UBC9 knockdown in bladder cancer T24 cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE117143 | GEO | 2018/12/25
REPOSITORIES: GEO
Similar Datasets
Project description:UBC9 knockdown in bladder cancer T24 cell lines
| PRJNA481271 | ENA
Project description:Ageing and mutations of transthyretin (TTR), the thyroid hormones and retinol transporting protein lead to amyloidosis by destabilizing the structure of TTR. Because protein structure is regulated through posttranslational modifications, we investigated the Small Ubiquitin-like Modifier (SUMO)ylation of TTR. We chose the widely used Ubc9 fusion-directed SUMOylation system, which is based on a fusion of the SUMOylation substrate of interest with Ubc9, a sole SUMO conjugating enzyme. Surprisingly, despite our presumptions, we found that Ubc9 fused to TTR was SUMOylated at a unique set of lysine residues. Three unknown SUMOylation sites of Ubc9—K154, K18 and K65—were revealed by mass spectrometry (MS). The previously reported SUMOylation at K49 of Ubc9 was also observed. SUMOylation of the lysine residues of TTR fused to Ubc9 was hardly detectable. However, non-fused TTR was SUMOylated via trans-SUMOylation by Ubc9 fused to TTR. Interestingly, mutating the catalytic residue of Ubc9 fused to TTR did not result in complete loss of the SUMOylation signal, suggesting that Ubc9 linked to TTR is directly cross-SUMOylated by the SUMO-activating enzyme E1. Ubc9, TTR or fusion proteins composed of TTR and Ubc9 specifically affected the global SUMOylation of cellular proteins. TTR or Ubc9 alone increased global SUMOylation, whereas TTR and Ubc9 together decreased the amount of high-molecular weight (HMW) SUMO conjugates. Our data suggest that TTR may influence the SUMOylation of Ubc9, thereby altering signalling pathways in the cell.
2016-08-15 | PXD004515 | Pride
Project description:Ageing and mutations of transthyretin (TTR), the thyroid hormones and retinol transporting protein lead to amyloidosis by destabilizing the structure of TTR. Because protein structure is regulated through posttranslational modifications, we investigated the Small Ubiquitin-like Modifier (SUMO)ylation of TTR. We chose the widely used Ubc9 fusion-directed SUMOylation system, which is based on a fusion of the SUMOylation substrate of interest with Ubc9, a sole SUMO conjugating enzyme. Surprisingly, despite our presumptions, we found that Ubc9 fused to TTR was SUMOylated at a unique set of lysine residues. Three unknown SUMOylation sites of Ubc9—K154, K18 and K65—were revealed by mass spectrometry (MS). The previously reported SUMOylation at K49 of Ubc9 was also observed. SUMOylation of the lysine residues of TTR fused to Ubc9 was hardly detectable. However, non-fused TTR was SUMOylated via trans-SUMOylation by Ubc9 fused to TTR. Interestingly, mutating the catalytic residue of Ubc9 fused to TTR did not result in complete loss of the SUMOylation signal, suggesting that Ubc9 linked to TTR is directly cross-SUMOylated by the SUMO-activating enzyme E1. Ubc9, TTR or fusion proteins composed of TTR and Ubc9 specifically affected the global SUMOylation of cellular proteins. TTR or Ubc9 alone increased global SUMOylation, whereas TTR and Ubc9 together decreased the amount of high-molecular weight (HMW) SUMO conjugates. Our data suggest that TTR may influence the SUMOylation of Ubc9, thereby altering signalling pathways in the cell.
2017-03-29 | MSV000080754 | MassIVE
Project description:Most human cancers present hyperactivated sumoylation, and cancer cell lines are usually highly sensitive to the lack of it, supporting potential application of sumoylation chemical inhibitors in cancer therapy. Here, we explored the impact of hyposumoylation (Ubc9 haploinsufficiency) on cancer development in mice using Apc loss-driven intestinal tumorigenesis model. We used microarrays to compare the global program of gene expression in intestinal polyps and normal tissue from mice homozygous (+/+) and heterozygous (+/-) for Ubc9, which encodes the unique SUMO E2-conjugating enzyme. This analysis was performed in the context of a conditional ablation of tumor suppressor Apc all along the crypt-villus axis through expresion of Cre recombinase driven by the intestinal specific promoter Villin
2020-09-14 | GSE146039 | GEO
Project description:The Lgr5+ intestinal stem cell, Paneth and transit-amplifying cell compartment constitute the intestinal crypt which is the constant source of differentiated epithelial cells that replenish the intestinal villi ensuring organ maintenance and regeneration. The Lgr5+ crypt-based columnar (CBC) cells have been identified as the intestinal stem cells (ISCs) and, importantly, as cells-of-origin of intestinal cancer. We used microarrays to detail the global program of gene expression in normal ISCs describing a mild downregulation of the sumoylation (post-translational modification (PTM) of proteins by SUMO) imposed by the loss of one allele of the unique E2-conjugating enzyme (Ubc9) of the pathway.
