Fig. 4: Chromatin landscape of migrated LCs enriches for EICE, AICE and ISRE motifs.

Human steady-state migrated LCs were subjected to whole-genome chromatin profiling of H3K4me3 and H3K27Ac. a Proportion of DEG with H3K27Ac mark at 2 h in clusters of co-expressed genes upregulated early (2 h, clusters 3) and late (24 h, cluster 2) following stimulation with TNF. Changes in H3K27Ac acetylation were calculated using MANorm algorithm embedded in BioWardrobe tool. Genes were filtered to include unique common entry across the biological replicates (consensus value from n = 3 independent donors). Genes with detected changes in acetylation were intersected with DEGs identified by EdgeR analysis. Source data are provided as a Source Data file. b UCSC genome browser tracks of H3K27Ac mark changes in human migrated LCs over the time course of stimulation with TNF. Early ubiquitin C, UBC (top) and CD40 (bottom) and late sequestosome SQSTM1 (top) and TRIM21 (bottom) induced genes. Red rectangle denotes promoter site, a representative example. c Promoter sites of genes acetylated at H3K27 in migrated human LCs are enriched in IRF-binding composite DNA elements. EICE is the top human motif enriched at steady-state LCs (HOMER de novo motif detection analysis, median –log P-value shown). d Peaks H3K4Me3 and H3K27Ac T0 datasets were scanned for ISRE/AICE/EICE binding motifs. In total, 1193 consensus transcripts (present in all three biological replicates with both chromatin marks) were identified. Biological processes enriched in those genes were detected using ToppGene based on FDR-corrected P-values for GO categories and collapsed to overarching categories. Source data are provided as a Source Data file.