Fig. 5: Splicing regulation by CELF2. | Leukemia

Fig. 5: Splicing regulation by CELF2.

From: EZH2 modulates mRNA splicing and exerts part of its oncogenic function through repression of splicing factors in CML

Fig. 5

A Differential splicing events in K562 cells after CELF2 over-expression determined with our in-house perl script. Plot on the left gives differential splice indices (ΔSI) of annotated isoforms (ISO), skipped exons (SE), and retained introns (RI), table on the right summarizes up- and down-regulated events, as well as the number of associated genes. B Heatmaps presenting ΔSI values at differential slicing events found after EZH2 inhibition, together with the corresponding ΔSI values observed after CELF2 over-expression. Red: up, blue: down. The black square highlights splicing events significantly up- or down-regulated in both scenarios. C The CDC14B isoform ex12-16 is increased upon EZH2 inhibitor treatment or CELF2 overexpression (perl script). D Analysis of exon-junction covering reads reveals that EZH2 inhibition or CELF2 expression leads to a shift from CDC14B isoforms containing exon 3 with a premature stop codon (shown as inverted red triangle), to isoforms skipping exon 13. Left panel: overview of CDC14B isoforms distinguishable by diagnostic exon-junction covering reads (shown as lines underneath the boxes that represent exons). Right panel: black numbers: reads covering the relevant diagnostic junctions were counted, and are given as ratio between treated samples (EZH2 inhibitor, pL-CELF2) over corresponding controls (DMSO, pL). Note that treatment leads to a relative enrichment of isoforms lacking exon 13 (see orange numbers, showing their increased presence relative to exon 13 containing isoforms). E DsiRNA (Dicer-Substrate Short Interfering RNA) mediated knock-down of exon 13 containing isoforms (ex13), but not the exon 13 skipping isoform ex12-15, leads to reduced cell viability and colony formation ability in K562 cells. * p value < 0.05 (t test, paired, 2-tailed). F Volcano plot showing differential gene-expression after CELF2 expression in K562 cells. G Gene set enrichment analysis of top ranked “Hallmark” genes upon CELF2 over-expression.

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