Polymorphism and divergence in the beta-globin replication origin initiation region

DNA sequence polymorphism and divergence was examined in the vicinity of th e human beta-globin gene cluster origin of replication initiation region (I R), a 1.3-kb genomic region located immediately 5' of the adult-expressed b eta-globin gene. DNA sequence variation in the replication origin IR and 5 kb of flanking DNA was surveyed in samples drawn from two populations, one African (from the Gambia, West Africa) and the other European (from Oxford, England). In these samples, levels of nucleotide and length polymorphism i n the IR were found to be more than two times as high as adjacent non-IR-as sociated regions (estimates of per-nucleotide heterozygosity were 0.30% and 0.12%, respectively). Most polymorphic positions identified in the origin IR fall within or just adjacent to a 52-bp alternating purine-pyrimidine (( RY)(n)) sequence repeat. Within- and between-population divergence is highe st in this portion of the IR, and interspecific divergence in the same regi on, determined by comparison with an orthologous sequence from the chimpanz ee, is also pronounced. Higher levels of diversity in this subregion are no t, however, primarily attributable to slippage-mediated repeat unit changes , as nucleotide substitution contributes disproportionately to allelic hete rogeneity. An estimate of helical stability in the sequenced region suggest s that the hypervariable (RY)(n) constitutes the major DNA unwinding elemen t (DUE) of the replication origin IR, the location at which the DNA duplex first unwinds and new strand synthesis begins. These findings suggest that the beta-globin IR experiences a higher underlying rate of neutral mutation than do adjacent genomic regions and that enzyme fidelity associated with the initiation of DNA replication at this origin may be compromised. The si gnificance of these findings for our understanding of eukaryotic replicatio n origin biology is discussed.