Fig. 1: Morphological and chromatin state dynamics of THP-1 cells during differentiation and M.tb infection. | Nature Communications

Fig. 1: Morphological and chromatin state dynamics of THP-1 cells during differentiation and M.tb infection.

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

Fig. 1: Morphological and chromatin state dynamics of THP-1 cells during differentiation and M.tb infection.

a Cartoon of Thp1-mono, Thp1-macro, and Thp1-M.tb. b Reconstruction of the three-dimensional structure of the nucleus. The nuclei were stained with Hochest and reconstructed. The different colors indicate different depths. c MA plot for gene differential expression analysis during Thp-1 cell differentiation. X-axis represents the mean of normalized counts, and Y-axis represents the log2 fold changes of gene expression level. Important transcription factors related to cell proliferation and differentiation are highlighted. d MA plot for gene differential expression analysis during M.tb infection. X-axis represents the mean of normalized counts, and Y-axis represents the log2 fold changes of gene expression level. Marker genes and important transcription factors for macrophages and M1 macrophages are highlighted. e Chromatin state definitions and histone mark probabilities, average genome coverage, genomic annotation enrichment levels, and gene expression levels in each chromatin state of Thp1-mono, Thp1-macro, and Thp1-M.tb cells. Box-plot showing the log2 (FPKM) of genes in each chromatin state. Box-plot with midline = median, box limits = Q1 (25th percentile)/Q3 (75th percentile), whiskers = minimum and maximum values, points = outliers (>1.5 interquartile range). The sample sizes (n) in each chromatin state are labeled in the figure. The difference in the chromatin state in each sample was highlighted with an arrow. f Dynamics of promoter states during differentiation and M.tb infection. The arrows indicate the chromatin states changed from one state (tails of the arrows) to another state (heads of the arrows). g KEGG pathway analysis of the 423 genes whose promoter status changed from repressive to active after M.tb infection. KEGG analysis used the ClueGO plug-in in Cytoscape software (Version: 2.5.8). h Genome Browser view of gene expression levels, chromatin accessibility and histone modifications at the TNFSF10 gene region in Thp1-macro and Thp1-M.tb cells.

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