Conserved structural features of the lncRNA HOTAIR in breast cancer cells

One such lncRNA, HOTAIR (Hox transcript antisense intergenic RNA), is a ~2.1 kb mammalian transcript whose overexpression promotes invasion and metastasis in breast cancer. However, the mechanisms by which HOTAIR influences gene regulation in cancer are poorly understood.

To approach this problem through a structural lens, we determined the full-length in cellulo secondary structure of HOTAIR using chemical probing in a metastatic breast cancer cell line. The resulting structure shows that HOTAIR adopts a multidomain architecture and has local structural features unique to the cellular context. Comparison between in vitro and in cellulo chemical probing identifies regions of differential accessibility that may indicate context-dependent molecular interactions or folding.