Additional file 8.

Analysis and comparison of PAR-CLIP-identified Puf3p targets. (A) Puf3p PAR-CLIP identified crosslinking sites in 147 (67%) of the 220 Puf3p target mRNA identified by RIP-Chip; 174 Puf3p RIP-Chip-identified target mRNAs contain the Puf3p recognition motif UGUAAAUA [12,13]. Puf3p PAR-CLIP identified motif-containing crosslinking sites in 76 (44%) of these mRNAs and in 265 additional mRNAs, suggesting post-transcriptional regulation by Puf3p for these 265 novel targets. (B) GO enrichment analysis of 265 PAR-CLIP-identified, motif-containing Puf3p targets. Results are consistent with Puf3p's role in localization, deadenylation, and repression of mRNAs encoding proteins destined for the mitochondria [29]. (C) Individual replicate coverage of COX17 3' UTR in gPAR-CLIP with average coverage as shown in Figure 2b.

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Freeberg et al. Genome Biology 2013 14:R13   doi:10.1186/gb-2013-14-2-r13