Fig. 4: RNAPII stalling in IDH2 and SRSF2 double-mutant AML and contribution of INTS3 loss to leukaemogenesis.
From: Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis
a, Metagene plot of genome-wide RNAPII Ser5 phosphorylation (Ser5P) in isogenic SRSF2WT or SRSF2P95H mutant K562 cells. b, c, RNAPII pausing index20 in primary AML samples calculated as the ratio of normalized ChIP–seq reads of RNAPII Ser5P on transcription start sites (TSSs) ( ± 250 bp) over that of the corresponding bodies (+500 bp to +1000 bp from TSSs) (b) and RNAPII abundance over the differentially spliced regions between SRSF2 single-mutant and IDH2 and SRSF2 double-mutant AML determined by RNAPII Ser2P ChIP–seq (y axis shows log2(counts per million (CPM))) (c). x axis shows patient ID. Box plots were generated from ChIP–seq data from an individual primary AML sample; the line represents mean, box edges represent 25th and 75th percentiles and whiskers show 2.5th and 97.5th percentiles. One-way ANOVA with Tukey’s multiple comparison test. d, Colony numbers from serial replating assays of either Mx1-cre Idh2+/+ or Idh2R140Q/+ BM cells transduced with shRNA targeting Ints3 (shInts3-1 or shInts3-4) or control shRNA (shControl). n = 3 biologically independent experiments; mean ± s.d.; two-way ANOVA with Tukey’s multiple comparison test. ***P < 0.004. e, g, Kaplan–Meier survival analysis of recipients. n = 5 per group; log-rank (Mantel–Cox) test (two-sided). In e: shInts3-1 versus shControl, P = 0.0018; shInts3-4 versus shControl, P = 0.0018. In g, P = 0.034 (INTS3 versus empty vector control). f, RNA-seq read coverage between exons 4–6 of INTS3 and 1,000 bp either side of INTS3 is scaled and shown as mean (line) ± s.d. (shaded region) (generated from TCGA datasets; sample list shown in legend for Extended Data Fig. 10e).
