Centromeric α-satellite DNA at euchromatin/heterochromatin boundary of human chromosome 21

A clone covering the euchromatin/heterochromatin boundary was isolated from a cosmid library specific for the human chromosome 21. This DNA contained a long block of the centromeric α-satellite DNA, unique nucleotide sequences, and dispersed Alu and L1 repeats. The α-satellite block constituted about a half of total length (about 45 kb) of the cloned DNA. It was adjacent to, but not overlapping with the nonsatellite region. The border between alphoid and nonalphoid domains was found in the longest subclone of 11 kb. This subclone was completely sequenced, and the sequence analyzed. The primary structure of an alphoid DNA of about 12 kb was shown to be different from the known chromosome 21-specific alphoid families and from the other described sequences. It was attributed to the suprachromosomal family 4 characterized by monomeric organization of the ancestral repeat. This alphoid DNA had no higher-order repeated structures typical of satellites. Insertions of one Alu repeat and three truncated L1 repeats were detected. One of the latter was flanked by direct repeats, as common for the mobile elements of the human genome.