Oncotarget

Priority Research Papers:

MYC regulates the non-coding transcriptome

Jonathan R. Hart, Thomas C. Roberts, Marc S. Weinberg, Kevin V. Morris, Peter K. Vogt _

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Oncotarget. 2014; 5:12543-12554. https://doi.org/10.18632/oncotarget.3033

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Abstract

Jonathan R. Hart1,*, Thomas C. Roberts1,2,*, Marc S. Weinberg1,3, Kevin V. Morris1,4 and Peter K. Vogt1

1 Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA

2 Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom

3 Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS, South Africa

4 School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW, Australia

* These authors contributed equally to this work

Correspondence:

Peter K. Vogt, email:

Keywords: Transcriptional regulation, RNA-seq, promoter occupancy, bidirectional promoter, nuclear run-on, quantitative PCR

Received: December 23, 2014 Accepted: December 24, 2014 Published: December 30, 2014

Abstract

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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