Cell fate decisions and the maintenance of cellular identity relies on cell-specific coordination of gene regulatory networks. Besides the known role of transcriptional regulators in this process, the spatial organization of chromatin has emerged as additional layer of transcriptional control, and mutations in proteins mediating genome folding have been associated with developmental disorders known as cohesinopathies. However, how ubiquitously expressed transcription regulators achieve cell-specificity, and the complex relationship between higher-order structure and physiologic development remains unclear. Here, we define two uncharacterized roles for Bromodomain-containing protein 4 (BRD4) in the regulation of a cardiomyocyte-specific gene program and in the maintenance of genome folding. To understand the cell-specific role of BRD4, we used conditional mouse genetics to show that cardiomyocyte-specific deletion of Brd4 in adult mice leads to impaired cardiac contractility accompanied by decreased expression of genes critical for mitochondrial bioenergetics. Genome-wide occupancy data show that BRD4 enriches at downregulated genes and preferentially co-localizes with GATA4, a lineage-determining cardiac transcription factor not previously implicated in regulation of cardiac metabolism. BRD4 and GATA4 form an endogenous complex in cardiomyocytes, revealing a new interaction partner for BRD4 that directs its locus and tissue specificity to regulate a gene program governing bioenergetic homeostasis in the adult heart. In an interrelated work, we also show that genetic deletion of the BRD4 in murine neural crest cells recapitulates key features observed in cohesinopathies. We leverage on this finding and demonstrate that BRD4 interacts with NIPBL, a positive cohesin regulator and commonly mutated in patients with cohesinopathies. Acute depletion of BRD4 or loss of the BRD4-NIPBL interaction reduces NIPBL-occupancy, elucidating the importance of BRD4 in stabilizing NIPBL on chromatin. Genome-wide chromatin interaction mapping and quantitative imaging studies demonstrate that BRD4-depletion results in aberrant genome folding, specifically loss of a subset of chromatin loops, weakening of TADs, and compromised loop extrusion. Finally, loss of BRD4 or the interaction with NIPBL attenuates neural crest differentiation. Remarkably, differentiation defects resulting from BRD4 depletion can be rescued by concomitant loss of WAPL, a negative cohesin regulator. Collectively, our data elucidate mechanisms of tissue-specific gene regulation and the physiological relevance of genome organization on differentiation.