Developmental and Evolutionary Comparative Analysis of a Regulatory Landscape in Mammals and Birds

The study analyzed the regulation of Hoxd genes in murine vibrissae and chicken feather primordia, comparing them to the regulatory mechanisms in the elongation of the posterior trunk in amniotes. It found that distinct subsets of Hoxd genes in these skin appendages are contacted by different lineage-specific enhancers, likely due to an ancestral chromatin topology. In contrast, the regulations in the mouse and chicken embryonic trunk partially relied on conserved cis-regulatory elements (CREs). Despite the divergence in CRE sequences between species, transcriptional robustness was maintained, suggesting functional divergence of non-coding sequences active in the trunk. This was supported by a genome-wide comparative approach.