Fig. 5

mRNA half-life analysis of CPEB4 target genes. A Transcriptome-wide mRNA decay was measured by RNA-Seq analysis of actinomycin D chase experiments in HeLa cells treated with 20 nM RMD or an equal volume of DMSO for 16 h. The graph depicts the distribution of mRNA half-lives grouped by the sum of diagnostic events in all CPEB4 binding sites per gene. B Western blot analysis of CPEB4 expression following KD with a control or two CPEB4-targeting siRNAs in HeLa cells. Cells were treated with 20 nM RMD or equal volume of DMSO for 16 h. C Scatter plot depicting mRNA half-lives determined by transcriptome-wide mRNA decay measurements in control vs. CPEB4 KD HeLa cells in the DMSO-treated condition. Average mRNA half-lives were calculated for the two CPEB4 siRNAs and for the two control conditions (control siRNA and untransfected HeLa cells). Immediate early gene (IEG) mRNAs are highlighted in blue. D The cumulative distribution of log₂-transformed changes in mRNA half-lives upon CPEB4 KD is shown for a literature-curated set of IEGs and all other genes. E The cumulative distribution of log₂-transformed changes in mRNA half-lives upon CPEB4 KD is shown for all genes grouped by the sum of diagnostic events in all CPEB4 binding sites per gene. F Gene set enrichment analysis showing enrichment of IEG mRNAs among CPEB4 target genes ranked by the sum of diagnostic events per gene. G Examples of CPEB4 PAR-CLIP coverage over the three IEGs EGR1, FOS, and JUNB. Only the longest gene model is depicted. H Scatter plot depicting the ribosome density of each mRNA based on Ribo-Seq analysis in CPEB4 KO clone #44 and parental HeLa cells (n = 2). IEG mRNAs are highlighted in blue