Figure 3.

Regulatory reallocations. Real-time PCR comparisons of gene expression levels in presumptive digits of either wild-type embryos (light-blue bars) or embryos homozygous for deletions of Hoxd loci located in 5′ of the cluster. The levels are always shown as a proportion of Hoxd13 wild-type RNA level. To better visualize the results, different scales are used for either Lnp and Evx2, or “posterior” Hoxd genes. (A) Deletions of the Hoxd13 locus, either alone [del(13), red bars] or in combination with either Hoxd12 [del(13–12), yellow bars] or Hoxd12 and Hoxd11 loci [del(13–11), green bars]. The deletions lead to up-regulations of the remaining genes. Regulatory reallocations are more important on the 3′ side (Hoxd genes) than on the 5′ side (Evx2) of the deletion. Lnp shows a significant up-regulation in the largest deletion, exclusively. In all cases, the newly positioned 5′-most Hoxd gene (rank 1) shows the strongest expression. (B) Similar genetic configurations, but combined in cis with a deletion of conserved RXII. Deleting RXII (dark-blue bars) results in both a decrease in Evx2 transcription and an overall higher expression of posterior Hoxd genes. Deleting RXII together with Hoxd13 [del(RXII)–del(13), orange bars], or Hoxd13 and Hoxd12 [del(RXII)–del(13-12), green bars] lead to partial recovery of Evx2 levels, together with an increase of the remaining Hoxd gene expression. However, quantitative collinearity is maintained in all configurations.