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Detection of RNA–DNA binding sites in long noncoding RNAs

ABSTRACT: Triple helix is a potential mechanism how lncRNAs interact with the genome. Our in silico method (Triplex Domain Finder) is able to predict the binding sites of lncRNA MEG3 and GATA6-AS in the genome. In order to validate these predictions, we develop DBD-Capture-Seq to capture the DNA loci where the given RNA oligo binds to via triplex. Method: Different RNA oligos are used The biotinylated RNA oligos (MEG3 TFR1, MEG3 TFR2, and GATA6-AS TFR1) were incubated with sheared genomic DNA to allow for triplex formation. After binding to streptavidin-coated beads, RNA-associated DNA was eluted and subjected to deep sequencing. Control experiments were conducted in the absence of biotinylated RNA oligos.

ORGANISM(S): Homo sapiens

PROVIDER: GSE119638 | GEO | 2019/01/15

REPOSITORIES: GEO

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