CpG Islands Are Associated with Conserved Core Functions and Gene Family Evolution in Vertebrates

CpG islands (CGIs) are key genomic features enriched in the promoters of vertebrate genes. Compared with cold-blooded animals, CGIs are markedly enriched in the promoters of warm-blooded animals and are present in the majority of mammalian housekeeping genes, highlighting their importance in transcriptional regulation. Although the distribution and physiological roles of CGIs are well characterized, their role in gene and genome evolution remains poorly understood. Here, we show that genes containing CGIs in their promoters (GCPs) are evolutionarily conserved, whereas non-GCP genes evolve under comparatively relaxed constraint. We further show that GCPs are predominantly associated with core cellular processes, including nuclear and metabolic functions, whereas non-GCP genes are enriched in specialized functions such as immune response and sensory perception. At the level of gene families, we observe phylogenetic heterogeneity among paralogs, with a preferential enrichment of GCPs in ancient, core-function genes and their depletion in more recently derived, specialized genes. Furthermore, we identify a relationship between gene family size and GCP frequency, with implications for both genome organization and evolutionary dynamics. We propose that the association of CGIs with gene conservation, together with their biased distribution among genes of different phylogenetic origins within gene families, may reflect the distinct regulatory and functional constraints acting on these genes rather than a direct causal effect of CGIs on gene conservation. Collectively, these findings provide new insights into the relationship between promoter CGIs, gene function, and vertebrate genome evolution.