Fig. 2

Genome-wide multidimensional clusters in RA and non-RA genomes. a A total of 125 genome-wide 5 kb multidimensional clusters were grouped into nine sections based epigenetic marks. From left to right of the upper panel shows the aligned 125 clusters, each of which includes 11 RA and 11 OA FLS lines: (1) the organization of clusters into epigenetically defined sections (see text); (2) genome annotation heatmap with coverage of each cluster, with 22 separate FLS lines shown within each cluster; (3) 125 cluster IDs; (4) the number of 5 kb regions in each epigenetic cluster (log10 scale); (5) the characteristics of each region within the clusters, such as the relative abundance of transcription start sites (TSS), gene bodies, or introns; (6) chromosome location of each region within the clusters (box shows high occupancy at chromosome 19); (7) differences in signals of epigenetic marks between RA and OA; and (8) percentage of DMERs each cluster. In the middle panel, boxplot examples of clusters in different sections corresponding to LBH regions in the genome browser (bottom panel) demonstrating differences between RA and OA and how the FLS marks can be categorized as sections I, II, IV, and VII¹⁴. b DMERs with enhancer and promoter histone marks account for the most common differences between RA and OA. The red and yellow lines connect H3K27ac and H3K4me3 bars to the genome browser, which shows an example of how those marks are differentially modified between RA and OA