Transcriptomics

Dataset Information

37

Gene expression analysis to identify long noncoding RNAs deregulated in Myc-driven B cell lymphoma


ABSTRACT: 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. Expression of all known mRNAs and >10 000 lncRNAs was assessed in primary lymphoma tissue with high c-myc levels (Burkitt lymphoma; BL) and low c-myc levels (chronic lymphocytic leukemia; CLL)

ORGANISM(S): Homo sapiens  

SUBMITTER: Gertrud Kortman  Melanie Winkle   Debora de Jong   Jantine Sietzema   Martijn Terpstra   Arjan Diepstra   Klaas Kok   Masoumeh Tayari   Lydia Visser   Anke van den Berg   Joost Kluiver    

PROVIDER: E-GEOD-59479 | ArrayExpress | 2015-02-08

SECONDARY ACCESSION(S): GSE59479PRJNA255407

REPOSITORIES: GEO, ArrayExpress

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