We found that the MSY heterochromatin encompasses at least six distinct sequence species (Supplementary Table 10), each forming long, rather homogenous tandem arrays, and two of which are located in the centromeric region. One centromeric array (DYZ3), based on a 171-bp alphoid primary unit with a 5.9-kb secondary periodicity, gradually merges, across a distance of 50 kb, with the euchromatic sequences of Yp (Supplementary Fig. 7f). On the opposite side of the centromere, an unrelated heterochromatic array (DYZ17), based on a GGAAT repeat unit, abruptly adjoins the euchromatic sequences of Yq (Supplementary Fig. 7h). Within the centromeric region, the alphoid (DYZ3) and GGAAT (DYZ17) arrays meet cleanly and without intermixing (Supplementary Fig. 7g). Another species of MSY heterochromatic sequences, the newly identified DYZ19 repeats, form a sharply demarcated island of tandemly repeated 125-bp units in the midst of the euchromatic sequences of proximal Yq (Supplementary Fig. 7i,j). This DYZ19 island, comprised of >3,000 repeat units, is roughly 400 kb in length and is remarkably homogeneous, with no Alu, LINE-1, or other insertions identified. When human metaphase chromosomes are stained with DAPI, the euchromatic region of Yq exhibits a single, thin pale band (Yq11.22), which we suspected might correspond to the DYZ19 island. This hypothesis was confirmed by hybridizing a fluorescent DYZ19 probe to DAPI-stained metaphase chromosomes in situ (FISH analysis; Supplementary Fig. 3a). The DYZ19 island can now serve as a cross-referenced landmark linking the light microscopic (cytogenetic) and sequence-based maps of the Y chromosome. The massive heterochromatic region of distal Yq, also known as Yq12, is extraordinarily polymorphic in length (1-3) and typically spans 40 Mb, or more than 1% of the haploid genome (4). We found that the Yq12 heterochromatin is comprised of at least three distinct sequence species (Supplementary Table 10). Immediately distal to the euchromatic sequences of Yq is a relatively homogenous array (DYZ18), not previously described, that is based on a GGAAT primary unit with a 2.9-kb secondary periodicity (Supplementary Fig. 7L). Chromosomal FISH analysis indicates that the DYZ18 sequences are restricted to this interface with Yq euchromatin and are not found elsewhere in the Yq12 heterochromatin (Supplementary Fig. 2b). The DYZ1 arrays, based on a GGAAT primary unit with a remarkably regular 3.6-kb secondary periodicity (Supplementary Fig. 7m), may comprise the bulk of the Yq12 heterochromatin (FISH studies not shown). The DYZ1 repeats were the first male-specific DNA sequences to be identified in the human genome (5, 6). We identified no BACs containing DYZ2, a third sequence species in Yq12 (Supplementary Table 10), and here only limited sequence information is available. Our FISH studies suggest the existence of at least two DYZ2 arrays that are separated by a large mass of DYZ1 repeats (not shown). We have not sequenced the entirety of any of the three heterochromatic regions, and thus additional sequence species may reside within one or more of these regions. In particular, our efforts to identify the distal boundary of the Yq12 heterochromatin were unsuccessful (Supplementary Fig. 1). In the course of these efforts, however, we discovered 65 kb of euchromatic, male-specific DNA that is located distal to the Yq12 heterochromatin but proximal to the long-arm pseudoautosomal region (Fig. 2). These most distal MSY sequences exhibit little similarity to the X chromosome or to other regions of the Y chromosome, but they are remarkably similar (as much as 98.5% identical) to sequences in human chromosomes 1, 2, 7, 10, and 16. We found no evidence of functional genes among these most distal MSY sequences. 1. Bobrow, M., Pearson, P.L., Pike, M.C. & el-Alfi, O.S. Length variation
in the quinacrine-binding segment of human Y chromosomes of different
sizes. Cytogenetics 10, 190-198 (1971). 2. Robinson, J.A. & Buckton, K.E. Quinacrine fluorescence of variant and
abnormal human Y chromosomes. Chromosoma 35, 342-352 (1971). 3. Schnedl, W. Flurescenzuntersuchungen ueber die Langenvariabilitaet des
Y-Chromosoms beim Menschen. Humangenetik 12, 188-194 (1971). 4. Morton, N.E. Parameters of the human genome. Proc. Natl. Acad. Sci. U.S.A.
88, 7474-7476 (1991). 5. Kunkel, L.M., Smith, K.D. & Boyler, S.H. Human Y-chromosome-specific
reiterated DNA. Science 191, 1189-1190 (1976). 6. Cooke, H. Repeated sequence specific to human males. Nature 262, 182-186