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MYC Transactome Mapped by Global Array-based Nuclear Run-on (ANRO)

ABSTRACT: We describe and illustrate the use of a method to measure nascent nuclear gene transcription with an Array-based Nuclear Run-On (ANRO) assay using a commercial microarray platform. ANRO measurements in an inducible c-Myc expressing human P493-6 B cell model reveals time-dependent waves of transcription, with a transactome early after c-Myc induction that does not persist at a late, steady-state phase, when genes that are regulated by c-Myc and E2F predominate.

ORGANISM(S): Homo sapiens

PROVIDER: GSE17109 | GEO | 2010/01/01

SECONDARY ACCESSION(S): PRJNA119793

REPOSITORIES: GEO

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MYC Transactome Mapped by Global Array-based Nuclear Run-on (ANRO - Affymetrix)

Project description:We describe and illustrate the use of a method to measure nascent nuclear gene transcription with an Array-based Nuclear Run-On (ANRO) assay using commercial microarray platforms. ANRO measurements in an inducible c-Myc expressing human P493-6 B cell model was performed following 48 hours with or without MYC gene induction. Samples were prepared from either nuclear run-on or total RNA and were applied to Affymetrix Exon arrays and similarly regulated, full length transcripts were demonstrated from each preparation type.

2010-01-01 | GSE17239 | GEO

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Project description:P493-6 cells are immortalized human peripheral B cells that carry a conditional, tetracycline-regulated myc gene. We present ChIP-seq analysis of key transcritional regulators in P493-6 cells expressing various levels of c-Myc: 0hr (low c-Myc levels), 1hr (intermediate c-Myc levels), 24hr (very high c-Myc levels) and No Tet (steady-state c-Myc levels). Brd4, c-Myc, Max, Med1, RNAPII, and the chromatin modification H3K27Ac were profiled in P493-6 cells

2012-11-14 | E-GEOD-42262 | biostudies-arrayexpress

Chromatin occupancy of key transcriptional regulators in P493-6 cells with various levels of c-Myc expression

2012-11-14 | GSE42262 | GEO

Gene expression analysis in cytoplasmic and nuclear fractions of P493-6 B cells with low c-myc expression to assess long noncoding RNA localization

Project description:Myc is a well known transcription factor with important roles in cell cycle, apoptosis and cellular transformation. Long non-coding (lnc)RNAs have recently emerged as a important class of regulatory RNAs. Here, we show that lncRNAs are an extensive component of the Myc-regulated transcriptional program. Using the P493-6 inducible Myc model we demonstrate that both Myc-induced mRNAs and lncRNAs were significant enriched for Myc binding sites. In contrast to Myc-repressed mRNAs, Myc-repressed lncRNAs were significantly enriched for Myc binding sites. Subcellular localization analysis revealed that Myc-repressed lncRNAs and mRNAs are enriched in the nucleus while Myc-induced lncRNAs and mRNAs are enriched both in the cytoplasm and nucleus. Parallel analysis of differentially expressed lncRNAs and mRNAs identified 105 lncRNA-mRNA pairs that were in close vicinity, indicative for regulation in cis. To support the potential relevance of the Myc-regulated lncRNAs in cellular transformation, we analyzed their expression in primary Myc-high and Myc-low B-cell lymphomas. In total, 54% of the lncRNAs differentially expressed between the lymphoma subsets were identified as Myc-regulated in P493-6 cells. This study is the first to show that lncRNAs are an important factor within the Myc-regulated transcriptional program and indicates a marked difference between Myc-repressed lncRNAs and mRNAs. Arrays: The total, cy3 labeled fraction and the cytoplasmic or nuclear, cy5 labeled fraction was hybridized on the same array. Data was imported and analyzed as a single color array. Expression of all known mRNAs and >10 000 lncRNAs was assessed in P493-6 B cells with low c-myc levels

2015-02-01 | E-GEOD-59478 | biostudies-arrayexpress

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2014-07-07 | E-GEOD-51004 | biostudies-arrayexpress

Ectopic Myc expression

Project description:Ectopic Myc Expression in P493-6 B-cells at three levels: High Myc, Low Myc and No Myc

2010-02-25 | GSE19703 | GEO

MYC Targeted Long Noncoding RNA DANCR Promotes Cancer in Part by Reducing p21 Levels.

Project description:p493 RNA-seq in the MYC on and MYC off conditions

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Gene expression from human B-lymphocytes (P493-6)

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2011-09-18 | E-GEOD-32219 | biostudies-arrayexpress

Ectopic Myc expression

Project description:Ectopic Myc Expression in P493-6 B-cells at three levels: High Myc, Low Myc and No Myc High Myc, Low Myc and No Myc expressions

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