Figure 4: Genome-wide mapping of MEG3 lncRNA binding sites. | Nature Communications

Figure 4: Genome-wide mapping of MEG3 lncRNA binding sites.

From: MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

Figure 4

(a) RT–qPCR analysis showing specific enrichment (presented as percentage of input) of MEG3 but not MALAT1 RNA in the ChOP pull-down assay with MEG3 antisense probes. The ChOP pull-down with GFP antisense oligo, used as a negative control, did not show any enrichment of MEG3 and MALAT1 RNAs. (b) Genomic tracks showing ChOP-seq (MEG3, GFP and input) and ChIP-seq (H3K4me1) intensities, visualized in log scale. The MEG3 binding site is located upstream of the TGFBR1 gene (falls within the intron of the COL15A1 gene) and it overlaps with H3K4me1 peaks in BT-549 cells. (c) ChIP–qPCR showing enrichment of H3K27me3 chromatin marks, presented as percentage of input, over the MEG3 peaks associated with the TGF-β genes in Ctrlsh and MEG3sh cells (±s.d., n=3). (d) Schematic outline of the TGFBR1 gene showing MEG3 peaks and the location of 3C primers (P1–P9), as indicated by arrows. EcoRI restriction sites are shown as blue vertical lines. Each error bar represents ±s.d. from three experiments. Looping events between the upstream MEG3 binding site (corresponding to P2 primer) and the TGFBR1 promoter detected by 3C–qPCR in Ctrlsh and MEG3sh cells. The P values were calculated using Student’s t-test (two-tailed, two-sample unequal variance), *P<0.05.

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