These diverse functional mechanisms summarily indicate that jointly with TFs, lncRNAs are key regulators of protein-coding genes – including those that encode TFs. A prerequisite toward understanding the biology of lncRNAs is their assignment into tractable gene regulatory networks. We previously showed [14] that TFs – in particular, Oct4 and Nanog, which are essential for stem cell pluripotency [15] – bind directly at the promoters or within gene bodies of hundreds of lncRNA genes. ChIP-qPCR validation of TF binding to lncRNA gene promoters has elucidated numerous targets of key TFs, including non-conserved lncRNAs repressed by REST/NRSF in the human DiGeorge Syndrome critical region and in mouse [16]. We have used forward and reverse genetics to validate the regulation of lncRNAs by these TFs, uncovering feedback loops in the network that also use the lncRNAs to regulate these TFs during cell lineage specification [14]. More recently, we have assigned lncRNAs into deterministic regulatory networks, using reverse genetic approaches to show that a primate-specific antisense lncRNA regulates neuronal activity-dependent epileptogenesis in the in vivo human brain [17]. However, despite this progress, a genome-wide understanding of the lncRNA regulatory network – including the characterization of TF/lncRNA interactions – has to date remained elusive.
