Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci

Abstract

Hox genes are required during the morphogenesis of both vertebrate digits and external genitals. We investigated whether transcription in such distinct contexts involves a shared enhancer-containing landscape. We show that the same regulatory topology is used, yet with some tissue-specific enhancer-promoter interactions, suggesting the hijacking of a regulatory backbone from one context to the other. In addition, comparable organizations are observed at both HoxA and HoxD clusters, which separated through genome duplication in an ancestral invertebrate animal. We propose that this convergent regulatory evolution was triggered by the preexistence of some chromatin architecture, thus facilitating the subsequent recruitment of the appropriate transcription factors. Such regulatory topologies may have both favored and constrained the evolution of pleiotropic developmental loci in vertebrates.

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

“…Here, by concomitantly labeling series of BACs spanning specifically the two TADs, we demonstrate that such configurations indeed exist as dense and separate objects in individual cells, as previously seen on a specific locus at the X-chromosome (10), with a low level of partial overlap consistent with the reduced number of interactions observed in 4C between the two TADs (16,17). This observation was confirmed by structured illumination microscopy.…”

“…between Hoxd11 and Hoxd12), with each TAD containing enhancers required to regulate different subgroups of genes in developing organs or structures (9,16,19) such as distal limbs, proximal limbs, genitals, or the cecum. Interestingly, all enhancers sharing a particular specificity are found within the same TAD, and thus far, no cell type or tissue was reported where these two opposite regulatory landscapes would operate concomitantly (8,16,17,19), suggesting a functional switch occurs between these two TADs in their capacity to regulate subsets of target Hoxd genes.…”

“…Hox gene clusters have been successfully used to study the functional organization of TADs (15)(16)(17), as well as the relationship between the progressive decompaction of both genes and enhancers and their transcriptional read-out. Studies of the mouse HoxD cluster have provided insights into the global regulation of its nine consecutive genes during limb development, including the presence of multiple regulatory sequences spanning a 2-megabase large DNA interval (18).…”

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

“…Consequently, specific subgroups of Hox genes, at least within the HoxA and HoxD clusters, are controlled by the same series of global enhancers; hence, they are coregulated in different contexts, which provide the system with both quantitative and qualitative modulations. This regulation has been well documented for the HoxD cluster, which contains a range of long-acting enhancers of different specificities within its two large flanking gene deserts (17)(18)(19)(20).…”

“…Within the T-DOM, series of enhancers are found, which regulate groups of genes lying in the central part of the cluster, as if the regulatory sequences would contact a chromatin pocket encompassing Hoxd8 to Hoxd11 (18). These large and apparently constitutive chromosome domains (TADs) may facilitate the required regulatory switches at important developmental loci, and were also proposed to have triggered the evolution of pleiotropy by providing the regulatory context for evolving novel enhancers (16,19).…”