In addition to sustaining an exponentially increasing rate of gene finding (Collins 1995), yeast artificial chromosome/sequence-tagged site (STS/YAC)-based maps (Burke et al. 1987;Olson et al. 1989) have begun to reveal additional features of chromosome structure and dynamics. For example, during the development of maps for subportions of the X chromosome, the existence of a second "pseudoautosomal" region at the Xq terminus of the chromosome was demonstrated (Freije and Schlessinger 1992;Li and Hamer 1995), followed by the discovery that the region shows a unique phenomenon of gene inactivation on both the X and Y homologs (D'Esposito et al. 1996). In another instance, it was shown that a cluster of genes in a delimited segment of XpI 1 escape X inactivation (Miller et al. 1995). As the density of markers across the chromosome has increased beyond the 100-kb resolution goal suggested for the 1Corresponding author. E-MAIL davids@sequencer.wustl.edu; FAX (314) 362-3203."genome initiative," additional features are revealed, as described here.The average inter-STS distance of-75 kb has been achieved by the placement of 2091 STSs on cognate YACs across the 160 Mb of the chromosome. Collectively, the STSs sample -1% of Xspecific sequences. About half of the STSs (962) are made from YAC insert ends (Kere et al. 1992), and another 592 are from randomly derived unique Xchromosomal sequences. However, the STSs also include 97 expressed sequence tags (ESTs) and 190 gene-specific STSs from known genes, as well as 192 dinucleotide and 38 tri-and tetranucleotide repeat markers that detect polymorphism. As a result, the YAC/STS map can be integrated with transcriptional and genetic maps. RESULTS Mapping Strategy and PerformanceWe used a modified "all-walking" form of STS content mapping (Kere et al. 1992) in which STSs were
Forty-three yeast artificial chromosomes (YACs) from the X chromosome have been overlapped across the 4-Mb Xq21.3 region, which is homologous to a segment in Yp11.1. The region is formatted to 60-kb resolution with 57 STSs and is merged at its edges with contigs specific for X. This allows a direct comparison of marker orders and distances on X and Y. In addition to some sequence variation and possible differences in marker order, two larger evolutionary divergencies between the X and Y homologs were revealed: (1) The X homolog is interrupted by a small X-specific region detected by a 3-kb plasmid probe for locus DXS214. An STS was developed from one end of the probe, but the sequence at the other end was highly homologous to an L1 repetitive element. This suggests that the interpolation of the X-specific segment may have involved an L1-mediated event. (2) A 250-kb portion containing DXYS1 is several megabases away from the rest of the homologous DNA on the Y but is contiguous with the remainder of the homologous region on X. Marker orders are consistent with the origin of the Y-specific 250-kb region in a paracentric inversion after the initial transfer of X DNA to the Y chromosome.[All sequence data for the STSs are in the Genome Database and on the Washington University web site at http://genome.wustl.edu/cgm/cgm.html.]In addition to several smaller regions , three major regions of homology are shared by the human X and Y chromosomes ( Fig.1). Two of them comprise the pseudoautosomal regions at the tips of the p and q arms, respectively 2.5 and 0.35 Mb in length. The other homologous region, in Xq21.3 and Yp11.1 Vollrath et al. 1992; Affara and FergusonSmith 1994), differs from the pseudoautosomal segments in several respects. First, it is more extensive, on the order of 4 Mb. Second, unlike the pseudoautosomal portions, the homologous X and Y segments are not thought to pair during meiosis. In the chimpanzee and lower vertebrates, this region only exists on the X chromosome (Page et al. 1984;Geldwerth et al. 1985;Koenig et al. 1985;Affara and Ferguson-Smith 1994). Hence, the XY homology region is unique to humans and presumably arose by translocation of the region from the X to the Y chromosome relatively recently on the evolutionary time-scale.A clone map of the XY homology region on both X and Y can help to determine features of the evolution of the sex chromosomes and to initiate a comparison of their genetic content. Most of the euchromatic region of the human Y chromosome has been cloned in yeast artificial chromosomes (YACs) and formatted with sequence-tagged sites (STSs) Vollrath et al. 1992). A more recent map of the Y chromosome is provided by Jones et al. (1994), although marker order within the XY homology region is essentially the same as in Foote et al. (1992). On the Y chromosome, the corresponding DNA includes STSs sY20, sY21...sY52, in numerical order across a 4-Mb region, and a relatively small segment containing DXYS1, located ∼2 Mb more proximal.The homologous region on the X chromosome ha...
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