Epigenetic and evolutionary features of ape subterminal heterochromatin

Many African great ape chromosomes possess large subterminal heterochromatic caps at their telomeres that are conspicuously absent from the human lineage. Leveraging the complete sequences of great ape genomes, we characterize the organization of subterminal caps and reconstruct the evolutionary history of these regions in chimpanzees and gorillas. Detailed analyses of the composition of the associated terminal 32 bp satellite array from chimpanzee (termed pCht) and intervening segmental duplication (SD) spacers confirm two independent origins in the <i>Pan</i> and gorilla lineages. In chimpanzee and bonobo, we estimate these structures emerged ∼7.7 million years ago (MYA) in contrast to gorilla, in which they expanded more recently, ∼5.0 MYA, and now make up 8.5% of the total gorilla genome. In both lineages, the SD spacers punctuating the pCht heterochromatic satellite arrays correspond to pockets of decreased methylation, although in gorilla such regions are significantly less methylated (<i>P</i> < 2.2 × 10^-16) than in chimpanzee or bonobo. Allelic pairs of subterminal caps show a higher degree of sequence divergence than euchromatic sequences, with bonobo showing less divergent haplotypes and less differentially methylated spacers. In contrast, we identify virtually identical subterminal caps mapping to nonhomologous chromosomes within a species, suggesting ectopic recombination potentially mediated by SD spacers. We find that the transition regions from heterochromatic subterminal caps to euchromatin are enriched for structural variant insertions and lineage-specific duplicated genes. Our findings suggest independent evolution of subterminal caps converging on a common genetic and epigenetic structure that promoted ectopic exchange as well as the emergence of novel genes at transition regions between euchromatin and heterochromatin.