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Unknown,Transcriptomics,Genomics,Proteomics

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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

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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

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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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Lamming PC3 human TMT proteomics

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