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GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data]

ABSTRACT: We have found that histone H2B is GlcNAcylated at residue S112 by O-GlcNAc transferase and that H2B S112 GlcNAcylation fluctuates in response to extracellular glucose level. We have also found that H2B S112 GlcAcylation promotes H2B K120 ubiquitination. To investigate whether these histone modification correlate to transcriptional activation, we performed comprehensive gene expression analysis using Affymetrix GeneChip in HeLa cell cultured with different conditions, i.e. without glucose, with glucose and with FBS. HeLa cells were cultured in DMEM with the following three conditions, 1) DMEM without glucose for 24 hours, 2) DMEM without glucose for 24 hours and followed by treatment with 4.5 g/L glucose for another 24 hours, 3) normal culture condition (DMEM with FBS). Total RNA was purified from these cells and each RNA was linearly amplified and hybridized to Affymetrix GeneChip.

ORGANISM(S): Homo sapiens

SUBMITTER: Ryoji Fujiki

PROVIDER: E-GEOD-33050 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data]

Project description:We have found that histone H2B is GlcNAcylated at residue S112 by O-GlcNAc transferase and that H2B S112 GlcNAcylation fluctuates in response to extracellular glucose level. We have also found that H2B S112 GlcAcylation promotes H2B K120 ubiquitination. To investigate whether these histone modification correlate to transcriptional activation, we performed comprehensive gene expression analysis using Affymetrix GeneChip in HeLa cell cultured with different conditions, i.e. without glucose, with glucose and with FBS.

2011-10-27 | GSE33050 | GEO

GlcNAcylation of histone H2B facilitates its monoubiquitination

Project description:This SuperSeries is composed of the following subset Series: GSE33049: GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data] GSE33050: GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data] Refer to individual Series

2011-10-26 | E-GEOD-33051 | biostudies-arrayexpress

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GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data]

Project description:We report that histone GlcNAcylation of H2B S112 is a vital histone modification which facilitates histone monoubiquitination (ub). In a genome-wide analysis, H2B S112 GlcNAcylation sites were observed widely distributed over entire chromosomes including transcribed gene loci, together with co-localization of H2B S112 GlcNAcylation and K120 ub. Examination of H2B S112 GlcNAc and H2B K120 ub in HeLa S3 cells

2011-10-27 | E-GEOD-33049 | biostudies-arrayexpress

RNA-seq of human patient-derived xenograft pancreatic cancer PancA6L cells cultured for 14 days with Galactose versus PancA6L cells cultured for 14 days with Glucose

Project description:The goal of the study was to identify genes and pathways that were altered when human pancreatic ductal adenocarcinoma (PDAC) cancer cells are cultured with different carbon source (Glucose versus Galactose). Primary adherent cultures established from patient-derived xenograft passaged in mice were established (PancA6L). Low passage (< 15) PDX-derived primary PDAC PancA6L cultures were trypsinized and seeded at a concentration of 800,000 cells in p100 plates with RPMI medium supplemented with 10% fetal bovine serum (FBS) and 50 units/mL of penicillin and streptomycin. After 24 h, cells were cultured with either 1) glucose-free DMEM medium (Dulbecco´s Modified Eagle Medium, Thermo Fisher Scientific) supplemented with 5mM glucose (0.9 g/L), 10% FBS, 50 units/mL of penicillin and streptomycin and 1mM of pyruvate [Glucose: OXPHOS-independent conditions] or 2) glucose-free DMEM medium (Thermo Fisher Scientific) supplemented with 5mM galactose (0.9 g/L), 10% FBS, 50 units/mL of penicillin and streptomycin and 1mM of pyruvate [Galactose: OXPHOS-competent enriched conditions]. Sugar concentrations of 5mM were chosen to mimic physiological sugar levels (glucose, 5mM) and to avoid potential biological artifacts mediated by supraphysiological sugar levels. Media for both conditions were changed every day Following 14 days in culture as spheres, Total RNA was isolated by the guanidine thiocyanate (GTC) method using standard protocols. PolyA+ RNA fraction was processed as in Illumina’s ‘‘TruSeq RNA Sample Preparation v2 Protocol’’. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer’s protocols. RNA-seq data sets were analyzed using the tool Nextpresso.

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2019-09-12 | GSE103689 | GEO

Fibroblast secretome proteomic analysis

Project description:LV fibroblasts were isolated from control (day 0), and infarcted regions at day 1, day 3, and day 7 after myocardial infarction (MI). Cells were isolated in DMEM in 10% fetal bovine serum and were seeded into 6-well plates and were allowed to grow to 80% confluence in DMEM supplemented with 10% fetal bovine serum (FBS). Cells were serum starved (DMEM + 0.1% FBS) for 18 h and then media was changed and secretome was collected after 24 h. The sample sizes are n=3 biological replicates for each time point.

2019-10-25 | PXD011778 | Pride

Lamming PC3 human TMT proteomics

Project description:PC3 cells were grown in 10% DMEM with FBS and treated with vehicle (DMSO), 100 nM rapamycin, or 100 nM DL001 for 24 hours

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RNAPolII CUT&Tag profiles of MDA-MB-231 cell line with repression of CDK genes and PRMT5

Project description:A clonal doxycycline inducible dCas9-KRAB MDA-MB-231 cell line to control repression of CDK genes and PRMT5. On day 1 of the experiment cells were infected with lentiviruses containing the appropriate targeting/NTC sgRNAs driven by the human U6 promoter at an MOI of ~3 for each virus to ensure all cells were transduced. Cells were transduced in DMEM + 10% FBS with the addition of 8 μg/mL polybrene. 16 hours after the time of transduction, media was changed to DMEM +10% FBS. 24 hours after this, the cell culture media was switched to DMEM + 10%FBS containing 2μg/mL puromycin to ensure no uninfected cells remain. 48 hours after this, cell culture media was changed to DMEM + 10%FBS containing 2 μg/mL puromycin and 1 μg/mL doxycycline to induce dCas9-KRAB expression. 48 hours after this, cells were processed for CUT&Tag library prep following the manufacturer's recommendations.

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Thrombospondin-1: A Pro-Atherosclerotic Protein Augmented by Hyperglycemia

Project description:Diabetes is associated with a more aggressive form of atherosclerosis. Thrombospondin-1 (TSP-1), an extracellular matrix protein, is an acute phase reactant that induces vascular smooth muscle (VSMC) migration and proliferation in areas of vascular injury, and is also upregulated in VSMCs exposed to hyperglycemia. We hypothesized that hyperglycemia amplifies the expression of genes induced by TSP-1 in VSMCs. Human aortic VSMCs were cultured in DMEM supplemented with 10 % FBS and 1% antibiotics, cells were used between passages three and five. VSMCs were preincubated in DMEM containing 0.2% FBS with 5 mM glucose (normoglycemia), 25 mM glucose (hyperglycemia), 25 mM mannose (osmotic control), TSP-1 (20µg/mL), 25 mM glucose + TSP-1 (20µg/mL) or 25 mM mannose + TSP-1 (20µg/mL). Data analysis revealed that TSP-1 stimulates gene expression relevant to the pathogenesis of atherosclerosis and diabetic vascular disease.

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