Extended Data Fig. 9: Triplex formation tested by EMSA.
From: In vivo single-molecule analysis reveals COOLAIR RNA structural diversity
a, Potential triplex sequence content formed by pyrimidine Y-RNA or purine R-RNA within hyper-variable region. The Watson strand DNA and Crick strand DNA, shown in red, pair with each other via Watson-Crick bonds. The triplex-forming oligo RNA (Y-RNA or R-RNA) are shown in green and can bind FLC double-stranded DNA via Hoogsteen bonds. The Y-RNA corresponds to COOLAIR RNA with the same sequence content, while R-RNA corresponds to FLC RNA with the same sequence content. The red triangle indicates the site corresponding to FLC TSS. b, The panels show signal for DNA end-labelled with Cy5 (red colour) and RNA end-labelled with FAM (green colour). DNA/RNA bw, black and white projection of the colour image; FLC dsDNA around TSS, Triplexator-predicted45 triplex target site at FLC TSS within the hyper-variable region (corresponding to the red shadows in Extended Data Fig. 4e, f and Extended Data Fig. 5c); Negative control, oligonucleotide sequence upstream of FLC TSS (asterisks marks impurity in ssDNA oligo); Positive control, triplex-forming oligonucleotide sequence of human rDNA enhancer En3 with lncRNA PAPAS21. DNA-RNA triplex samples are shown in increasing ssRNA concentration with dsDNA:ssRNA ratios of 1:1, 1:2 and 1:4. For the positive control, the triplex sample is fixed at a ratio of 1:4. Data are representative of at least three independent experiments. For gel source data, see Supplementary Fig. 1.
