Fig. 4: Remodeling of the chromatin configuration of guanylate-binding protein (GBP) gene clusters. | Nature Communications

Fig. 4: Remodeling of the chromatin configuration of guanylate-binding protein (GBP) gene clusters.

From: Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation

Fig. 4: Remodeling of the chromatin configuration of guanylate-binding protein (GBP) gene clusters.

a Comparison of TAD DoD value, chromatin interaction matrices, chromatin loops, RNA expression levels, and epigenetic modifications around the GBP loci in bulk cells before and after M.tb infection. b Comparing the single-cell chromatin contact differences using merged single-cell chromatin contact matrix. Each color of the dots in the matrix represents the chromatin contact from the same cell. c Single-cell chromatin contacts between GBP2, GBP4, GBP5, and GBP7 and RNA expression before and after M.tb infection. d Depiction Hi-C chromatin loops before and after infection and BRD4 and MED1 ChIP-seq peaks around GBP gene clusters. e Colocalization between BRD4 and the GBP gene cluster by IF and DNA-FISH in Thp1-macro and Thp1-M.tb cells. IF, DNA-FISH, and merged channels (overlapping signal in white) are shown in separate images. The dashed line highlights the nuclear periphery, determined by DAPI staining. The rightmost column shows the area in the yellow box in greater detail. For each cell type, we counted 60 GBP gene loci. 18.3% (11/60) GBP loci were colocated with BRD4 in Thp1-macro cells and 65.0% (39/60) GBP loci were colocated with BRD4 in Thp1-M.tb cells. Each experiment was replicated three times.

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