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The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output

ABSTRACT: The aim of the experiment was to determine if changes in nuclear phosphoinositides induced by depletion of PIP4K2B impacts on gene expression through a specific phosphoinositide interaction site on TAF3. TAF3 is a core promoter complex protein that contains a PHD finger that interacts with H3K4me3. We determined that The TAF3 PHD finger also interacted with phosphoinositides and generated mutants of TAF3 that were unable to interact with phosphoinositides but still were capable of interacting with H3K4me3. PIP4K2B depletion enhances C2C12 myoblast differentiation. We depleted the endogenous TAF3 from C2C12 myoblast cells and rescued the cells with either a wild type TAF3 or a mutant unable to interact with PI (KK-TAF3). These cells were then maintained as controls or depeleted of PIP4K2B. The cells were then differentiated for two days or were treated wtih a etoposide. We aimed to identify genes that were reguated by PIP4K2B that required an intact phosphoinositide binding site. Triplicate biological samples were analysed for each point after differentiation for three days or etoposide treatment for seven hours.

ORGANISM(S): Mus musculus

SUBMITTER: nullin divecha

PROVIDER: E-GEOD-66353 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output

Project description:The aim of the experiment was to determine if changes in nuclear phosphoinositides induced by depletion of PIP4K2B impacts on gene expression through a specific phosphoinositide interaction site on TAF3. TAF3 is a core promoter complex protein that contains a PHD finger that interacts with H3K4me3. We determined that The TAF3 PHD finger also interacted with phosphoinositides and generated mutants of TAF3 that were unable to interact with phosphoinositides but still were capable of interacting with H3K4me3. PIP4K2B depletion enhances C2C12 myoblast differentiation. We depleted the endogenous TAF3 from C2C12 myoblast cells and rescued the cells with either a wild type TAF3 or a mutant unable to interact with PI (KK-TAF3). These cells were then maintained as controls or depeleted of PIP4K2B. The cells were then differentiated for two days or were treated wtih a etoposide. We aimed to identify genes that were reguated by PIP4K2B that required an intact phosphoinositide binding site.

2015-02-28 | GSE66353 | GEO

Application of recombinant PHD domain instead of anti-H3K4me3 antibody

Project description:Application of recombinant Taf3 PHD domain instead of anti-H3K4me3 antibody in ChIP-seq-like experiments (CIDOP-seq)

2016-05-31 | E-MTAB-4103 | biostudies-arrayexpress

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation [HIT-Seq]

Project description:Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription through interactions with effector proteins that include initiation factor TFIID. We demonstrate that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53 targets. Further analyses show that (i) H3K4me3 enhances p53-dependent transcription by stimulating preinitiation complex (PIC) formation; (ii) H3K4me3, through TAF3 interactions, can act either independently or cooperatively with the TATA box to direct PIC formation and transcription; and (iii) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of p53 in response to genotoxic stress. Our findings indicate a mechanism by which H3K4me3 directs PIC assembly for the rapid induction of specific p53 target genes Examination of genome wide binding sites of TAF3 full length protein vs TAF3 PHD domain alone (Full vs PHD), with or without M880A mutation (WT vs mut) in mouse MEF cells using HITseq method (PNAS 2010, 107:3135-3140, PMID: 20133638)

2013-03-02 | E-GEOD-43540 | biostudies-arrayexpress

Systematic analysis of cis-elements in unstable mRNAs demonstrates that CUGBP1 is a key regulator of mRNA decay in muscle cells

Project description:This SuperSeries is composed of the following subset Series: GSE21233: Expression data from C2C12 mouse myoblast with treatment actinomycin D GSE21235: mRNA immunoprecipitated with CUGBP1 in C2C12 Refer to individual Series

2010-07-08 | E-GEOD-21236 | biostudies-arrayexpress

Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy

Project description:1) 144 intact-mass and top-down raw LC-MS and LC-MS/MS files (myoblast and myotube, 3 biological replicates, 6 fractions, 2 top-down MS/MS technical replicates and 2 MS1-only technical replicates) from 12% GELFrEE fractions of C2C12 mitochondrial extracts. 2) 12 intact-mass raw LC-MS files from unfractionated C2C12 mitochondrial extracts (myoblast and myotube, 3 biological replicates, 2 MS1-only technical replicates). 3) 12 bottom-up raw LC-MS/MS files from unfractionated C2C12 mitochondrial extracts digested with trypsin (myoblast and myotube, 3 biological replicates, 2 technical replicates).

2018-05-16 | MSV000082366 | MassIVE

Mus musculus

Project description:C2C12 myoblast vs myotube

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Transcriptomic profiling of wild-type C2C12 cells and C2C12 cells with Myod1 gene knockout by RNA-sequencing

Project description:C2C12 is a myoblast cell line usually used for study of muscle differentiation. Myod1 is a pro-differentiation factor for myogenesis. We found that CRISPR/Cas9-mediated Myod1 gene knockout in C2C12 cells led to the loss of myoblast identity and gain of neural properties.

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Comprehensive analysis of the proteome, phosphoproteome and N-linked sialylated glycoproteome of C2C12 myoblasts

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2020-11-27 | PXD011334 | Pride

Ethanol effect on myoblast differentiation

Project description:Expression profiling of C2C12 myoblast cells treated with ethanol during differentiation. Ethanol inhibits C2C12 differentiation. Results provide insight into signaling pathways altered by ethanol during differentiation.

2013-04-30 | GSE46492 | GEO

C2C12 myoblast vs myotube

Project description:Comparison of undifferentiated C2C12 myoblast to 4 day differentiated myotubes. Keywords: other

2005-09-07 | GSE3243 | GEO