Figure 3: Human lncRNAs directly regulated by p53.
(a) Summary table of lncRNAs directly regulated by p53. Different shades of blue indicate the RNA expression values for each lncRNA under the different conditions of treatment. The presence of p53 binding to the lncRNA loci in HCT116 cells at 0 and 12 h of 5-FU treatment or in MEFs treated with doxorubicin is indicated in orange, and the p53-binding sequence motif obtained by MEME analysis is shown. The relative subcellular localization of the lncRNAs determined by subcellular fractionation followed by qRT–PCR is indicated with colours from white to dark blue according to increasing RNA levels. Values are the average of three biological replicates. (b–d) Schematic representation of the chromosomal locations of the PR-lncRNA-1 and PR-lncRNA-10 gene loci. RNA expression (RNA-seq signal), p53, H3K4me3 and H3K4me1 ChIP-seq peaks and transcript structures as assembled by Cufflinks (grey) or annotated by Gencode (black). Validation by qRT–PCR of the PR-lncRNA-1 (c) and PR-lncRNA-10 (e) in an independent experiment with HCT116 p53+/+ and p53−/− untreated or treated with DNA damage for 4 and 12 h. Values represent the mean±s.d. of three biological replicates. (f) Subcellular localization. Percentage of total RNA found in the nuclear fraction bound to chromatin, nuclear soluble and cytoplasmic fractions in the HCT116 p53+/+ cells determined by qRT–PCR. Values represent the mean±s.d. of three biological replicates. (g) RNA fluorescence in situ hybridization of PR-lncRNA-1 and PR-lncRNA-10 in HCT116 p53+/+ cells untreated (−5-FU) or treated (+5-FU) with 5-FU for 12 h. White line indicates 10 μm.
