RUNX2 associated long non-coding RNA characterization

RUNX2 is a lineage-specific transcription factor (TF) known to promote cancer progression. However, the molecular mechanisms that control RUNX2 expression in cancer remain widely unknown. Long non-coding RNAs (lncRNAs) are a novel class of transcripts that do not code for proteins and are often engaged in gene expression regulation. Using the ENCODE annotation data, we identified a previously uncharacterized family of lncRNAs within the RUNX2 locus, that we named RAIN (RUNX2 Associated Intergenic Non-coding RNA). We showed that RAIN comprises 4 major variants that share a common central region but differ at the 5'- and 3'- ends. The longest isoform (l-RAIN) is nuclear and strongly associated with chromatin, suggesting a role of RAIN in gene expression regulation. Expression analysis in cancer cell lines and patient samples demonstrated that RAIN correlates with RUNX2. Furthermore, RAIN silencing resulted in a significant RUNX2 repression demonstrating that this lncRNA is required for the expression of this TF in cancer. We showed that RAIN promotes RUNX2 expression at least through two distinct mechanisms. Interacting with WDR5 and directing its recruitment to the P2 promoter, RAIN modifies its transcriptional activation status, bursting transcription initiation. In parallel, RAIN sequesters NELFe preventing the binding of the NELF complex to the RUNX2 P2 promoter and restraining its inhibitory function on nascent transcripts elongation. Finally, we investigated the RAIN associated transcriptional profile in thyroid cancer showing that beside RUNX2, this lncRNA controls a panel of cancer associated TFs. Overall, our data characterize the function of novel lncRNA and identify an additional layer in the complex RUNX2 regulation in cancer.