Developmental and Evolutionary Comparative Analysis of a Regulatory Landscape in Mouse and Chicken

The study examined the regulatory landscape of Hoxd genes in mice and chickens, focusing on their expression in skin appendages and the embryonic trunk. It found that while the overall chromatin structure was conserved, cis-regulatory elements (CREs) exhibited high plasticity, allowing for species-specific regulatory activities. Different subsets of Hoxd genes were expressed in mouse vibrissae and chicken feather primordia, driven by lineage-specific enhancers. The research highlighted the evolutionary divergence in regulatory elements, with conserved gene expression occurring despite sequence divergence. The study concluded that the regulatory architecture of TADs provides a structural framework for the evolution of new enhancer sequences, contributing to lineage-specific regulatory evolution.