Long noncoding RNA-dependent control of Myc transcriptional bursting [HiC]

Genes are transcribed in short periods of activity, called bursts. Bursts are initiated by enhancer-promoter contacts and dynamically controlled by the levels of enhancer- and promoter-produced RNAs through a negative feedback mechanism. Here, by direct visualization of nascent transcripts, we show that chromatin-associated long noncoding RNAs (lncRNAs) contribute to the regulation of transcriptional bursting. We find that production of Pvt1 raises the baseline of RNA concentration in the locus of the Myc proto-oncogene and acts locally and in a dose-dependent manner to decrease the duration of Myc bursting. Premature termination of Pvt1 led to higher Myc expression and transcriptional activities, resulting in increased cellular proliferation and advanced tumor development in autochthonous models of lung cancer. These findings point to a critical lncRNA-mediated mechanism for Myc regulation and suggest a potentially widespread role for lncRNAs in fine-tuning gene expression through local control of transcriptional bursting. Primary Pvt1+/+ and Pvt1aP/P MEFs were isolated from littermate E13.5 MEFs and cultured in DMEM supplemented with 15% FBS, Pen/Strep, L-glutamine, NEAA, and b-ME. Samples were harvested in two biological replicates from two independent littermate pairs. For RNA-seq, total RNA was isolated using the Qiagen RNeasy Kit and submitted for library preparation and sequencing at the Yale Center for Genome Analysis (YCGA). For ATAC-seq and Hi-C, cryopreserved cells were submitted for library prepation and sequencing at YCGA.