In mammals, both testes and ovaries derive from a bipotential organ. Sex determination is triggered by the early expression of either SRY or RSPO1/FOXL2 in the XY or XX gonad respectively (for a review, see Capel, 2017). Upon commitment of the gonad to a specific fate, a complex genetic and hormonal cascade controls the progressive transformation of the internal and external genitalia in a process denominated sexual differentiation. Many genes are involved in the male or female pathway, whose disruptions can result in a wide range of effects, from minor alterations of the reproductive function to complete sex reversal. These effects can even take place in the adult life, long after development has occurred, demonstrating the intrinsic reprogramming capability of gonadal cell types and their genetic pathways.

During development, genes undergo through complex and specific patterns of expression that are critical for the formation and maintenance of the different structures present in an organism. Pleiotropic gene effects are often achieved through combination of tissue-specific regulatory elements, being sexual development-associated genes no exception to this. For example, non-sense mutations disrupting SOX9 or GATA4 proteins are embryonic lethal, while structural variants affecting their genomic deserts can give rise to viable individuals but with gonadal pathologies such as sex reversal or impaired reproductive function.


To trigger gene expression, regulatory elements are physically bought into the vicinity of promoters in a process called “looping”. Although the process of gene transcription has been largely studied, the principles of how regulatory elements engage into loops and find their appropriate partner, often ignoring other nearby genes are still largely unknown.

The exhaustive study of the mammalian interactome though Chromosome Conformation Capture (3C) and derivatives (for a review, see de Wit and de Laat, 2012) revealed that these enhancer-promoter associations are usually confined inside what was defined as Topologically Associating Domains (TADs). These megabase sized domains represent broad DNA regions containing loci that interacting more frequently with themselves than with the rest of the genome (Dixon et al., 2012; Nora et al., 2012). The position of these domains are almost invariant between species and relatively unchanged upon cell differentiation, highly overlapping with previously described regulatory landscapes where enhancers are able to exert their influence.

Based on this, it was thought that TADs represent fundamental genomic modules that facilitate regulatory elements to find their cognate promoters. Confirming this notion, we recently demonstrated that TAD disruption allows the interaction between previously independent domains, causing novel associations between otherwise segregated enhancer and promoter pairs (Lupiáñez et al., 2015). Remarkably, this results in aberrant patterns of gene expression inducing a wide range of congenital malformations, thus confirming the biological relevance of these structures (Lupiáñez et al., 2016).