Extended Data Fig. 8: In vitro DNA-binding analysis and in vivo ChIP–seq and scATAC-seq analysis of GFI1(R412X).
From: Mouse models of neutropenia reveal progenitor-stage-specific defects
a–e, EMSA using nuclear extracts of 293T cells transfected with a GFI1, GFI1(R412X), or empty expression vector. Arrows indicate bound (shift) and free probe. All data represent one experiment. a–c, A probe containing a high-affinity GFI1-binding site (R21) was incubated with a titration of nuclear extracts (a) or a titration of cold competitors with (R21) or without (MutR21) a high-affinity GFI1-binding site (b, c).d, e, Nuclear extracts were incubated with probes containing a GFI1-binding site taken from the Mmp8 (d) or Cbx3 (e) locus. These loci contain a GFI1 ChIP–seq peak and the corresponding genes are differentially expressed in Gfi1R412X/− Fluidigm scRNA-seq data. f, Heat map of ChIP–seq read coverage at GFI1-specific peaks, in which each row represents one peak that was called in the wild-type and each column represents a DNA-base position of the peak centred on each GFI1 called peak in the indicated ChIP samples. The cluster colour (left) indicates loci bound by GFI1 alone (white) or by GFI1 and GFI1(R412X) (black). g–l, Schematics of the indicated genomic loci displaying scATAC-seq pseudobulk accessibility in the colour-coded clusters (top) or ChIP–seq reads and called peaks (bottom), with differentially accessible regions bound by GFI1 shaded.
