Fig. 3

AC004540.4 is enriched in the nucleus of melanoma cells. a-b) Representative images of ISH-signals (RNAscope) derived from D04 (a) and MM415 (b) cell pellets. Fluorescent signals are either produced by DAPI DNA staining to mark the nuclear regions (blue) or probes that stain the lncRNA AC004540.4 (green). c) Subcellular RNA enrichment analysis of D04 and MM415 cells. QRT-PCR was used to compare the ratio of nuclear versus cytoplasmic RNA levels of AC004540.4, GAPDH mRNA and H19 lncRNA, which served as cytoplasmic enriched controls and the MALAT1 lncRNA, which served as nuclear enriched control. The nuclear-to-cytoplasmic ratios of GAPDH, H19 and AC004540.4 were further normalized to the nuclear-to-cytoplasmic ratio of MALAT1. The data are presented as fold-change of nuclear to cytoplasmic ratio (n = 3). Compared to MALAT1, GAPDH (D04: 0.08-fold, MM415: 0.34-fold) and H19 (0.33-fold, MM415: 0.49-fold) present a lower ratio, and AC004540.4 presents a higher ratio (6.71-fold, MM415: 5.2-fold)