Figure 1.

Promoter interacting regions were enriched for regulatory elements. A, Three types of Hi-C with sequence capture-established interactions; promotor (P)-distal (D), P-P and genome-wide association studies (GWAS)-P (G-P), respectively; for the Gene A promoter. In P-D is analyzed probed promoters’ interaction with D element (DEs); the latter separated by restriction sites. In P-P and G-P both ends of the interaction are probed. B, The largest connected subgraph in chr9 in aortic endothelial cell (AEC). There are 22 promoters, 3 GWAS SNPs and 271 DE (only those overlapping with H3K27ac marks are included). The blue track represents gene expression levels, gray boxes represent transcripts, and innermost layers represent H3K27Ac marks (2 replicates). Purple arcs represent G-P or P-P, and orange arcs represent P-D interactions respectively. C, Principal component analysis of P-D interaction of genes not expressed in none of the cell types D, Overlap enrichment relative to a segment-length and distance-from-P controlled random set. The AEC P-D and G-P datasets were overlapped with general cardiovascular, HUVEC, and HAEC transcription factor marker data from ChipAtlas. E, Three hundred and fifty-seven kilobase region containing MTAP-rs944797 interaction and (F) 393 kb region containing BMP6-rs9328448 interaction visualized using Gviz package.⁴⁶ Overlap with H3K27Ac marks are shown in the lower panes as well as the signal from the input chromatin. P-D (including P-G) and P-P interactions are colored as green and purple respectively. ASMC indicates aortic smooth muscle cells; BMP6, Bone Morphogenetic Protein 6; HAEC, human aortic endothelial cell line; HUVEC, Human umbilical vein endothelial cells; LPS, lipopolysaccharides; MTAP, Methylthioadenosine Phosphorylase; mTHP, macrophage–THP-1; and SNP, single nucleotide polymorphism.