GSE202405
The lncRNA Firre functions as a rapid regulator of transcription [RNA-seq]
There are currently over 16,000 long-noncoding RNAs (lncRNAs) annotated in mammalian genomes, a number on par with protein-coding genes. Numerous studies have demonstrated that lncRNAs can influence gene expression programs but lack the temporal resolution to identify the immediate regulatory events. Thus, even for the most well studied the early and primary targets of lncRNAs remains elusive. Here we describe a multifaceted effort to determine the primary targets of a lncRNA and the underlying temporal dynamics. Our approach combines several genetically defined loss-of and gain-of-function, rescue, and inducible lncRNA models. We further resolved gene regulatory events temporally (30 min to four days). Applying this approach, we find that the lncRNA Firre is an RNA-based transcriptional activator.  These transcriptional activation events are not mediated by the epigenetic regulators PRC2, WDR5, or G9A, nor are they due to the proximal binding of the Firre lncRNA. Instead, Firre activates transcription by increasing chromatin accessibility (approximately 30 min after induction) and activating primary target genes (about an hour later). Overall, this study suggests Firre functions as an RNA-based transcriptional activator. Overall design: RNA-seq time courses in mESCs after inducing the lncRNA Firre using doxycyline in a Firre KO and WT background. Dataset includes a long (96-hour) time course with 5 time points and three replicates and a short timecourse (5.5-hour) with 12 time points and two replicates. Cell lines with an inducible Firre transgene were compared to genetically matched controls to control for the effect of doxycycline on gene expression.