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E-GEOD-59477 - Gene expression analysis to identify Myc-regulated long noncoding RNAs in B cells with variable Myc levels

Status
Released on 1 February 2015, last updated on 8 February 2015
Organism
Homo sapiens
Samples (8)
Array (1)
Protocols (7)
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. P493-6: 72h Tet treated (low c-myc levels), t=4h (intermediate c-myc levels), t=24h (high c-myc levels), untreated (steady state c-myc levels) Expression of all known mRNAs and >10 000 lncRNAs was assessed in P493-6 B cells with different c-myc levels
Experiment type
transcription profiling by array 
Contacts
Anke van den Berg, Arjan Diepstra, Debora de Jong, Gertrud Kortman, Jantine Sietzema, Joost Kluiver, Klaas Kok, Lydia Visser, Martijn Terpstra, Masoumeh Tayari, Melanie Winkle
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-59477.idf.txt
Sample and data relationshipE-GEOD-59477.sdrf.txt
Raw data (1)E-GEOD-59477.raw.1.zip
Processed data (1)E-GEOD-59477.processed.1.zip
Array designA-GEOD-18959.adf.txt
Links