There is a growing perception that long non-coding RNAs (lncRNAs) modulate cellular function. In this study, we analyzed the role of the lncRNA HOTAIR in mesenchymal stem cells (MSCs) with particular focus on senescence-associated changes in gene expression and DNA-methylation (DNAm). HOTAIR binding sites were enriched at genomic regions that become hypermethylated with increasing cell culture passage. Overexpression and knockdown of HOTAIR inhibited or stimulated adipogenic differentiation of MSCs, respectively. Modification of HOTAIR expression evoked only very moderate effects on gene expression, particularly of polycomb group target genes. Furthermore, overexpression and knockdown of HOTAIR resulted in DNAm changes at HOTAIR binding sites. Five potential triple helix forming domains were predicted within the HOTAIR sequence based on reverse Hoogsteen hydrogen bonds. Notably, the predicted triple helix target sites for these HOTAIR domains were also enriched in differentially expressed genes and close to DNAm changes upon modulation of HOTAIR. Electrophoretic mobility shift assays provided further evidence that HOTAIR domains form RNA–DNA–DNA triplexes with predicted target sites. Our results demonstrate that HOTAIR impacts on differentiation of MSCs and that it is associated with senescence-associated DNAm. Targeting of epigenetic modifiers to relevant loci in the genome may involve triple helix formation with HOTAIR.
BackgroundUnderstanding carboplatin resistance in ovarian cancer is critical for the improvement of patients’ lives. Multipotent mesenchymal stem cells or an aggravated epithelial to mesenchymal transition phenotype of a cancer are integrally involved in pathways conferring chemo-resistance. Long non-coding RNA HOTAIR (HOX transcript antisense intergenic RNA) is involved in mesenchymal stem cell fate and cancer biology.MethodsWe analyzed HOTAIR expression and associated surrogate DNA methylation (DNAme) in 134 primary ovarian cancer cases (63 received carboplatin, 55 received cisplatin and 16 no chemotherapy). We validated our findings by HOTAIR expression and DNAme analysis in a multicentre setting of five additional sets, encompassing 946 ovarian cancers. Chemo-sensitivity has been assessed in cell culture experiments.ResultsHOTAIR expression was significantly associated with poor survival in carboplatin-treated patients with adjusted hazard ratios for death of 3.64 (95 % confidence interval [CI] 1.78–7.42; P < 0.001) in the discovery and 1.63 (95 % CI 1.04–2.56; P = 0.032) in the validation set. This effect was not seen in patients who did not receive carboplatin (0.97 [95 % CI 0.52–1.80; P = 0.932]). HOTAIR expression or its surrogate DNAme signature predicted poor outcome in all additional sets of carboplatin-treated ovarian cancer patients while HOTAIR expressors responded preferentially to cisplatin (multivariate interaction P = 0.008).ConclusionsNon-coding RNA HOTAIR or its more stable DNAme surrogate may indicate the presence of a subset of cells which confer resistance to carboplatin and can serve as (1) a marker to personalise treatment and (2) a novel target to overcome carboplatin resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0233-4) contains supplementary material, which is available to authorized users.
Long (>200bps) non-coding RNAs (lncRNA) can act as a scaffold promoting the interaction of several proteins, RNA and DNA. Some lncRNAs interact with the DNA via a triple helix formation. Triple helices are formed by a single stranded RNA/DNA molecule, which binds to the major groove of a double helix following a canonical code. Recently, sequence analysis methods have been proposed to detect triple helices for a given RNA and DNA sequences. We propose the Triplex Domain Finder (TDF) to detect DNA binding domains in RNA molecules. For a candidate lncRNA and potential target DNA regions, i.e. promoter of genes differentially regulated after the knockdown of the lncRNA, TDF evaluates whether particular RNA regions are likely to form DNA binding domains (DBD). Moreover, the DNA binding sites from the predicted DBDs are used to indicate potential target DNA regions, i.e. genes with high binding site coverage in their promoter. The command line tool provides results on a user friendly and graphical html interface. A case study on FENDRR, an lncRNA known to form triple helices, demonstrates that TDF is able to recover both previously discovered DBDs and DNA binding sites. Source code, tutorial and case studies are available at www.regulatory-genomics.org/tdf.
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