Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

Abstract

Vertebrate Hox genes encode transcription factors operating during the development of multiple organs and structures. However, the evolutionary mechanism underlying this remarkable pleiotropy remains to be fully understood. Here, we show that Hoxd8 and Hoxd9, two genes of the HoxD complex, are transcribed during mammary bud (MB) development. However, unlike in other developmental contexts, their coexpression does not rely on the same regulatory mechanism. Hoxd8 is regulated by the combined activity of closely located sequences and the most distant telomeric gene desert. On the other hand, Hoxd9 is controlled by an enhancer-rich region that is also located within the telomeric gene desert but has no impact on Hoxd8 transcription, thus constituting an exception to the global regulatory logic systematically observed at this locus. The latter DNA region is also involved in Hoxd gene regulation in other contexts and strongly interacts with Hoxd9 in all tissues analyzed thus far, indicating that its regulatory activity was already operational before the appearance of mammary glands. Within this DNA region and neighboring a strong limb enhancer, we identified a short sequence conserved in therian mammals and capable of enhancer activity in the MBs. We propose that Hoxd gene regulation in embryonic MBs evolved by hijacking a preexisting regulatory landscape that was already at work before the emergence of mammals in structures such as the limbs or the intestinal tract.enhancers | TAD | mammalian development | mammary gland

The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

“…For instance, in both proximal limb bud cells and the intestinal cecum where the T-DOM is active, the border is established between Hoxd11 (positive) and Hoxd12 (negative) (Andrey et al 2013;Delpretti et al 2013). In the mammary gland, however, this boundary seems to form between Hoxd9 (positive) and Hoxd10 (negative) (Schep et al 2016). In contrast, when the C-DOM is activated in either distal limb cells or the developing genitals, the boundary is found somewhere between Hoxd10 (active) and Hoxd9 (weakly active) (Lonfat et al 2014).…”

“…This region contains enhancers for limbs, the cecum, and mammary glands as well as a bidirectional transcription start site for the hotdog (Hog) and twin of hotdog (Tog) long noncoding RNAs (lncRNAs) (Delpretti et al 2013;Schep et al 2016). CS38-41 was specifically contacted by the central part of the HoxD cluster in proximal cells only (Fig.…”

“…It is not contacted in brain cells where Hoxd genes are inactive (Montavon et al 2011). In contrast, the CS38 bait belongs to the CS38-41 region of the T-DOM, a conserved region with multiple enhancer activities in the intestinal cecum, limbs, and mammary buds (Delpretti et al 2013;Beccari et al 2016;Schep et al 2016). Of note, this region contains three occupied CTCF sites, all oriented toward the cluster, and is also enriched in cohesin (Fig.…”

The Hoxd Cluster Is a Dynamic and Resilient Tad Boundary Controlling the Segregation of Antagonistic Regulatory Landscapes

“…Hoxd10 (negative) (Schep et al 2016). In contrast, when C-DOM is activated, either in distal limb cells or in the developing genitals, the boundary is found somewhere between Hoxd10 (active) and Hoxd9 (weakly active) (Lonfat et al 2014).…”

Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

“…For example, the subset of Hoxd genes transcribed in the developing caecum or in mammary buds interacts only with the 3 ′ TAD, whereas another subset of genes expressed in the developing genitalia is regulated by sequences located within the 5 ′ TAD (Delpretti et al 2013;Lonfat et al 2014;Schep et al 2016). This selectivity and exclusiveness in TAD functions (the 5 ′ TAD and 3 ′ TAD are never active at the same time) underlie collinear regulation during the development of our appendicular axes.…”