MRNA-Seq of primary MEFs untreated or treated with auxin for OGT degradation
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB65054 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11829900.fastq.gz | Fastqsanger.gz | |||
| ERR11829901.fastq.gz | Fastqsanger.gz | |||
| ERR11829902.fastq.gz | Fastqsanger.gz | |||
| ERR11829903.fastq.gz | Fastqsanger.gz | |||
| ERR11829904.fastq.gz | Fastqsanger.gz |
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Project description:Primary mouse embryonic fibroblasts (MEFs) were derived from E12.5 embryos from the breeding of male mice which are homozygous for the insertion of the OsTIR1 transgene and females which are heterozygous for the AID knock-in at the endogenous Ogt locus (OgtAID/WT). The resulting MEFs clones were genotyped for sex and presence of the insertions and three pairs of OsTIR1-het;OgtAID/Y and control OsTIR1-het;OgtWT/Y male clones were used for the experiment, each pair coming from a different litter. The experiment consisted in treating each clone with auxin (IAA) for 24 hours, 48 hours or 96 hours and collecting them for single-end mRNA-Seq. One plate per clone was left untreated and also collected for mRNA-Seq.
2024-08-15 | E-MTAB-13298 | biostudies-arrayexpress
Project description:SMART-Seq of untreated and auxin-treated blastocysts for OGT degradation
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Project description:Evaluation of change in gene expression upon degradation of OGT by siRNA
2024-08-31 | E-MTAB-14313 | biostudies-arrayexpress
Project description:Zygotes were recovered from crosses of OgtAID/WT females with OsTIR-homozygous males and cultured ex vivo for 72 hours in standard culture conditions, then the morulae were divided in two groups and one was treated with 250 micromolar auxin for 24 hours. After that, all blastocysts were collected for single embryo mRNA-Seq. The 119 blastocysts in the sequencing library come from five replicates of breeding-treatment-collection. Then, cDNA library was prepared from all of them at the same time and they were all pooled in the same run of a NextSeq500 (75 bp SE mode). Sex and genotype of the embryos was identified in silico from the sequencing data (see paper Methods).
2024-08-15 | E-MTAB-13297 | biostudies-arrayexpress
Project description:Total RNA-seq upon degradation of OGT by siRNA
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Project description:O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is the sole enzyme that catalyzes all O-GlcNAcylation reactions intracellularly. Previous investigations have found that OGT levels oscillate during the cell division process. Specifically, OGT abundance is downregulated during mitosis, but the underlying mechanism is lacking. Here we demonstrate that OGT is ubiquitinated by the ubiquitin E3 ligase, anaphase promoting complex/cyclosome (APC/C)-cell division cycle 20 (Cdc20). We show that APC/CCdc20 interacts with OGT through a conserved destruction box (D-box): Arg-351/Leu-354, the abrogation of which stabilizes OGT. As APC/CCdc20-substrate binding is often preceded by a priming ubiquitination event, we also used mass spectrometry and mapped OGT Lys-352 to be a ubiquitination site, which is a prerequisite for OGT association with APC/C subunits. Interestingly in The Cancer Genome Atlas, R351C is a uterine carcinoma mutant, suggesting that mutations of the D-box are linked with tumorigenesis. Paradoxically, we found that both R351C and the D-box mutants (R351A/L354A) inhibit uterine carcinoma in mouse xenograft models, probably due to impaired cell division and proliferation. In sum, we propose a model where OGT Lys-352 ubiquitination primes its binding with APC/C, and then APC/CCdc20 partners with OGT through the D-box for its mitotic destruction. Our work not only highlights the key mechanism that regulates OGT during the cell cycle, but also reveals the mutual coordination between glycosylation and the cell division machinery.
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Project description:TET2 directly interacts with OGT, which is important for the chromatin association of OGT in vivo. Although this specific interaction does not regulate the enzymatic activity of TET2, it facilitates OGT-dependent histone O-GlcNAcylation. Moreover, OGT associates with TET2 at transcription starting sites (TSS). Down-regulation of TET2 reduces the amount of H2B S112 GlcNAc marks in vivo, which are associated with gene transcription regulation. We found that OGT interacts with TET2 tightly. Using ChIP-seq with specific antibodies, we tested the co-localization of TET2 and OGT in genome level.
2012-12-11 | E-GEOD-41720 | biostudies-arrayexpress
Project description:Ogt catalyzed O-linked N-acetylglucosamine (O-GlcNAcylation, O-GlcNAc) plays an important function in diverse biological processes and diseases. However, the roles of Ogt in regulating neurogenesis remain largely unknown. Here, we show that Ogt deficiency or depletion in adult neural stem cells (aNSCs) leads to the diminishment of aNSCs pool and the aberrant neurogenesis, and consequently impairs cognitive function of adult mice. RNA sequencing reveals that Ogt deficiency alters the transcription of genes relating to cell cycle, neurogenesis, and neuronal development. Mechanistic studies show that Ogt directly interacts with Notch1 and catalyzes the O-GlcNAc modification of Notch TM/ICD fragment. The decreased O-GlcNAc modification of TM/ICD increases the binding of E3 ubiquitin ligase Itch to TM/ICD and promotes its degradation. Itch knockdown rescues neurogenic defects in Ogt-deficient mice. OGT also regulates human cortical neurogenesis in forebrain organoids derived from induced pluripotent stem cells. Our findings reveal the essential roles and mechanisms of Ogt and O-GlcNAc modification in regulating mammalian neurogenesis and cognition.
2020-12-15 | GSE163141 | GEO
Project description:O-GlcNAc transferase (OGT) has been reported to participate in the development of various cancers, but its role in clear cell renal cell carcinoma (ccRCC) remains unclear. In this study, we found that OGT was upregulated in ccRCC compared with paired nontumor renal tissues and was associated with worse survival. Moreover, OGT promoted the proliferation, clone formation, and invasive abilities of VHL-mutated ccRCC cells. Mechanistically, OGT promoted the expression of hypoxia-inducible factor-2α (HIF-2α) (the main driver of the clear cell phenotype) by repressing ubiquitin‒proteasome system-mediated degradation. Interestingly, the OGT/HIF-2α axis confers ccRCC sensitivity to ferroptosis, rendering it vulnerable. In conclusion, OGT promotes the progression of VHL-mutated ccRCC by inhibiting the degradation of HIF-2α. On the other hand, the OGT/HIF-2α axis renders ccRCC vulnerable to ferroptosis, suggesting that ferroptosis inducers are a promising therapy for patients with upregulated OGT and mutated VHL ccRCC.
2023-04-29 | GSE230386 | GEO
Project description:O-linked N-acetylglucosamine (O-GlcNAc ) transferase (OGT) activity is essential for embryonic stem (ES) cell viability and mouse development. OGT is present in both cytoplasm and nucleus of different cell types and mediates serine or threonine glycosylation. The Ogt gene locus resides on the X-chromosome and its activity is required for the viability of male ES cells. Using Ogt conditional knock out (KO) ES cells it was shown the failure of establishing stable KO ES clones further suggesting that Ogt activity is required for ES cell self-renewal and pluripotency. For understanding these changes, we performed global gene expression upon silencing of Ogt mediated by esiRNA in mouse Embryonic Stem Cells. Total RNA was extracted from E14 ES cells (derived from Ola129 mice) transiently transfected with Ogt specific and control esiRNA oligos 48 hrs. post-transfection.
2013-01-06 | E-GEOD-39321 | biostudies-arrayexpress