Fig. 6

Proteins associated with CLK2 and implicated in CG expression. a Volcano plot ranking proteins associated with CLK2 IP identified by four pull downs of N-terminal FLAG tagged, one untagged CLK2 and one control empty vector, determined by TMT mass spectrometry. The log₂ mean fold enrichment (horizontal axis) and enrichment p-value were determined by linear model fits to MS determined peptide abundance. Known CLK2 interactors^34,35,36, orange dots; known spliceosome-associated proteins (PantherGO⁵²), green dots; factors associated with RNA-binding motifs enriched in CG exons are boxed and their dots blue; factors associated with 3′-end processing highlighted in red. Threshold is adjusted to <0.05 and log₂(mean enrichment) >0. b Number of CG events above expression threshold after siRNA knockdown. siRNA to splicing factors (vertical axis, highlighted red: 3′-end processing factors) assessed by a quantitative, targeted NGS sequencing panel for specific CG events was used to quantify CG expression in relation to non-targeting controls. The plot displays the number of CG events per knockdown condition, expressed more than 2 SD above the mean of ≥3 non-targeting controls or the number of CG events per knockdown condition where CG expression in the non-targeting controls was undetectable (see also Supplementary Fig. 36). c Heatmap showing distribution of individual CG event occurrence (vertical axis) above the control expression threshold (as in panel b). The presence of a black square indicates one or more CG events