Fig. 4: CENPB is the major downregulated gene upon loss of circMAN1A2(2,3,4,5).
a Computational pipeline to identify differentially expressed genes and circRNAs after KD of circMAN1A2(2,3,4,5). b KD of circMAN1A2(2,3,4,5) reduced circMAN1A2(2,3,4,5) expression but not linear MAN1A2. FPBcirc of circMAN1A2(2,3,4,5) (top panel) and FPBlinear of linear MAN1A2 (bottom panel) were shown in corresponding HT29, DLD-1, HeLa, A549, and 293FT cell lines with circMAN1A2(2,3,4,5) KD. c KD of circMAN1A2(2,3,4,5) reduced CENPB, BCL2L2-PABPN1 and PABPN1 mRNA expression. FPKM of each mRNA was shown in corresponding HT29, DLD-1, HeLa, A549, and 293FT cell lines with circMAN1A2(2,3,4,5) KD. d, e KD of circMAN1A2(2,3,4,5) led to downregulated CENPB expression in HT29 (d) and DLD-1 cells (e), as shown by RT-qPCR (left panels) and WB (right panels). f Designed sgRNA-c1 and sgRNA-c2 specifically targeting the BSJ site of circMAN1A2(2,3,4,5) for RfxCas13d system. g KD efficiency of circMAN1A2(2,3,4,5) by RfxCas13d in DLD-1 cells. h KD of circMAN1A2(2,3,4,5) by RfxCas13d led to downregulated CENPB expression in DLD-1 cells detected by RT-qPCR (left panel) and WB (right panel). Images are representative of three independent experiments (d, e, h). RNA levels were detected by RT-qPCR, normalized to ACTB and presented as mean ± s.d., with biologically individual data points shown (d, e, g, h). P values were determined by ordinary one-way ANOVA test with Dunnett’s post-hoc comparisons versus scramble control (FDR-adjusted P values) (d, e) and unpaired two-tailed Student’s t-test (h). Source data are provided as a Source Data file.
