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

The study investigated the role of cis-regulatory elements (CREs) in the evolution of gene regulation by examining Hoxd genes in mouse vibrissae and chicken feather primordia. These skin appendages expressed different Hoxd gene subsets, influenced by lineage-specific enhancers, which likely utilized an ancestral chromatin topology for evolutionary changes. In contrast, gene regulation in the embryonic trunk of both species relied on conserved CREs, although many non-coding sequences active in the trunk had functionally diverged between species. This divergence suggested that transcriptional robustness was maintained despite significant enhancer sequence changes.