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Sumoylation-deficient bone marrow derived dendritic cells transcriptomic analysis after LPS stimulation

ABSTRACT: Bone marrow derived dendritic cells were generated from Ubc9[fl;-] and Ubc9[+/+] mice. After in vitro derivation in the presence of GM-CSF, dendritic cells were treated with tamoxifen for four days to cause CreERT2 activation, and induce Ubc9 floxed allele deletion. This allowed comparative transcriptomic analysis of Ubc9[+/+] and Ubc9[-/-] dendritic cells unstimulated or stimulated with 10ng/ml LPS for one hour and six hours.

ORGANISM(S): Mus musculus

PROVIDER: GSE66178 | GEO | 2015/12/14

SECONDARY ACCESSION(S): PRJNA276071

REPOSITORIES: GEO

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Sumoylation-deficient bone marrow derived dendritic cells transcriptomic analysis after LPS stimulation

Project description:Bone marrow derived dendritic cells were generated from Ubc9[fl;-] and Ubc9[+/+] mice. After in vitro derivation in the presence of GM-CSF, dendritic cells were treated with tamoxifen for four days to cause CreERT2 activation, and induce Ubc9 floxed allele deletion. This allowed comparative transcriptomic analysis of Ubc9[+/+] and Ubc9[-/-] dendritic cells unstimulated or stimulated with 10ng/ml LPS for one hour and six hours. Three biological replicates of each conditions were used. Analyzed bone marrow derived dendritic cells were Ubc9 WT or Ubc9 KO. Cells were left unstimulated or stimulated with LPS 10 ng/ml for one hour and six hours.

2015-12-14 | E-GEOD-66178 | biostudies-arrayexpress

H3K4me3 chromatin profiling in SUMOylation-competent and -deficient bone marrow derived dendritic cells unstimulated or stimulated with LPS

Project description:Purpose: To determine H3K4me3 chromatin profile in UBC9WT and UBC9KO BMDC before and after LPS stimulation. Methods: H3K4me3 chromatin profile was determined by sequencing UBC9 WT and UBC9 KO BMDC chromatin immunoprecipitated with antibody specific for H3K4me3. Results: We show differential chromatin profile for H3K4me3 on the ifnb1 locus between UBC9 KO cells and UBC9 WT. Conclusions: Loss of SUMOylation causes a deregulation of ifnb1 transcription activation mark. A study of H3K4me3 chromatin profile in UBC9 WT and UBC9 KO Bone Marrow derived Dendritic Cells.

2015-12-14 | E-GEOD-66338 | biostudies-arrayexpress

SUMO safeguards somatic and pluripotent cell identities by enforcing distinct chromatin states [SUMO-ChIP-seq]

Project description:Mouse embryonic fibroblasts (MEFs) were generated from Ubc9fl/- and Ubc9+/+ embryos (E13.5). MEFs were treated with tamoxifen for six days to cause CreERT2 activation, and induce Ubc9 floxed allele deletion. We determined the ChIP-seq profiles of SUMO-1 and SUMO-2 using chromatin of wild-type MEFs Ubc9+/+ and of the corresponding Ubc9 KO MEFs which are entirely depleted for sumoylation. The analysis revealed the nearly complete absence of genome-wide binding of SUMO-1 and SUMO-2 in Ubc9-/- MEFs, attesting for antibody specificities.

2018-10-24 | GSE115842 | GEO

H3K4me3 chromatin profiling in SUMOylation-competent and -deficient bone marrow derived dendritic cells unstimulated or stimulated with LPS

2015-12-14 | GSE66338 | GEO

Kinetics of LPS induction in wt and Cop1-ko BMDMs

Project description:Bone marrow was extracted from mice that are COP1-wt Rosa26-CreERT2 or COP1-floxed Rosa26-CreERT2 BMDMs were obtained by culturing bone marrow precursors in media containing 20% of supernatant from L929 cells. At day 4 of differentiation 4-OHT was added at 1uM to induce deletion of COP1 in BMDMs derived from COP1-floxed mice. At day 7 of differentiation, BMDMs were treated with 100 ng/ml of LPS or not. BMDMs were directly harvested in lysis buffer (from Qiagen RNeasy mini kit) at different time points (0h, 2.5h, 2.5h, 4h, 6h, 9h and 13h) following LPS stimulation. Three BMDMs preparations per group: G1: BMDMs from COP1-wt mice (expressing the wt allele of COP1) CRE positive. G2: BMDMs from COP1-floxed mice (expressing the floxed allele of COP1) CRE positive

2018-10-03 | GSE114762 | GEO

SUMOylation promotes survival and integration of neural stem cell grafts in stroke

Project description:In this study we sought to determine the effect of overexpressing the SUMOylation E2 conjugase Ubc9 on the response of murine Neural Stem Cells (NSCs) to oxygen-glucose-deprivation and restoration of oxygen/glucose (OGD/ROG). We established stably-expandable lines of NSCs from the subventricular zones (SVZ) of adult wild-type mice (WT NSCs) and Ubc9-overexpressing mice (Ubc9 NSCs) and profiled their transcriptional changes in response to OGD/ROG as well as in response to differentiation.

2019-04-11 | E-MTAB-7428 | biostudies-arrayexpress

Is transthyretin a regulator of Ubc9 SUMOylation?

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

Gene expression profile of GM-CSF derived bone marrow dendritic cell subsets after LPS stimulation

Project description:GM-CSF derived bone marrow cultures contain several subsets of CD11c+MHCII+ mononuclear phagocytes Using Affymetrix microarrays we compared gene expression of the different mononuclear phagocytes within the bone marrow culture. The different populations are left unstimulated or are stimulated with LPS

2015-09-01 | GSE62746 | GEO

Protein SUMOylation is required for regulatory T cell expansion and function

Project description:Foxp3-expressing regulatory T (Treg) cells are essential regulators in the immune system; molecular mechanisms underlying Treg cell expansion and function are still not well understood. SUMOylation is an important post-translational modification characterized by covalent attachment of SUMO moieties to lysine within proteins. UBC9 is the only E2 conjugation enzyme involved in this process and loss of UBC9 completely impairs the SUMOylation pathway. Here we report that selective deletion of Ubc9 within the Treg cell lineage resulted in fatal early-onset autoimmunity as the Foxp3 mutant mice. Ubc9-deficient Treg cells exhibited severe defects in TCR-driven homeostatic proliferation, accompanied by impaired activation and compromised suppressor function. Importantly, TCR-enhanced SUMOylation of IRF4, a critical regulator of Treg cell function downstream of TCR signals, regulates its stability in Treg cells. Our data thus have demonstrated an essential role of SUMOylation in the expansion and function of Treg cells.

2016-05-31 | GSE82031 | GEO

Is transthyretin a regulator of Ubc9 SUMOylation?

2017-03-29 | MSV000080754 | MassIVE

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