2020-09-14 | GSE146106 | GEO
Project description:Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. This increase is essential for the survival of aged cells and CR-mediated lifespan extension
2024-04-17 | GSE253055 | GEO
Project description:The reproductive lifespan in mammals is largely determined by the abundance and quality of oocytes residing within the primoridial ovarian follicular pool. Critical oocyte-expressed genes driving ovarian function have been identified, buta role for post-translational modifications, such as SUMOylation of these key factors is not well understood. Oocyte-specific genetic ablation of the sole E2 SUMOylation enzyme, UBC9, cause female sterility. Preantral and antral stage ovarian follicles are depleted by sexual maturity, and loss of the ovarian reserve in early adulthood causes premature ovarian failure, a condition associated with infertility in women. Gene expression changes indicate atered function of multiple POI candidate genes, including the transcription factors, NOBOX and SOHLH1. Together, these studies show that SUMOylation is required in the mammalian oocyte for regulating key genetic determinants of oocyte growth and differentiation.
2019-11-15 | GSE133179 | GEO
Project description:Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. This increase is essential for the survival of aged cells and CR-mediated lifespan extension
2024-04-17 | GSE254981 | GEO
Project description:Many transcription-related proteins are known to be modified by SUMO post-translational modification in yeast, plants, humans and other eukaryotes. We are interested in understanding how cells use sumoylation to regulate transcription of specific genes and globally. To explore this, we carried out ChIP-seq analysis to determine how genomic levels of RNA polymerase II (RNAPII) change when cellular levels of sumoylation are greatly reduced in budding yeast. Compared to wild-type yeast, RNAP occupancy in the sumoylation-deficient ubc9-6 strain was significantly altered for hundreds of genes. Among the genes with the most elevated levels of RNAPII are those involved in translation and ribosome biogenesis, including most ribosomal protein genes. On the other hand, many genes involved in small molecule and amino acid metabolism and biosynthesis showed reduced RNAPII levels in ubc9-6. Exposure of yeast to heat shock is known to cause a widespread change to RNAPII occupancy across the genome. To examine whether cellular sumoylation plays a role in this process, RNAPII ChIP-seq was performed in wild-type and ubc9-6 strains after a brief heat shock. Strikingly, the sumoylation deficient strain showed a far more dramatic redistribution of RNAPII across the genome, with significantly more genes showing a heat-shock induced increase or decrease in RNAPII occupancy. These results imply that cellular sumoylation levels have a significant impact on the regulation of transcription genome-wide, and that normal sumoylation levels are needed to restrain the vast redistribution of RNAPII that occurs in response to heat shock.
2021-09-21 | GSE167424 | GEO
Project description:Transcription related proteins are among the most frequently identified targets of SUMO post-translational modification, but the gene-specific and genome-wide effects of transcription machinery sumoylation are not well-understood. To explore this, we examined whether dramatically reducing cellular sumoylation levels affects the levels of mRNAs in budding yeast. RNA-seq was performed using polyadenylate (polyA)-enriched RNAs from the sumoylation-deficient ubc9-6 strain and its wild-type parent. Indeed, the abundance of hundreds of mRNAs were upregulated or downregulated in the mutant strain, implying that sumoylation has a widespread influence on RNA polymerase II (RNAPII) transcription or mRNA stability. Interestingly, about one third of mRNAs that were significantly upregulated in the ubc9-6 strain encode proteins that are involved in small molecule metabolic processes, suggesting that sumoylation is normally involved in restricting these pathways. As part of our analysis of transcription-related sumoylation, we determined that the large subunit of TFIIF, Tfg1, is a major target of sumoylation among the general transcription factors (GTFs) of RNAPII. To determine whether sumoylation of Tfg1 specifically is involved in regulating mRNA levels, we performed RNA-seq on polyA-enriched RNAs derived from strains expressing wild-type (Tfg1-HA) or sumoylation-deficient (Tfg1-K60,61R-HA) forms of Tfg1. However, with few exceptions, impairing Tfg1 sumoylation had no effect on the mRNA transcriptome. Together, our data demonstrate that gene expression is extensively regulated by sumoylation, but this likely involves the coordinated modification of multiple proteins at multiple levels.
2021-09-21 | GSE167427 | GEO