Integration of Shh and Fgf signaling in controlling Hox expression in cultured limb cells [ChIP-seq]

During embryonic development, fields of progenitor cells form complex spatial structures through dynamic interactions with external signaling molecules. However, how complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood. For instance several critical signals have been well characterized in the early limb bud, including Sonic hedgehog (Shh) and Fibroblast growth Factor 8 (Fgf8). While the former is expressed in the distal posterior mesenchyme where it acts as the mediator of anterior to posterior (AP) patterning, the latter is produced by the apical ectodermal ridge (AER) at the distal tip of the limb bud and directs the outgrowth and the proximal to distal (PD) organization of the limb. Here we use cultured limb mesenchyme cells to try and assess the response of the target Hoxd genes to these two factors. We find that they act synergistically and that both factors are required to get activation of Hoxd13 in limb mesenchymal cells. However, the analysis of the enhancer landscapes flanking the HoxD cluster reveals that the bimodal regulatory switch observed in vivo is not fully achieved under these in vitro conditions, suggesting the requirement for other factors. ChIP-seq analysis of H3K27ac in cultured distal-anterior mesenchymal cells from chick forelimb buds at HH21.