The analysis of the spatial genome organization reveals the complexity of chromosomal interactions on a 3D level. These interactions regulate gene expression in many flavors, including long-range enhancers and repressors’ control or epigenomic modifications. Therefore, chromosome conformation has a central role in gene expression control. Despite the relevance of the changes in the spatial genome organization, gene-associated diseases are poorly understood.

This project has aimed to discern how changes in the promoter interactome are associated with modifications in gene regulation that result in pathological phenotype like dilated and ischemic cardiomyopathy (DCM, ICM).

The latest techniques for mapping the contact regions in the chromatin were chosen for the experimental approach, HiC (High-throughput Genome-Wide Chromosome Conformation Capture) for uncovering how cells control the accessibility of the chromatin and PCHiC (Promoter Capture HiC) for a specific selection of distal promoter interacting regions. Both techniques have been applied to a large cohort of heart tissue samples: controls (n=9), DCM (n=13), and ICM (n=10). Besides, random-primer based RNA-Seq has been performed.

To our knowledge, this is the first comprehensive HiC - PCHiC analysis in left ventricular heart tissue in a large cohort. In the mean, we find 92.4% valid read pairs (± 4.6) from interacting genomic loci in controls, 93.1% (± 2.6) in DCM, and 94.3% (± 1.0) in ICM. After stringent quality control, including removal of artifacts, on average 120.0 (± 30.9) million reads per sample were detected as high-quality reads. From all detected interactions, 39.3% (± 4.0) were trans-chromosomal, resembling cell-heterogeneity of the tissue compared to cell culture experiments (20%). We were able to successfully detect important regulatory elements such as enhancers, CTCF binding sites, histone methylation or acetylation associated with activation (H3K4me1, H3K4me3, H3K27ac) and silencing (H3K27me3, H3K9me3) of genes. Those motifs were significantly enriched. Finally, we find 1484 and 8177 interactions (cis) to be significantly (p-value < 0.005) different in DCM or ICM compared to controls. Interestingly, those significant interactions harbour many regulatory regions related to genes associated with cardiomyopathies or heart failure and correlates with differential expression of distinct genes. Novel DCM/ICM-related regulatory regions are associated with genes involved in important molecular mechanisms such as protein tyrosine kinase activity, hemodynamic regulation and metabolism.   

We here provide for the first time a comprehensive genome-wide interaction promoter-capture map of the human left-ventricle from patients with cardiomyopathies and controls. Important regulatory regions can be shown to be dysregulated in disease, which adds another layer to the understanding of the molecular complexity of the disease and enables the identification of novel potential therapeutic targets.