Extended Data Fig. 3: CFL1 promotes seRNA m6A formation.
a, Metagene plot shows RPKM values of m6A-seq over m6A-seRNA. b, The number (histogram plot) and proportion (pie plot) of CFL1 PAR-CLIP peaks in different genomic regions based on m6A-seq of total RNA. c, The top 2 motifs identified by CFL1 CLIP peak analysis, with enrichment P values by Homer based on binomial distribution. d, The overlap between the CFL1-binding peaks in seRNAs and the hyper-m6A seRNAs in PDAC. e, The effect of CFL1 KO on seRNA m6A formation. Data were determined by m6A-seq of nuclear RNA from PANC-1 cells. f, The number (histogram plot) and proportion (pie plot) of CFL1 PAR-CLIP peaks in different genomic regions by PAR-CLIP-seq of PANC-1 nuclear RNA. g, Distribution of CFL1 PAR-CLIP-seq tags around the m6A sites of seRNAs in PANC-1 cells and top 1 motif enriched by CFL1 PAR-CLIP-seq of nuclear RNA (P value by Homer based on binomial distribution). h, Metagene plots showing the distribution of m6A peaks in mRNA in CFL1 KO or KO-control cells. i, Histogram showing the m6A enrichment alterations at mRNA m6A peaks in CFL1 KO or KO-control cells. Red, hyper-m6A (n = 541); gray, m6A unchanged (n = 14,137) and blue, hypo-m6A (n = 768). j, LC-MS/MS quantification of m6A abundance in poly A+ RNA from CFL1 KO or KO-control cells. Data are mean ± SD of three replications. P by two-sided Student’s t-test. k, Dot blots of m6A in different amounts of poly A+ RNA from CFL1 KO or KO-control cells. MB: methylene blue as loading control. l, Heatmap showing differentially expressed genes in corresponding pathways between CytoD treated cells and control cells. m, The effect of CytoD treatment on seRNA m6A formation of PANC-1 cells determined by m6A-seq.
