In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms
Fig 3
iPSC-CVPC-specific exons are enriched for RBP binding and canonical splice sites.
(A) Barplot showing the differential expression of 38 RBPs with experimentally determined (eCLIP) binding sites between iPSC-CVPC and adult heart. Colors represent p-values (S3 Table). Each row represents one RBP. (B) Plot showing the enrichment of genomic loci encoding iPSC-CVPC-specific isoforms and adult-heart specific isoforms for overlapping experimentally determined (eCLIP) RBP binding sites. Each line corresponds to an eCLIP experiment. The X axis corresponds to log2 ratio thresholds (mean isoform usage in iPSC-CVPC/mean isoform usage in adult heart; FDR < 0.05). Enrichment was calculated by comparing the proportion of genes with differentially expressed isoforms passing the log2 ratio thresholds described on the X axis (S5 Table) and overlapping eCLIP peaks against the proportion of genes without any differentially expressed isoforms (FDR > 0.05 for all isoforms) overlapping eCLIP peaks. The thick lines represent the mean enrichments across all RBP experiments for iPSC-CVPC-specific isoforms (blue) or adult heart-specific isoforms (purple). The plot shows that, at all thresholds, iPSC-CVPC-specific isoforms are more likely to overlap eCLIP peaks than adult heart-specific isoforms. (C) Shown is the sequence logo of the 50 bp upstream of the splice acceptor site (left of gray bar) and the 20 bp downstream of the splice donor site (right of gray bar). Gray bar represents the location of the exon. Only the first nucleotide of the exon is shown. Log2 ratio between the use of the most common nucleotide at each position between (D) iPSC-CVPC-specific and adult heart-specific exons, (F) iPSC-CVPC-specific and adult arteria-specific exons and (H) adult heart-specific and adult arteria-specific exons. Circles represent the estimate and segments represent the 95% confidence interval as calculated using the fisher.test function in R. (E, G, I) Barplots showing the–log10 (p-values, Fisher’s exact test) of the enrichments shown in (D, F, H). The Y axis is the same across similar panels: in panel I, three positions have significant differences between adult heart and arteria, with p-values close to 0.05 (dotted line), whereas the majority of comparisons between iPSC-CVPC and each of the two adult tissues are significant in panels E and G. At each position, test results are shown only for the most common nucleotide. Each color represents the tested nucleotide, as shown in Panel C (A = green; C = blue; G = yellow; T = red). Enrichment results for all the nucleotides at all positions are shown in S10 Table.