During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis‐regulatory elements that are located far away in the linear genome. How sequences located hundreds of kilobases away from a promoter can influence its activity has been the subject of numerous speculations, which all underline the importance of the 3D‐organization of the genome. The recent advent of chromosome conformation capture techniques has put into focus the subdivision of the genome into topologically associating domains (TADs). TADs may influence regulatory activities on multiple levels. The relative invariance of TAD limits across cell types suggests that they may form fixed structural domains that could facilitate and/or confine long‐range regulatory interactions. However, most recent studies suggest that interactions within TADs are more variable and dynamic than initially described. Hence, different models are emerging regarding how TADs shape the complex 3D conformations, and thereafter influence the networks of cis‐interactions that govern gene expression during development. WIREs Dev Biol 2016, 5:169–185. doi: 10.1002/wdev.218This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms