Comparative Regulatory Evolution of HIGD1A and HIGD2A Reveals Divergent Cis-Regulatory Architectures within the Human HIGD Gene Family

The HIGD gene family encodes mitochondrial proteins involved in hypoxia adaptation, mitochondrial homeostasis, and cellular stress responses. Although HIGD1A and HIGD2A perform related biological functions, the evolutionary divergence of their regulatory architectures remains poorly understood. Here, we performed a comparative in silico analysis of the human HIGD1A and HIGD2A loci using publicly available genomic resources, including UCSC Genome Browser annotations, ENCODE candidate cis-regulatory elements (cCREs), ReMap ChIP-seq datasets, EP300 occupancy profiles, TFAP2A binding sites, CTCF-associated regions, and vertebrate conservation tracks. Both loci contained promoter-like and enhancer-like regulatory signatures. However, HIGD2A displayed increased enhancer-associated complexity, stronger evolutionary conservation, and a conserved boundary-associated enhancer candidate near the NOP16–HIGD2A locus. In contrast, HIGD1A exhibited a broader but less conserved regulatory landscape. These observations support a model in which members of the HIGD gene family underwent cis-regulatory divergence following gene family evolution while retaining related mitochondrial functions. The identified candidate regulatory regions provide a framework for future functional studies investigating regulatory specialization within mitochondrial gene families.