Fig. 1: NQO1-AS interacts with the 3′-UTR of NQO1 and regulates NQO1 expression.
a, Volcano plot showing antisense RNAs in MDA-Par and MDA-LM2 cells. b, Fold change in expression level of antisense RNAs and their corresponding sense RNAs in MDA-LM2 cells relative to MDA-Par cells. NQO1 is indicated by the red dot. c, Tracks showing GRO-seq peaks in MDA-LM2 cells, along with RNA-seq in the MDA-LM2 and MDA-Par cell lines. d, RT–qPCR of NQO1-AS and NQO1 in MDA-Par and MDA-LM2 cell lines. n = 3 independent cell cultures. e, Psoralen-mediated RNA crosslinking followed by ligation. RT–qPCR was used to detect the interactions between the NQO1 sense 3′-UTR with NQO1-AS RNA. Samples without the proximity ligation step were used as controls. f, Relative NQO1 decay rate in MDA-Par and MDA-LM2 cell lines from our metabolomic pulse-chase labeling of these cell lines3. n = 4 independently treated cell cultures. g, Relative NQO1 mRNA levels in MDA-LM2 cells with GapmeR-mediated NQO1-AS knockdown (n = 6 independent cell cultures), CRISPRi-mediated NQO1-AS suppression (n = 3 independent cell cultures) and CRISPRa-mediated NQO1-AS overexpression (n = 3 independent cell cultures), measured using RT–qPCR. sg, single-guide. h, Relative NQO1 mRNA levels in BT-20 cells after GapmeR-mediated NQO1-AS knockdown, measured using RT–qPCR. n = 3 independent cell cultures. All P values were calculated using a one-tailed Mann–Whitney U-test.
