Skin regional specification and higher-order <i>HoxC</i> regulation.

Abstract

The integument plays a critical role in functional adaptation, with macro-regional specification forming structures like beaks, combs, feathers, and scales, while micro-regional specification modifies skin appendage shapes. However, the molecular mechanisms remain largely unknown. Craniofacial integument displays dramatic diversity, exemplified by the Polish chicken (PC) with a homeotic transformation of comb-to-crest feathers, caused by a 195-base pair (bp) duplication in <i>HoxC10</i> intron. Micro-C analyses show that HoxC-containing topologically associating domain (TAD) is normally closed in the scalp but open in the dorsal and tail regions, allowing multiple long-distance contacts. In the PC scalp, the TAD is open, resulting in high <i>HoxC</i> expression. CRISPR-Cas9 deletion of the 195-bp duplication reduces crest feather formation, and <i>HoxC</i> misexpression alters feather shapes. The 195-bp sequence is found only in Archelosauria (crocodilians and birds) and not in mammals. These findings suggest that higher-order regulation of the <i>HoxC</i> cluster modulates gene expression, driving the evolution of adaptive integumentary appendages in birds.