Analysis of the effect of PSF on the gene expression profile in neuronal cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE256401 | GEO | 2024/12/19
REPOSITORIES: GEO
Similar Datasets
Project description:Proline- and glutamine-rich (PSF) has been identified as an important driver of aggressive cancers, in which PSF-RNA interactions promotes the expression of numerous oncogenic transcripts by modulating epigenetic and splicing systems. To develop small compounds targeting PSF as next generation therapeutic agents for hormone therapy refractory cancers, we performed small molecule library screen and identified the compound designated as No.10-3 as a potent PSF inhibitor. We further describe another small molecule C-30, an improved analog of No.10-3. PSF inhibits p53 epression in prostate cancer cells by epigenetic regulation. We then performed ChIP-seq analysis to determined PSF and p53 binding regions.
2024-09-01 | GSE244040 | GEO
Project description:We sought to identify the transcripts that responded to changes in cellular SFPQ/PSF (polypyrimidine tract-binding protein (PTB)-associated splicing factor) protein levels by expression profile analysis of PSF knockdown cells. We constructed clonal HeLa cell lines stably expressing small hairpin RNAs (shRNA) targeted to various regions within the PSF CDS. For microarray studies, we chose two clones (#s 1_1 and 3_1) harboring independently targeted shRNAs that showed ~50% reduction of the endogenous PSF protein. As controls, we used two independent clones harboring a non-targeting shRNA (#s 6_2 and 6_4). Microarray analysis of total cellular RNA identified the transcripts that were reproducibly upregulated (>1.5 fold, n=284) and downregulated (< 0.66 fold, n=121) in both independent knockdown cell lines, and hence were likely enriched in the nonrandomly responding species. We next studied the effects of PSF depletion on particular gene categories. Analysis of the transcripts with unique RefSeq identifiers (n=15805) using PANTHER tools at http://www.pantherdb.org (Molecular Function) revealed significant nonrandom responses of transcripts encoding ribosomal proteins (RP) (downregulation, n=150, P=2.9E-04), while other subgroups exhibited higher P-values. We wondered whether the nonrandomly affected transcripts shared nucleotide sequence features that might account for their response to PSF depletion. To extract such features, we analyzed the mRNAs representing the top up- and downregulated species (n=100 each) as well as the “ribosomal protein” category retrieved from PANTHER database (n=150) for the presence of shared sequence motifs, by using Gibbs motif sampling and dscan software at http://bayesweb.wadsworth.org/gibbs/gibbs.html. The Gibbs sampling returned very similar shared signatures for the up- and downregulated species; and a very similar signature (motif #3) was elicited from the combined up and downregulated datasets (n=200). Notably, a related signature was also elicited from RP sequences. In order to assign unbiased probabilities to the nonrandomness of motif occurrence, we used nucleotide frequency matrices representing motif #3 and dscan utility to calculate the hit scores in the up and downregulated mRNAs. As a control, the same procedure was performed on samplings (n=100) randomly extracted from human EST sequence databases, and the hit scores were evaluated using the Mann-Whitney test. We found that the random samplings featured only low scores, while the PSF-repressed and, to even greater extent, the PSF-activated samplings exhibited significantly higher scores (P=0.01 and P=0.0001, respectively; α=0.05), and similar P-values were obtained when using different control samplings. These data revealed a correlation between PSF-responsiveness and high occurrence of a particular sequence signature, and suggested that the presence of such sequences could contribute to the response. Because PSF can directly bind mRNA in vivo, it was plausible that it recognized the motifs directly, as part of mRNA. Indeed, comparison of motif #3 to the direct PSF-binding sites in pre-mRNA revealed a similarity that included a common UGNAGC signature, whereas the SELEX-derived PSF aptamers shared the core GYYG signature. In addition, the motif #3 also exhibited, albeit to a different extent, direct repeats of a trinucleotide CUG that were not found in the CLIP and SELEX signatures. Since such sequences have not been previously noted in PSF-binding RNA, their significance was not clear. However, the pre-mRNA CLIPs were nonrandomly enriched in CUG‘s constituent dinucleotides CU and UG, possibly reflecting a shared recognition determinant. In summary, our results showed that PSF regulates specific subsets of human genes, and suggested that PSF-mRNA recognition could contribute to the regulation.
2008-12-09 | GSE13857 | GEO
Project description:Recent transcriptome analysis indicates that >90% of human genes undergoes alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now revealed that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells.
