TGF-beta-upregulated Lnc-Nr6a1 acts as a reservoir of miR-181 and mediates assembly of a glycolytic complex [ChIP-seq]

Long noncoding RNAs (lncRNAs) have emerged as key regulators in a wide range of biological processes. The involvement of lncRNAs in epithelial-to-mesenchymal transition (EMT) has been well stablished; however, the role as immediate-early regulators is still unclear. Here, we identified a mouse miRNA-host gene lncRNA (lnc-Nr6a1) early upregulated during EMT. We show that this lncRNA is processed giving rise to abundant polyadenylated isoforms, lnc-Nr6a1 and lnc-Nr6a1-2, and a longer non-polyadenylated microprocessor-driven lnc-pri-miRNAS containing clustered pre-miRNA-181a2 and pre-miRNA-181b2 hairpins. Ectopic expression of lnc-Nr6a1-1/2 isoforms enhance cell migration and invasive capacity of the cells, whereas the expression of isoforms and miR-181a2/b2 confers anoikis resistance. Lnc-Nr6a1 gene deletion results in cells with lower adhesion capacity and reduced glycolytic metabolism which are restored by lnc-Nr6a1-1 isoform expression. We perform identification of direct RNA interacting proteins (iDRIP) to identify proteins interacting directly with lnc-Nr6a1-1 isoform. We define a network of interacting proteins, including glycolytic enzymes, desmosome proteins and chaperone proteins and we demonstrated that lnc-Nr6a1-1 isoform directly binds and acts as a scaffold molecule for the assembly of ENO1, ALDOA, GAPDH, PKM glycolytic enzymes along with LDHA, supporting substrate canneling for efficient glycolysis. Our results unveil a role of lnc-Nr6a1 as a multifunctional lncRNA acting as a backbone for multiprotein complexes formation and as a primary microRNAs reservoir. Binding profiles of Lamin A/C from NMuMG mouse glandular epithelial cells (control and KO cells) were generated by deep sequencing.