A 36-base hairpin within lncRNA DRAIC, which is modulated by alternative splicing, interacts with the IKKα coiled-coil domain and inhibits NF-κB and tumor cell phenotypes

A tumor-suppressive long-noncoding RNA (lncRNA) DRAIC (downregulated RNAin cancers) inhibits NF-κB activity and physically interacts with IKKα, a kinase component of the IKK complex, in several cancer types. Here we explore the precise molecular mechanism involved in this interaction and suppression. Using SHAPE-MaP, we identified a 36-nucleotide hairpin (A + B) within DRAIC that is necessary and sufficient for its anti-oncogenic function. RNA immunoprecipitation (RIP) and Electrophoretic mobility shift assays (EMSA) confirmed that this hairpin physically interacts with the coiled coil domain of IKKα. A + B RNA has a high-binding affinity (KD ∼1-7 nM) to IKKα. The binding of A + B disrupts the dimerization of NEMO and IKKα coiled-coil domains, a critical step for IKK action. Consistent with this, A + B inhibits the phosphorylation of the NF-κB inhibitor IκBα and suppresses NF-κB activity. Publicly available tumor RNAseq data revealed that alternative splicing modulates the presence of this critical hairpin: The inclusion of exon 4a (encoding one side of the A + B hairpin) in lung tumors correlates with reduced NF-κB activity. By demonstrating that the A + B hairpin is both necessary and sufficient to inhibit IKK and oncogenic phenotypes, this study underscores the centrality of IKKα interaction and NF-κB inhibition in DRAIC-mediated cancer suppression and indicates that the activity of this lncRNA is regulated by alternative splicing. This study also reveals the first example of a short RNA disrupting coiled-coil dimerization, offering a new approach to disrupt such dimerization in cancer biology.