HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex

DNA:DNA:RNA triplexes that are formed through Hoogsteen base-pairing of the RNA in the major groove of the DNA duplex have been observed in vitro, but the extent to which these interactions occur in cells and how they impact cellular functions remains elusive. Using a combination of bioinformatic techniques, RNA/DNA pulldown and biophysical studies, we set out to identify functionally important DNA:DNA:RNA triplex-forming long non-coding RNAs (lncRNA) in human endothelial cells. The lncRNA HIF1 alpha-AS1 was retrieved as a top hit. Endogenous HIF1 alpha-AS1 reduces the expression of numerous genes, including EPH Receptor A2 and Adrenomedullin through DNA:DNA:RNA triplex formation by acting as an adapter for the repressive human silencing hub complex (HUSH). Moreover, the oxygen-sensitive HIF1 alpha-AS1 is down-regulated in pulmonary hypertension and loss-of-function approaches not only result in gene de-repression but also enhance angiogenic capacity. As exemplified here with HIF1 alpha-AS1, DNA:DNA:RNA triplex formation is a functionally important mechanism of trans-acting gene expression control. Using a composite bioinformatics approach, the DNA:DNA:RNA triplex-forming lncRNAs HIF1 alpha-AS1 was identified in human endothelial cells which recruits an epigenetic silencing complex to limit expression of triplex target genes.

Automated summary

Using bioinformatic techniques and biophysical studies, we identified a functionally important DNA:DNA:RNA triplex-forming lncRNA HIF1 alpha-AS1 in human endothelial cells, which reduces the expression of multiple genes by inducing triplex formation as an adapter. Additionally, we found that HIF1 alpha-AS1 is down-regulated in pulmonary hypertension and loss-of-function enhances gene de-repression and angiogenic capacity.