HOTAIR ancient sequence suggests regulatory roles both in cis and trans

HOTAIR is a long noncoding RNA transcribed between HOXC11 and HOXC12 in mammals. The proposed function(s) of HOTAIR lacks consensus as to whether it regulates HoxD cluster genes in trans or HoxC cluster genes in cis. We have identified a 32-nucleotide long conserved noncoding element (CNE) as HOTAIR ancient sequence which has a paralogous copy embedded in HOXD11 noncoding transcript. All vertebrates except teleosts have two copies of CNE and the paralogous CNEs exhibit sequence complementarity in the transcribed orientation. Moreover, paralogous CNEs underwent compensatory mutations suggesting they co-evolved and might hybridize. In both human and mouse, HOTAIR CNE exhibits characteristic features of a poised enhancer in HOTAIR-unexpressed stem cells and of an active enhancer in HOTAIR-expressed cells. Tight correlation between the transcriptional activity of the CNE and HOTAIR promoter suggests HOTAIR transcription is crucial for enhancer activity. In HOTAIR-expressed cells, HOTAIR expression is positively correlated with HOXC11 in cis and negatively correlated with HOXD11 in trans, suggesting a dual modality of HOTAIR ancient sequence.