Genome-wide mapping of Acinus RNA-binding sites in HeLa cells using iCLIP-seq. (A) Cartoon displaying the three main Acinus protein isoforms (L, S, and S′), the apoptotic-generated p17 fragment, as well as the T7-tagged working construct T7-Acinus S*. Arrows on top represent the apoptotic cleavage sites, as previously described (Sahara et al. 1999) (cleavage by Caspase 3 is shown by the red arrowhead, whereas the black arrowhead indicates cleavage by an unknown activity). The different protein domains are highlighted: SAP domain, RNA recognition motif (RRM), RS-like domain, as well as the different N termini of Acinus S and S′ isoforms and the T7 tag. (B) Diagram showing the number of peaks for each Acinus iCLIP experiment that are unique to a specific iCLIP experiment or are also present in another experiment. Peaks were detected using Pyicoclip and peaks present in the control experiments were removed from our analysis. (C) Distribution of Acinus “common” binding peaks among coding exons, 5′UTR, 3′UTR, and introns. Acinus “common” peaks refer to the 36,271 peaks common to two out of three iCLIP experiments. (D) Two significant motifs discovered from the common Acinus peaks using the MEME tool. The search was done for a 6- to 10-nt motif in 20-nt sequences centered on the peak summit from 1000 randomly selected peaks. (E) Proportion of peaks from the common data containing motif 1, motif 2, or both motifs. We considered all peaks (n = 36,271), exonic peaks (n = 25,347), and intronic peaks (n = 6944).
