Extended Data Fig. 5: Effect of ZRSR2 loss on minor intron splicing.
From: Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition
a, ZRSR2 mutations in our cohort. ‘MDS 05–14’ are wild-type; ‘i-p’ are ZRSR2-mutant. VAF: variant allele frequency, fs: frameshift, ptc: premature termination codon, del: deletion, ins: insertion, ms: missense mutation. b, Comparison of U12-type intron retention in MDS samples vs. normal marrow. c, Differential splicing of U12-type introns. Each point corresponds to a single intron, illustrating percentage of mRNAs in which intron is spliced out. Blue/red dots: introns with significantly increased/decreased retention in ZRSR2-mutant vs. WT, with absolute change ≥10% or absolute log fold-change of ≥2 with p≤0.05 (two-sided Mann-Whitney U, without adjustments for multiple comparisons). d, Distribution of intron retention in samples with ZRSR2 mutations. Blue/red dashed lines: thresholds of −10% and 10% for differential retention; gold line: median change in intron retention. e, As (b), and (f) as (d), for U2-type introns. g, As (a), and (h) As (b), for Madan et al. (i) As (h), for U2-type introns. j, As (f), for Madan et al. (k) RNA-seq coverage plots of U12-type introns averaging samples with indicated genotypes. l, Splicing efficiencies of introns in (k) relative to normal marrow (median over n = 4 normal samples). P-values: two-sided Mann-Whitney U. Middle line, hinges, notches, and whiskers: median, 25th/75th percentiles, 95% confidence interval and most extreme points within 1.5x interquartile range from hinge. m, Expression of genes with retained U12-type introns between ZRSR2-mutant vs. WT. n, Immunoblot in K562 cells used for eCLIP-seq (repeated twice with similar results). o, eCLIP of ZRSR2-binding sites. Input-normalized peak signals as log2 fold-change. Purple points: eCLIP-enriched ZRSR2 peaks in biological replicates. p, Overlap of genes bound by ZRSR2 vs. differentially spliced in ZRSR2-mutant versus WT (‘ZRSR2 responsive’). P-value: Fisher’s exact test. q, U2 snRNA binding energy within ZRSR2 non-responsive and responsive minor introns.
