Fig. 2

Proteins bind RNA at various stages of RNA processing. The proteins varied on the proportion of intron alignments in the fRIP-Seq versus input. a The heat map shows the average proportion of a gene’s FPKM assigned to exon isoforms versus unspliced pre-RNA isoforms (“Materials and methods”). The scatter plots show every gene for ADAR and CHD4. Traditional RBPs ADAR, HNRNPH1, HNRNPU, and HUR likely bind co-transcriptionally; thus, they often immunoprecipitate with unspliced transcripts. b RBPs also varied on the degree to which the fRIP/input fold change correlated with input FPKM. The heat map plots the Spearman correlation of these values, and the scatter plots show every gene with a generalized additive model regression line. c Relationships between input FPKM and fold change were consistent between single and multi-exonic genes