Temporal transcriptomics identifies trans-regulation by multiple lncRNAs in human iPSCs

Some long noncoding RNAs (lncRNAs) are known to regulate gene expression. However, the underlying temporal dynamics of lncRNAs influencing gene and epigenetic regulation, as well as mechanisms of lncRNA regulation in trans, are less understood. To investigate this, we genetically engineer 17 doxycycline-inducible lncRNA transgenes for ectopic expression at the H11 safe harbor locus in human pluripotent stem cells (hiPSCs), and we generate high-density temporal RNA-seq and ATAC-seq profiles. Most lncRNA transgenes are induced at 2 h and maintain expression through the 96 h time course. Surprisingly, when we seek to identify gene expression changes owing to the lncRNAs, we find that the global transcriptional landscape is dominated by a strong systemic response triggered by doxycycline exposure. We rigorously define this cohort of genes as a doxycycline-responsive gene signature (DRGS). The DRGS is also present in at least 28 public data sets from dox-inducible transgene studies involving diverse cell types. Next, we determine which lncRNAs exhibit trans-regulatory events. We identify DANCR, FENDRR, LINC00667, LINC00847, LNCPRESS1, and LNCPNKY as lncRNAs that regulate specific transcript expression in trans The downstream target genes encode 53 mRNAs and 10 lncRNAs. None of the target lncRNAs alter gene expression proximal to their own loci (i.e., triggering secondary cis-effects). Surprisingly, the target genes of LINC00847 (transcribed from Chromosome 22) are substantially enriched on Chromosome 19, with a preponderance of target genes encoding RNA metabolism and RNA splicing factors. Collectively, our study provides a resource to discern artifacts in the doxycycline-inducible system and identifies temporally regulated targets of six lncRNAs for future mechanistic studies.