Abstract 067: Genome-wide Chromatin Conformation Map Of Human Induced Pluripotent Stem Cell-derived Vascular Endothelial Cells Reveals New Regulatory Insights

Abstract

Chromatin conformation influences gene transcription by changing the spatial organization and accessibility of DNA regulatory elements. Endothelial cells (ECs) play an important role in the regulation of blood pressure. We have shown that human induced pluripotent stem cell (iPSC)-derived ECs (iECs) exhibit robust expression of a large panel of EC marker genes. In this study, we developed genome-wide maps of chromatin conformation in iECs using Hi-C and Micro-C techniques. With Hi-C, we identified 309 and 1,584 loops at 5,000 base pairs (bp) and 10,000 bp resolution, respectively, from a total of more than 171 million chromatin contacts. We also identified 62 and 582 contact domains at the two levels of resolution. From a total of more than 356 million contacts in the Micro-C map of iECs, we identified 3,259 and 6,497 loops and 1,262 and 3,542 contact domains at 5,000 bp and 10,000 bp resolution, respectively, including many identified by Hi-C. A subsample of the Micro-C data that was similar to the Hi-C map in size identified four fold more loops and six fold more domains at 5,000 bp resolution. Using approaches that we published recently, we identified 54 overlapping genes between 1,278 genes known to be relevant to ECs and 251 genes known to be involved in blood pressure regulation. We searched the 3,259 loops in the Micro-C map of iECs for the 54 genes and 26,585 single nucleotide polymorphisms (SNPs) in 1,071 haplotypes associated with blood pressure. EDNRA (endothelin receptor type A) and SMAD3 (SMAD family member 3) were in the same loops as blood pressure-associated haplotypes, were the closest genes to the haplotype regions, and were expression quantitative trait locus (eQTL) genes for SNPs in the haplotypes. GJA1 (connexin-43) was in the same loop as the rs6925750 haplotype and an eQTL gene for some SNPs in the haplotype, but GJA1 was not the closest gene to the haplotype. In fact, the GJA1 promoter was 498,217 bp away from the haplotype region, indicating possible long-range regulation of GJA1 by SNPs in this blood pressure-associated haplotype. In summary, we have developed a genome-wide chromatin conformation map for human iECs, which may reveal new insights into the mechanisms underlying the regulation of endothelial gene expression and blood pressure.