2009-12-24 | GSE19323 | GEO
Project description:Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. We identified androgen-regulated long non-coding RNA, CTBP1-AS, located in the antisese region of CTBP1 gene. CTBP1-AS activate AR signaling by epigenetically repress AR-associated cofactors such as CTBP1 by interactign with RNA-binding protein PSF and recruiting HDAC complex to the target promoters. In order investigated the PSF target genes, we performed ChIP-seq analysis of PSF binding sites in prostate cancer cell line, LNCaP cells. We identified androgen dependent PSF binding regions in prostate cancer cell genome. We observed PSF bindings around the promoters of androgen repressed genes such as CTBP1, p53 and SMAD3. ChIP-sequence analysis of PSF binding sites in prostate cancer cells
2014-01-01 | E-GEOD-45124 | biostudies-arrayexpress
Project description:Recent transcriptome analysis indicates that >90% of human genes undergoes alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now revealed that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells. Examination of PTB-RNA binding in Hela cells using CLIP-seq (Cross-Linking ImmunoPrecipitation coupled with high-throughput sequencing) method. Peaks: The four alignment files (linked as supplementary files on Sample records) were combined together for peak finding, as we found that most of the monomeric and dimeric tags are similarly distributed in the genome with high pearson correlation coefficient. The method to detect the peaks above gene-specific randomized background was similar to (Yeo et al., 2009) and described in the paper (Xue et al., 2009).
2009-12-24 | E-GEOD-19323 | biostudies-arrayexpress
Project description:Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. We identified androgen-regulated long non-coding RNA, CTBP1-AS, located in the antisese region of CTBP1 gene. CTBP1-AS activate AR signaling by epigenetically repress AR-associated cofactors such as CTBP1 by interactign with RNA-binding protein PSF and recruiting HDAC complex to the target promoters. In order investigated the PSF target genes, we performed ChIP-seq analysis of PSF binding sites in prostate cancer cell line, LNCaP cells. We identified androgen dependent PSF binding regions in prostate cancer cell genome. We observed PSF bindings around the promoters of androgen repressed genes such as CTBP1, p53 and SMAD3.
2014-01-01 | GSE45124 | GEO
Project description:Drosophila PTB (Polypyrimidine Tract-binding protein dmPTB) regulates dorso-ventral patterning genes in embryos Comparison of wild type (yw genotype) and PTB mutant (heph03429) drosophila embryos
2014-05-10 | E-GEOD-57517 | biostudies-arrayexpress
Project description:Drosophila PTB (Polypyrimidine Tract-binding protein dmPTB) regulates dorso-ventral patterning genes in embryos
2014-05-10 | GSE57517 | GEO
Project description:Prostate cancer is the most common cancer in men and Androgen receptor (AR) downstream signalings promote prostate cancer cell proliferation. We identified androgen-regulated long non-coding RNA, CTBP1-AS, located in the antisese region of CTBP1 gene. CTBP1-AS activate AR signaling by epigenetically repress AR-associated cofactors such as CTBP1 by interactign with RNA-binding protein PSF and recruiting HDAC complex to the target promoters. In order to investigate the CTBP1-AS and PSF function in prostate cancer cells, we performed gene expression in AR-positive prostate cancer cell lines after siPSF or siCTBP1-AS treatment. We also treated cells with vehicle or androgen to analyzed the effects of CTBP1-AS and PSF on AR function. Observation of androgen dependent gene expression changes after treatmet with siRNAs targeting CTBP1-AS and PSF with microarray.
2014-01-01 | E-GEOD-44264 | biostudies-arrayexpress
Project description:Direct conversion of somatic cells into neurons holds great promise for regenerative medicine. However, neuronal conversion is relatively inefficient in human cells compared to mouse cells. It has been unclear what might be the key barriers to reprogramming in human cells. We recently elucidated an RNA program mediated by the polypyrimidine tract binding protein PTB to convert mouse embryonic fibroblasts (MEFs) into functional neurons. In human adult fibroblasts (HAFs), however, we unexpectedly found that invoking the documented PTB–REST–miR-124 loop generates only immature neurons. We now report that the functionality requires sequential inactivation of PTB and the PTB paralog nPTB in HAFs. Inactivation of nPTB triggers another self-enforcing loop essential for neuronal maturation, which comprises nPTB, the transcription factor BRN2, and miR-9. These findings suggest that two separate gatekeepers control neuronal conversion and maturation and consecutively overcoming these gatekeepers enables deterministic reprogramming of HAFs into functional neurons.
2016-04-25 | GSE77523 | GEO