Coordinated regulation by lncRNAs results in tight lncRNA–target couplings [ChIRP-Seq]

The determination of long non-coding RNA (lncRNA) function is a major challenge in RNA biology with applications to basic, translational, and medical research. Our efforts to improve the accuracy of lncRNA-target inference identified lncRNAs that coordinately regulate both the transcriptional and post-transcriptional processing of their targets. Namely, these lncRNAs may regulate the transcription of their target and chaperone the resulting message until its translation, leading to tightly coupled lncRNA and target abundance. Our analysis suggested that hundreds of cancer genes are coordinately and tightly regulated by lncRNAs and that this unexplored regulatory paradigm may propagate the effects of non-coding alterations to effectively dysregulate gene expression programs. As a proof-of-principle we studied the regulation of DICER1—a cancer gene that controls microRNA biogenesis—by the lncRNA ZFAS1, showing that ZFAS1 activates DICER1 transcription and blocks its post-transcriptional repression to phenomimic and regulate DICER1 and its target microRNAs. To identify ZFAS1-bound DNA regions (RNA-DNA interactions), we performed Chromatin Isolation by RNA Purification followed by DNA sequencing (ChIRP-Seq) in two cell lines, ECC-1 and NCI-H460. For each cell line, we generated two datasets: an input control and a ZFAS1 pulldown. We then identified DNA regions enriched in the ZFAS1 pulldown relative to the input control. These enriched regions were processed and output as standard narrowPeak format files.