Fig. 3

R-loops promote inflammatory gene expression in ddx41 mutants (A) Volcano plot displaying differentially expressed genes between cd41:gfp+ HSPCs from ddx41 mutants and siblings. Significant differences are defined as FDR < 0.05 and log2 fold change >1. Black vertical lines denote the fold-change threshold and the black horizontal line denotes the FDR threshold. Three biological replicates for both ddx41 mutants and siblings were used to generate RNA-sequencing data. (B and C) Representative charts of pathways significantly enriched in genes downregulated (B) or upregulated (C) in ddx41 mutant HSPCs compared with sibling controls as determined by MSigDB analysis. (D) Graph of RT-qPCR analysis of the expression of type I IFN-responsive genes between sibling controls and ddx41 mutants that are Tg(hsp70:M27RNASEH1-GFP)-negative versus Tg(hsp70:M27RNASEH1-GFP)-positive. Expression levels were normalized to β-actin levels. All levels are relative to the RNASEH1-GFP (RNH1) negative sibling controls expressed as ddCt values, with positive values reflecting higher expression and negative values reflecting lower expression. Graph displays means ± standard error mean with p values calculated with an unpaired t test, ∗p < 0.05. N = 4 replicates per experiment.