GENOMICS 11,15-23 (1991) Chromosome-Specific Alpha Satellites: Two Distinct Families on Human Chromosome 18 I. A. ALEXANDROV,* T. D. MASHKOVA,t T. A. AKOPIAN,$ L. I. MEDVEDEV,* L. L. KISSELEV,t S. P. MITKEVICH,* ANDY. B. YUROV* *All-Union Research Center of Mental Health, Moscow, USSR; tEngelhardt Institute of Molecular Biology, Moscow, USSR; and *All-Union Research Institute of Agricultural Biotechnology, Moscow, USSR Received October 22, 1990; revised March 8, 1991 Two types of human chromosome M-specific alpha satel- lite fragments have been cloned and sequenced. They repre- sent closely related but distinct alphoid families formed by two different types of the higher-order repeated units (1360-bp EcoRI and 1700-bp HindI fragments) that do not alternate in the genome. The individual repeats within each family are 99% identical and interfamily homology is about 78%. Sequence analysis shows that both repeats be- long to alphoid suprachromosomal family 2, but their ho- mology is not higher than that of family members located on different chromosomes. Therefore, the two repeats shared a common origin in the recent past, although they are not the direct offspring of one ancestral sequence. Our data indicate that these two 18-specific domains have ap- peared as a result of two separate amplification events. De- spite the high degree of homology, they are not undergoing intrachromosomal homogenization, although some varia- tion of this process might take place within each do- main. Q 1991 Academic Press, Inc. IN-I’RODUCl-ION Alpha satellite is a human repeated DNA localized in the pericentromeric regions of all chromosomes. The basic repeated unit is a monomer about 171 bp in length. Several related but not identical monomers may form a higher-order repeated unit that is reiter- ated tandemly. The chromosome-specific organization of human alpha satellite DNA is well characterized (see Willard and Waye, 1987a, for review). Its main features are two levels of homology corresponding to chromo- some-specific and suprachromosomal alphoid fami- lies. Chromosome-specific families are relatively ho- Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under Accession Nos. M65181 and M65182. mogeneous subsets of higher-order repeated units, which are distinct in different chromosomes. Su- prachromosomal families are groups of chromosome- specific variants that have originated recently from a common ancestor. The three main alphoid su- prachromosomal families of the human genome have been mapped in the following chromosomes: for fam- ily 1, chromosomes 1, 3, 5,6, 7, 10, 12, 16, and 19; for family 2, chromosomes 2,4,8,9,13,14,15,18,20,21, and 22; and for family 3 chromosomes 1, 11,17, and X (Manuelidis, 1978; Alexandrov et al. 198613, 1988; Willard and Waye, 1987b). Given the high homogeneity of chromosome-spe- cific families (usually 99-95%), it was proposed (Wil- lard and Waye, 1987a) that alphoid sequences of one chromosome undergo homogenization that fixes only one type of alphoid higher-order repeated unit per chromosome. However, the coexistence of two al- phoid subsets on chromosomes 7 (Waye et aZ., 1987), 1 (Alexandrov et aZ., 1988), and 15 (Choo et aZ., 1990) suggests that the subsets distinguished by a certain degree of divergence may not be homogenized within one chromosome. Here, we present a new example of two distinct but internally homogeneous alpha satellite domains on chromosome 18. These sequences share 78% homol- ogy and apparently are not homogenized within chro- mosome 18. The structure of the two 18-specific families and their relation to other alpha DNA types were com- pared using Southern analysis, in situ hybridization, and sequencing. Similar localization and common se- quence motifs proved that both families belong to al- phoid suprachromosomal family 2 (chromosomes 2,4, 8,9,13,14,15,18,20,21, and 22). Sequence compari- sons within this family confirm that the alphoid do- mains of the above-mentioned chromosomes have evolved from a single dimeric ancestral sequence, not identical to the ancestors of suprachromosomal fami- lies 1 and 3. 15 0888-7543/91$3.00 Copyright 0 1991 by Academic Press, Inc. AU rights of reproduction in any form reserved.