Fig. 3

Characterization of PTBP1 binding sites in flanking introns and the effects on circRNA expression. A Pie chart shows the distribution of PTBP1 RIP peaks in different genomic regions. B Motifs and p values enriched from PTBP1 RIP peaks are shown. C Profile of PTBP1 RIP-seq and input near the back splicing junction sites of all circRNAs and differentially expressed circRNAs. D The expression level of circRNAs with and without PTBP1 binding sites in flanking introns in K562 WT cell line. E Distribution of PTBP1-bound signals within 3 kb upstream and downstream of circSPPL3 was demonstrated by the Integrative Genome Browser. Blue squares mark the PTBP1 binding regions on introns. F Minigene reporter schematics for circSPPL3. The PTBP1-RIP peak motif is represented by two black triangular symbols, motifs unrelated to the PTBP1-RIP peak are represented by one black triangular symbol, and yellow triangular symbols indicates that the motif is mutated. G RT-qPCR quantification of circSPPL3 from minigene reporters co-transfected with PTBP1 expression plasmid (PTBP1-overexpression) or empty vector in 293 T cells. Linear transcript generated from the reporter was used for normalization. n = 3 biological replicates. Error bars are represented as mean ± standard error of means (SEM). * p < 0.05, ** p < 0.01, Student’s t-test, two-tailed and unpaired