Fig. 2

mRNAs bind to AtPABs with different efficiencies. a Schematic of the CLIP-seq experiment, which detects the direct RNA-binding targets of AtPABs. b AtPABs bind predominantly to consecutive A’s. Reads with ≥ 12 consecutive N’s were counted because the yeast Pab1p requires at least 12 consecutive A’s for binding. c mRNA is the major binding target of AtPABs. d CLIP-seq reads were mainly mapped to the 3′-ends of mRNAs. The length of each mRNA was scaled to 100%. “0” and “100” represent the transcription start and end, respectively. e The AtPAB-binding gene detected in CLIP-seq was validated by RIP-RT-PCR. The distribution of the AtPAB-CLIP reads is shown by the wiggle plots. The gene model shows the untranslated regions (gray boxes), coding sequences (black boxes), and introns (lines). The input and IP panels show the mRNA level of an AtPAB-binding gene in total RNA and RIP experiments (anti-HA antibody), respectively. The minus sign (−) indicates the negative control (the wild-type Col) in which the GFP-HA tagged AtPAB is absent. f The AtPAB2-binding efficiency significantly varies among genes in Col. Each dot represents a target gene of AtPAB2. The diagonal is shown by a blue dashed line. g The difference in AtPAB2-binding efficiency among genes was validated by RIP-RT-qPCR. Green bars and purple bars show the AtPAB2-binding efficiency estimated by CLIP-seq and RIP-RT-qPCR, respectively. The ~ 10-fold difference in AtPAB2-binding efficiency between At1G12110 and At4G40090 that was detected by CLIP-seq was validated by RIP-RT-qPCR. The error bar represents the standard deviation of three replicates. h The binding efficiencies of genes were highly correlated among AtPABs. P values were given by Pearson’s correlation analysis (P < 1 × 10⁻¹⁰⁰ in all three pairwise comparisons)