Fig. 6: Splicing landscape in CML.

A Alternative splicing events in CD34+ cells from CML patients exhibiting differential splicing compared to CD34+ from healthy donors (HD) 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 Percentage of differentially expressed genes from the GO categories “RNA-splicing” and “Development” in CD34 + CML patient samples compared to CD34+ control samples. Up-regulated genes are presented in red, down-regulated genes in blue. C Bar-graph showing the differential expression of selected splicing genes in CML patients. The blot encompassed genes previously identified as EZH2 targets in K562 cells. Red: up-regulated, blue: down-regulated. D Basal expression levels of genes from (E) in CD34+ control samples determined by RNA-seq. E Normalized read counts of CELF2 in CD34+ healthy donor (HD) and CML chronic phase (CP) patient samples. F H3K27me3 levels at the CELF2 promoter in CML (pink) and non-CML (grey) haematopoietic stem/progenitor cells (HSCs/HPCs) as determined by ChIP-seq. Figure was generated using the dataset PRJEB8291. Tracks represent normalized read counts and the same scale is used for all samples. BM: samples derived from bone marrow, PB: derived from peripheral blood, CP: chronic phase (G) CELF2 promoter H3K27me3 levels in non-CML (black, grey) and CML CD34+ cells in chronic phase (CP, pink) or blast phase (BP, green). Data was derived from the previously published ChIP-seq dataset PRJNA777969, tracks are shown using the same scale. BM: samples derived from bone marrow, PB: derived from peripheral blood.