Proportion of Acinus peaks associated with eIF4A3 peaks and enrichment at “canonical” EJC occupancy site (24-nt upstream of an exon junction). (A) Proportion of Acinus peaks found in close proximity of eIF4A3 peaks (eIF4A3+) (maximum distance of 10 nt between both peak summits). The analysis was done on “genomic” peaks (reads mapped to the genome) depending on their location: all peaks (n = 36,271), exonic peaks (n = 25,347), 5′UTR peaks (n = 1347), 3′UTR peaks (n = 2379), and intronic peaks (n = 6944), but also on “transcriptomic” peaks (reads mapped to a representative transcriptome data set) (n = 13,231). eIF4A3 CLIP-seq data described in Saulière et al. (2012) were downloaded from GEO: GSM1001331. (B) Distribution of the peak frequency according to the distance of the peak summit from the exon 5′ end or the exon 3′ end. This analysis was done using Acinus’ “common transcriptomic” peak data for all peaks (n = 10,735), peaks associated with eIF4A3 (n = 2000), or peaks not associated with eIF4A3 (n = 8735) (from left to right). Only internal exons were used. The iCLIP data are represented by a red line. The gray line corresponds to randomized peak summit positions.
