Functionally dissecting the regulatory genome of paralogous cardiac gene clusters

During heart development and function, precise gene expression patterns are established and maintained in different cellular, tissue and genomic contexts. Misregulation of gene expression programs can lead to congenital heart defects and cardiac diseases. A class of noncoding cis-regulatory DNA elements, called enhancers, play an important role in orchestrating the spatio-temporal expression of genes during development and disease. More than 80,000 putative enhancers have been identified in the human and mouse heart based on distinct epigenetic features. Functional enhancers are bound by lineage-specific and general transcription factors and usually engage with target genes present within the same structural chromatin domains also known as topologically associated domains. The regulatory relationship between enhancers is complex and less is known about their functional behavior in regulation of genes during development and disease. Although regulatory elements have been experimentally characterized in cell culture assays, insights into the in vivo function of regulatory elements in mammals and the impact of genetic variation on enhancer function and phenotype are limited. In this thesis we focused on the regulatory genome of the heart and we investigated the function and physiological roles of (super) enhancers in two clusters of paralogous genes, Nppa-Nppb and Scn5a-Scn10a, during heart development and disease. We show that the absence of functional enhancers in both gene clusters has impact on developmental and pathological gene regulation of the heart. The results of this thesis enhance our understanding of the general mechanisms by which (super) enhancers function to ensure appropriate expression and organization of the genome.