Fig. 4: ZC3H11A and TAF15 control multiple independent regulons through distinct regulatory programs.
From: Systematic identification of post-transcriptional regulatory modules
A Violin plots showing the normalized enrichment scores (NES) resulting from gene set enrichment analysis of proximity labeling data. Left subpanel: NES scores across all the GO-BP terms for ZC3H11A and TAF15 proteins. The five highest-scoring pathways are highlighted with color. Right subpanel: NES scores across all studied RBPs for the pathways GO:0000387, GO:0045727, and GO:0048255. ZC3H11A and TAF15 are highlighted with colored triangles. Dashed lines: quartiles; solid red line: 0.9 quantile. B Scatterplot showing changes in alternative splicing events (ASE) usage upon ZC3H11A knockdown as estimated by MISO. Individual subplots cover different classes of alternative splicing events: Skipped Exon (SE), Retained Intron (RI), Alternative 3’ Splice Site (A3SS), Alternative 5’ Splice Site (A5SS), and Mutually Exclusive Exon (MXE). Dashed lines indicate the following filters: Bayes factor ≥ 10 and the absolute value of isoforms levels difference ≥ 0.2. The ASEs passing these filters are shown in red. Source data are provided as a Source Data file. C Relative levels of two skipped exons from the transcripts WARS1 (left) and ASPM (right) were measured by RT-qPCR in control K562 and ZC3H11A-KD cells; n = 3 biological replicates. P-value from a one-sided t test performed on log-transformed isoform expression ratios, 0.0166 for WARS1 and 2.86·10−4 for ASPM. Source data are provided as a Source Data file. D Scatterplot showing changes in alternative splicing events in TAF15 knockdown cells, as in (B). Source data are provided as a Source Data file. E Relative levels of two retained introns from the transcripts CDC37 (left) and ZWINT (right) were measured by RT-qPCR in control K562 and ZC3H11A-KD cells; n = 3 biological replicates. P-value from one-sided t test performed on log-transformed isoform expression ratios, 8.03·10−5 for CDC37 and 2.883·10−4 for ZWINT. Source data are provided as a Source Data file. F Left: Sashimi plot illustrating the changes in intron retention event usage in ZWINT transcript upon TAF15 knockdown. Right: Genomic view of the ZWINT retained intron, RNA-seq profiles from WT and TAF15-KD cells, and TAF15 CLIP-seq peaks are shown at the bottom. Y-axis: counts per million (CPM). The region corresponding to the alternative splicing event is framed.
