Figure 5: RIP-Seq (RNA immunoprecipitation-sequencing) for the identification of CPEB4 targets in melanoma.

(a) Correlated results of Cuffdiff or EdgeR-based analysis of CPEB4 RIP-seq analyses in SK-Mel-103, using shCPEB4-derivatives as a reference. This comparison was performed in two independent replicates. Graph depicts differential expression changes (Log2 fold change, Log2FC) obtained with each method for replicate (1). Replicate (2) is shown in Supplementary Fig. 5c. (b) Differential expression of CPEB4-bound mRNAs in SK-Mel-103 versus the RWP1 pancreatic cancer cell line. RIP-seq data from RWP1 was obtained from ref. 35 and analysed as for melanoma cells by Cuffdiff. Two replicates were processed for each cell line. Data in this panel correspond to Replicate (1) of melanoma and pancreatic cancers. Other replicates are depicted in Supplementary Fig. 5d. (c) Relative expression of CPEB4-bound mRNAs identified by RIP-seq in SK-Mel-103 cells and mined by GSEA across the CCLE data set. Graph represents the enrichment score in melanoma versus other tumours. Positive correlated genes in melanoma and negatively correlated in other tumours are highlighted in red and blue, respectively. (d) Heatmap from the GSEA analysis shown in c, represented for each of the indicated tumour cell types. Note the distinct clustering in melanoma. Pearson coefficient (P), Spearman rank correlation coefficient (r) and FDR values are indicated in the corresponding panels.