Fig. 4
From: Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin
A-ROD is functional at its release from chromatin. a, b Expression levels of A-ROD and DKK1 assessed upon cell fractionation in the chromatin-associated (a) and nucleoplasmic fraction (b), in control (ctrl) and siRNA-treated MCF-7 cells. RT-qPCR measured RNA levels are normalized to GAPDH and control. Two different siRNA sequences targeting either the 5′ (A-ROD 5′si) or the 3′ (A-ROD 3′si2) of A-ROD were used. Error bars represent standard deviations from three independent experiments (n = 3 biological replicates, *p < 0.05 and **p < 0.01, two-tailed Student’s t-test). c Expression levels of A-ROD and DKK1 in the BrU-labeled nascent RNA (BrU IP done from the chromatin-associated RNA fraction) measured by RT-qPCR in control and A-ROD siRNA treated cells, assayed by two different siRNA sequences targeting either the 5′ (A-ROD 5′ si) or 3′ (A-ROD 3′ si2) of A-ROD. Values were normalized to GAPDH exon and control. Error bars represent standard deviations from three independent experiments (n = 3 biological replicates, *p < 0.05 and **p < 0.01, two-tailed Student’s t-test). d Transcriptional pausing index for A-ROD and DKK1 assessed by extracting the ratio 5′/3′ IP recovery (BrU-IP over Input for two distinct 5′ and 3′ RT-qPCR amplicons) in control and A-ROD siRNA treated cells
