The IPA:LE isoform ratio is widely and directly regulated by ELAVL1. (A) Western blot analysis of ELAVL1 protein levels in MCF-7 cells transfected with an siRNA targeting ELAVL1 (siELAVL1) or a negative-control siRNA (siCTRL). (B) Identification by 3′-seq on whole MCF-7 cells of abundant IPA isoforms, for which the IPA:LE ratio is regulated by siELAVL1 when compared to siCTRL. (C) Venn diagram comparing the peaks found in two biological replicates of ELAVL1 iCLIP in whole MCF-7 cells. Overlapping peaks were considered ELAVL1 binding sites. The most enriched motif is shown. (D) Venn diagram comparing the peaks found in two biological replicates of iCLIP using nonspecific immunoglobulin (IgG). (E) Density of ELAVL1 binding sites in exons, introns, 3′ UTRs overlapping introns, and 3′ UTRs overlapping the last exon of genes. (F) Fraction of genes that have an ELAVL1 binding site in the indicated IPA or LE region, among the genes that are either up- or down-regulated by siELAVL1 at the level of IPA:LE isoform ratio. (G) RT-qPCR analysis of the effect of ELAVL1 siRNA on the IPA:LE isoform ratio in the CELSR1 gene. (H) Visualization of 3′-seq, iCLIP, and total RNA-seq data for the CELSR1 gene in the UCSC Genome Browser.
