Studies on genome spatial organization have increased considerably in the past few decades, allowing for the detailed characterization of diverse genomic topological landscapes. Chromatin interactions between promoters and regulatory elements are crucial in controlling gene regulation during development, resulting in specific gene expression profiles characterized by transcript dosage and their distribution in time and space. Here, we describe both proximity-ligation-based and non-proximity-ligation-based new technologies, as well as their exciting findings in pluripotent cells and early embryogenesis. We also discuss examples of chromatin conformation disruption in disease and cancer.