Journal
ONCOTARGET
Volume 5, Issue 24, Pages 12543-12554Publisher
IMPACT JOURNALS LLC
DOI: 10.18632/oncotarget.3033
Keywords
Transcriptional regulation; RNA-seq; promoter occupancy; bidirectional promoter; nuclear run-on; quantitative PCR
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Funding
- National Institutes of Health [R01 CA153124, R01 CA151574, R01 CA078230]
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Using RNA-seq (RNA sequencing) of ribosome-depleted RNA, we have identified 1,273 lncRNAs (long non-coding RNAs) in P493-6 human B-cells. Of these, 534 are either up-or downregulated in response to MYC overexpression. An increase in MYC occupancy near their TSS (transcription start sites) was observed for MYC-responsive lncRNAs suggesting these are direct MYC targets. MYC binds to the same TSS across several cell lines, but the number of TSS bound depends on cellular MYC levels and increases with higher MYC concentrations. Despite this concordance in promoter binding, a majority of expressed lncRNAs are specific for one cell line, suggesting a determinant role of additional, possibly differentiation-specific factors in the activity of MYC-bound lncRNA promoters. A significant fraction of the lncRNA transcripts lack polyadenylation. The RNA-seq data were confirmed on eight selected lncRNAs by NRO (nuclear run-on) and RT-qPCR (quantitative reverse transcription PCR).
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