Lineage-specific regulatory evolution: insights from massively parallel reporter assays

Lineage-specific genetic variants play a key role in evolutionary divergence, particularly through changes in cis-regulatory elements that fine-tune gene expression. Massively parallel reporter assays (MPRAs) provide a powerful approach to characterize these variants at scale. This review highlights how MPRAs have been used to study lineage-specific regulatory activity in enhancer elements, including human accelerated regions, human adaptive quickly evolving regions, and short human-specific conserved deletions. We discuss the effects of enhancer variation on traits distinguishing modern humans, archaic hominins, and primates, as well as how MPRAs disentangle cis- and trans-regulatory contributions to gene expression divergence. As MPRA technology advances, integrating it with CRISPR-based validation and artificial intelligence–driven predictions will further illuminate the role of lineage-specific regulatory evolution.