Similarities and differences in the regulation of HoxD genes during chick and mouse limb development

Abstract

In all tetrapods examined thus far, the development and patterning of limbs require the activation of gene members of the HoxD cluster. In mammals, they are regulated by a complex bimodal process that controls first the proximal patterning and then the distal structure. During the shift from the former to the latter regulation, this bimodal regulatory mechanism allows the production of a domain with low Hoxd gene expression, at which both telomeric (T-DOM) and centromeric regulatory domains (C-DOM) are silent. These cells generate the future wrist and ankle articulations. We analyzed the implementation of this regulatory mechanism in chicken, i.e., in an animal for which large morphological differences exist between fore- and hindlimbs. We report that although this bimodal regulation is globally conserved between the mouse and the chick, some important modifications evolved at least between these two model systems, in particular regarding the activity of specific enhancers, the width of the TAD boundary separating the two regulations, and the comparison between the forelimb versus hindlimb regulatory controls. At least one aspect of these regulations seems to be more conserved between chick and bats than with mouse, which may relate to the extent to which forelimbs and hindlimbs of these various animals differ in their morphologies.

Chromatin topology and the timing of enhancer function at thehoxdlocus

“…In contrast to CS39, CS65 and CS93, however, these two early limb control regions (ELCR2 and ELCR3) were not found fully conserved in chicken, albeit they are present in all mammals ( Fig. S1 and (Andrey et al, 2013;Yakushiji-Kaminatsui et al, 2018)). Transgenic analysis of both ELCR2 and ELCR3 showed strong LacZ expression in E9 limb buds, which coincides with the expression of CS39 and CS65 transgenes (Fig.…”

“…1A, remains active at late (E12.5) embryonic stages. Most limb enhancers described thus far are located within this chromatin domain, in particular the CS39, CS65 and CS93 sequences (Andrey et al, 2013;Beccari et al, 2016;Yakushiji-Kaminatsui et al, 2018).…”

“…At this stage, the distribution of interactions with T-DOM shows a clear topological segregation, with 3'-located genes (Hoxd1 to Hoxd8) interacting mostly with the first sub-TAD, whereas 5'-located genes (Hoxd9 to Hoxd11) associate in priority with the more distant sub-TAD (Andrey et al, 2013;Rodríguez-Carballo et al, 2017), suggesting a functional compartmentalisation of T-DOM. All limb-specific enhancers were thus far associated to the distant sub-TAD, starting at the sub-TAD boundary and extending up to Hnrnpa3, including the CS65 and CS93 enhancers (Andrey et al, 2013;Yakushiji-Kaminatsui et al, 2018).…”

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes

“…At the level of gene regulation, topologically associating domains (TADs) [7–9] usually match large domains of long-range gene regulation referred to as regulatory landscapes [10]. These structures are globally detected in all cell types and conserved across vertebrate species [7, 11–15]. The experimental depletion of either CTCF or cohesin subunits leads to a loss of both loop organization and TAD structure.…”

Establishment and evolution of heterochromatin

“…114,185 Once established, the TAD structures seem to remain stable during development 117 and conserved during evolution. 96,155,186 For developmental and molecular biologists, the critical questions remaining to be answered include what factors are involved, and how do they interact with each other to recognize the genomic cis elements, probably with a different priority during early embryogenesis to establish the chromatin states and architectures? What are the distinct mechanisms for establishing and maintaining heterochromatin in different genomic regions?…”