Human alphoid family of tandemly repeated DNA. Sequence of cloned tetrameric fragments and analysis of familial divergence.

Three tetramers of the 170 base-pair monomer repeat unit of human centromeric DNA (alphoid DNA) have been cloned and sequenced. Adjacent subunits differed in sequence by 30 to 45%, while dimers varied by 13 to 20% whether adjacent or not. Divergence was distributed unevenly across the monomeric sequence, such that two highly conserved segments adjoined clusters of insertions/deletions. Divergence, calculated from the cloned sequences or measured in uncloned DNA by thermal destabilization of mismatched reassociated duplexes, was far greater than previously estimated for the total human alphoid family. The population of these repeats within the human genome was not uniformly diverged, however, since restriction subsets of alphoid DNA contained as little as one-tenth the overall level of divergence. This indicates a hierarchical or familial structure of the genomic repeat population. Using cloned probes, human alphoid DNA was shown to be highly methylated and transcriptionally inactive. These data, along with evidence of conserved segments and periodicities (dimeric and higher-order) overlying considerable sequence diversity, support a structural role for this DNA family.