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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

In a concerted effort to identify biomarkers for lung and colon carcinomas by genome-wide transcriptional profiling, we describe the identification and cloning of one such gene as well as two additional closely related genes. Due to the strong sequence homology to the C. elegans UNC-112 we call this gene URP1, for UNC-112 related protein. We have also isolated the full-length clones for another novel related gene, URP2 and the previously discovered MIG-2 gene. Collectively, these proteins, together with two from Drosophila, appear to form a novel membrane-associated FERM and PH domain-containing protein family. Transcriptional analysis shows that only URP1 is significantly differentially regulated, being over-expressed in 70% of the colon carcinomas and 60% of the lung carcinomas tested. Quantification of URP1 expression by qRT-PCR showed up-regulation of the gene by 60-fold in lung tumors and up to nearly 6-fold in colon tumors. Northern blot analysis of URP1 indicates that normal expression is restricted to neuromuscular tissues. In contrast, the expression of URP2 appears to be confined primarily to tissues of the immune system. SNP analysis of URP1 reveals that it is highly polymorphic, containing seven sites, four of which are in the coding region and one position that results in the interchangeable substitution of glutamic acid and lysine. Finally, we have shown that the genomic structure for all three genes is nearly identical with all encoded by 15 exons although URP1 gene localized to chromosome 20p13, URP2 to 11q12 and MIG-2 to 14q22. This conserved exon structure suggests that all three members probably arose by gene duplication from one ancestral gene. The presence of multiple FERM domains characteristic of cytoplasmic plasma membrane to cytoskeleton linkers and a PH domain typical of membrane-anchored proteins involved in signal transduction suggest an important role for URP1 in tumorigenesis.

As large-scale sequencing accumulates momentum, an increasing number of instances are being revealed in which genes or other relatively rare sequences are duplicated, either in tandem or at nearby locations. Such duplications are a source of considerable polymorphism in populations, and also increase the evolutionary possibilities for the coregulation of juxtaposed sequences. As a further consequence, they promote inversions and deletions that are responsible for significant inherited pathology. Here we review known examples of genomic duplications present on the human X chromosome and autosomes.

ADAMTS-4 and ADAMTS-Aggrecanase-mediated degradation of aggrecan, the major aggregating proteoglycan of articular cartilage, is an early and sustained feature of osteoarthritis (OA (3, 4). Because of their preference for Glu at P1, both ADAMTS-4 and -5 are considered glutamyl endoproteinases. Whereas ADAMTS-5 is constitutively expressed in human cartilage, ADAMTS-4 is inducible by a number of inflammatory cytokines, such as interleukin-1␤ and tumor necrosis factor-␣ (5). Gene knockout of ADAMTS-5, but not ADAMTS-4, expression in mice has been shown to be chondroprotective in a surgical mouse model of OA (6, 7), yet in human OA cartilage explants both ADAMTS-4 and ADAMTS-5 mediate aggrecan breakdown (8). Inhibition of ADAMTS-4 and ADAMTS-5 activity may represent a viable option for slowing down the progression of cartilage deterioration in OA.Alignment of the known sequences flanking the ADAMTS-4 cleavage sites in the proteoglycan substrates, aggrecan, versican, and brevican, led to the proposal of a 24-amino acid consensus motif (9). Not surprisingly, a glutamic acid residue occupied P1 (100% conserved) with P2Ј occupied by the basic amino acids, Arg or Lys. The authors speculated that activity of ADAMTS family members toward proteoglycan substrates was primarily dictated by an extended 23-amino acid motif N-terminal to the scissile bond, and a short 3-amino acid motif downstream of the site of cleavage. However, unlike the scissile bonds in the aggregating proteoglycans, the site of ADAMTS-4 proteolysis in ␣ 2 -macroglobulin (␣ 2 M) is Met 690 /Gly 691 , with no requirement for Glu at P1 (10). Yet, P1Ј to P3Ј in ␣ 2 M, Gly-Arg-Gly, is remarkably similar to downstream sequences in aggrecan and brevican, implying that PЈ amino acids may be more important in recognition and catalysis than sequences upstream of the scissile bond. ADAMTS-4 has also been shown * The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.