Emergence and evolution of chimeric pseudogenes (φgenes) contribute to genetic and functional diversity of the human genome

Genome evolution through rearrangements and selection drives the emergence of new genes, gene families, and species. Although pseudogenes (φgenes) are often regarded as "dead on arrival" due to disruptive mutations or loss of regulatory elements, our earlier work revealed that several φgenes remain transcriptionally active, challenging this assumption. Here, we show that segmental duplications at proximal loci can generate chimeric φgenes comprising contiguous sequences from two or more genes, occasionally through intron fusions. These fused introns and flanking exons appear to have co-evolved from ancestral parent genes. Co-opting of 5' regulatory elements from the upstream parent likely drives chimeric φgene activation, while 3' modifications enhance transcript stability. Some chimeric φgenes retain strong coding potential, producing novel or truncated proteins that preserve parental domains. Notably, their expression is restricted to human tissues and exhibits signatures of purifying selection. Functional analysis identifies ANAPC1P2 (vA-202) as a coding-noncoding (cnc) RNA that regulates p53 stability and translation, while HYDIN2 knockdown impairs neuronal differentiation, underscoring the regulatory significance of these chimeric φgenes. Collectively, our findings suggest that chimeric φgenes and their emergent functions contribute to human-specific traits, speciation, and adaptive evolution.