Figure 4: Genetic variation affecting stable and transiently remodeled chromatin regions.

A) Fold change (FC) in chromatin accessibility in activated vs. naïve T cells (x-axis) and memory vs naïve T cells (y-axis). Peaks undergoing stable (red), transient (blue), or memory-specific (grey) changes are shown for B6/Cast F1, number of peaks in each group gaining (up) or losing (down) accessibility, relative to the naïve state, is indicated.

B) Mean ATAC-seq counts for peak groups shown in (A) in naïve and activated states. Number of stable and transiently responsive peaks in top left and bottom right quadrant are indicated.

C) Association between Runx1 motif mutations and allele-specific chromatin accessibility of transient up (top) and stable up (bottom) peaks. Individual lines indicate ATAC-seq peaks with a variant motif stronger on the B6 allele (blue) or stronger on the Cast allele (red). Grey lines indicate the distribution of allelic imbalances in ATAC-seq peaks containing invariant Runx1 motifs. P-value for two-sided t-test.

D) Effect of transcription factor (TF) binding motif variation on allele-specific chromatin accessibility in activated T cells. Motif-containing ATAC peaks were assigned to either the Ref. or Alt. allele based on the strength of the motif match. A t-test was used to compare the mean allelic ATAC-seq ratio between peaks with a stronger motif match on the ref. allele and peaks with a stronger motif match on the alt. allele as shown in panel (C). Motifs with a significant p-value (<0.05) and a difference in mean ATAC-seq ratio > 0.1 in both strains are highlighted. Motifs are colored according to their TF family.

E) Gene expression values for select TF families in B6/Cast in activated vs. naïve (top) and activated vs. memory T cells (bottom). Log2 FC is plotted against the mean count.