Computational prediction of HOTAIR binding to DNA

In Kalwa et al, 2016, we have applied for the first time the “Triplex Domain Finder” (TDF) to analyse DNA regions potentially regulated by HOTAIR, i.e. peaks of ChIRP-Seq experiments or regions with DNA methylation changes after siHOTAIR. TDF not only detected regions in HOTAIR potentially forming triple helices as we could detect target DNA regions in the promoter of PCDH7 and HOXB2. These triple helices were verified in vitro and are the first evidence HOTAIR target particular promoters on a sequence specific manner.