||
| SRR2071652.fastq.gz | Fastqsanger.gz | |||
| SRR2071653.fastq.gz | Fastqsanger.gz | |||
| SRR2071654.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Scaffold Matrix Attachment Region binding protein 1, SMAR1 has vital role to play as a general repressor of transcription. SMAR1 is known to retard cell cycle progression and delay tumor growth in mice. Further, it forms a ternary complex with p53-Mdm2 and inhibit p53-mediated transcription. Thus, SMAR1 can potentially alter p53 function and orchestrate different set of genes in p53-dependent and p53-independent manner. The present study aims to decipher the potential role of SMAR1 in global transcription regulation and to study role of p53 in the process. Towards this objective, chromatin immunoprecipitation combined Next-generation sequencing (ChIP-Seq) was performed using HCT116 and HCT116 p53-/- cell samples. The α-SMAR1 antibody was used for such ChIP experiments which was already tested by Wastern blot assays and found to be SMAR1 specific. The sequence data generated was then analyzed and the results obtained are (1) Higher genomic occupancy of SMAR1 in HCT116 (wild type) than HCT116 p53-/- (P53 null) data set (2) For peaks within ±5kb of TSS, SMAR1 had the highest predisposition to bind upstream of the TSS in close proximity, i.e., -1 to 0 kb that represents the promoter region of the gene (3) SMAR1 was found to target 5617 genes (unique in Wild type) , 8198 genes (unique in Null) and 1876 genes that were common in both the samples (4) In silico motif search indicated that SMAR1 binds to a dinucleotide T(C/G) repeat sequence (5) Functional Annotation of targets revealed that the predicted target genes are involved in apoptosis, epigenetics, cell cycle, cell signalling, neuronal genes, transcription, metabolism etc. The target also include noncoding RNAs genes such as microRNAs /lincRNAs.
2016-10-13 | GSE70058 | GEO
Project description:The present microarray studies the differential transcription levels of various genes upon overexpression of tumor suppressor protein SMAR1. The results will lead us to potential targets which are either up/downregulated by SMAR1.
2009-08-25 | GSE17795 | GEO
Project description:Maternally Expressed Gene 3 (MEG3) encodes a lncRNA which is suggested to function as a tumor suppressor. MEG3 functions as a tumor suppressor in hepatoma cells, whose action is mediated by interaction with p53 protein to activate p53-mediated transcriptional activity and influence the expression of partial p53 target genes. Total RNA was isolated from hepatoma cells (HepG2 and SK-Hep-1) transfected with either control or MEG3 overexpression/knockdown constructs for global expression analysis.
2015-06-17 | E-GEOD-69916 | biostudies-arrayexpress
Project description:The present microarray studies the differential transcription levels of various genes upon overexpression of tumor suppressor protein SMAR1. The results will lead us to potential targets which are either up/downregulated by SMAR1. Experiment Overall Design: Agilent two-color experiment,Organism: Human ,Slides, Agilent’s Human Microarray G4110B with 22000 features, Labeling kit: Agilents Low input RNA linear amplification Kit Cat # 5184-3523, Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA
2009-09-05 | E-GEOD-17795 | biostudies-arrayexpress
Project description:The tumor suppressor p53 prevents cancer development through regulation of dozens of target genes with diverse biological functions. Numerous p53 target genes have been identified to date, whereas the dynamics and function of the regulatory network centered on p53 have not yet been fully elucidated. To identify novel p53 target genes, we performed RNA sequencing and differential expression analysis on MCF7 cells treated with DMSO or Nutlin-3, a nongenotoxic small molecule that activates p53 through disruption of p53-MDM2 interaction. Among the top 15 differentially expressed genes, we found a potent transcriptional target of p53.
2024-03-26 | GSE254303 | GEO
Project description:Ceramides are important participants of signal transduction, regulating fundamental cellular processes. Here we report the mechanism for activation of p53 tumor suppressor by C16-ceramide. C16-ceramide tightly binds within the p53 DNA binding domain (Kd ~ 60 nM), in close vicinity to the Box V motif. This interaction is highly selective towards the ceramide acyl chain length with its C10 atom being proximal to Ser240 and Ser241. Ceramide binding stabilizes p53 and disrupts its complex with E3 ligase MDM2 leading to the p53 accumulation, nuclear translocation and activation of the downstream targets. This is a novel physiological mechanism of p53 activation, which is fundamentally different from the canonical p53 regulation through protein-protein interactions or post-translational modifications. The discovered mechanism is triggered by serum or folate deprivation implicating it in the cellular response to nutrient/metabolic stress. Our study establishes C16-ceramide as the first natural small molecule activating p53 through the direct binding.
2018-10-16 | PXD010783 | Pride
Project description:WTX encodes a tumor suppressor, frequently inactivated in Wilms tumor, with both plasma membrane and nuclear localization. WTX has been implicated in beta-catenin turnover, but its effect on nuclear proteins is unknown. We report an interaction between WTX and p53, derived from the unexpected observation of WTX, p53 and E1B 55K colocalization within the characteristic cytoplasmic body of adenovirus-transformed kidney cells. In other cells without adenovirus expression, the C-terminal domain of WTX binds to the DNA binding domain of p53, enhances its binding to CBP, and increases CBP/p300-mediated acetylation of p53 at Lys 382. WTX knockdown accelerates CBP/p300 protein turnover and attenuates this modification of p53. In p53-reconstitution experiments, cell cycle arrest, apoptosis, and p53-target gene expression are suppressed by depletion of WTX. Together, these results suggest that WTX modulates p53 function, in part through regulation of its activator CBP/p300. Affymetrix microarray gene expression profiling was performed to identify differentially expressed genes following overexpression of WTX in HEK293 clones after 12 hour induction of WTX
2012-01-01 | E-GEOD-34715 | biostudies-arrayexpress
Project description:Maternally Expressed Gene 3 (MEG3) encodes a lncRNA which is suggested to function as a tumor suppressor. MEG3 functions as a tumor suppressor in hepatoma cells, whose action is mediated by interaction with p53 protein to activate p53-mediated transcriptional activity and influence the expression of partial p53 target genes.
2015-06-17 | GSE69916 | GEO
Project description:WTX encodes a tumor suppressor, frequently inactivated in Wilms tumor, with both plasma membrane and nuclear localization. WTX has been implicated in beta-catenin turnover, but its effect on nuclear proteins is unknown. We report an interaction between WTX and p53, derived from the unexpected observation of WTX, p53 and E1B 55K colocalization within the characteristic cytoplasmic body of adenovirus-transformed kidney cells. In other cells without adenovirus expression, the C-terminal domain of WTX binds to the DNA binding domain of p53, enhances its binding to CBP, and increases CBP/p300-mediated acetylation of p53 at Lys 382. WTX knockdown accelerates CBP/p300 protein turnover and attenuates this modification of p53. In p53-reconstitution experiments, cell cycle arrest, apoptosis, and p53-target gene expression are suppressed by depletion of WTX. Together, these results suggest that WTX modulates p53 function, in part through regulation of its activator CBP/p300.
2012-01-01 | GSE34715 | GEO
Project description:A microRNA component of the p53 tumor suppressor network
| PRJNA100005 | ENA