Physical maps on chromosome 1q
FISH assignments
A total of 49 new and refined assignments to chromosome 1q were made by in situ hybridization (FISH) since the previous chromosome 1 workshop (Table 4). In addition, many more markers (genes, ESTs, STSs) have been localized on contigs of YAC and bacterial clones in 1q (Table 5). Of note is the long list of genes assigned to the gene-rich region 1q21. These include a novel gene encoding the T cell-specific adapter protein (TSAd) involved in the control of T cell activation (Spurkland et al., 1998); the human HPRP3 gene encoding U4/U6-associated splicing factors (Heng et al., 1997); the human MP70 (Cx50; connexin 50) gene (Geyer et al., 1997); the human homolog of the murine mammary transforming gene (HMAT1) associated with tumorigenesis (Hwang et al., 1997); the cathepsin K gene, residing within 150 Kb of an evolutionarily related cysteine protease, cathepsin S (Gelb et al., 1997); the large subunit of cytochrome b (SDHC) in human liver complex II (Hirawake et al., 1997); the BCL9 gene which may be the target of translocation in some B-cell malignancies with abnormalities of 1q21 (Willis et al., 1998); the human ROR gamma (RORC), a member of the nuclear orphan receptor subfamily ROR/RZR of the steroid and thyroid hormone/retinoid receptor superfamily (Medvedev et al., 1997); and DAP3, the death associated protein 3 (Kissil & Kimchi, 1997); In addition, autosomal dominant medullary cystic kidney disease (ADMCKD) has been mapped to an approximately 8 cM region between D1S498 and D1S2125 corresponding to its physical localization within 1q21 as confirmed by FISH mapping (Christodoulou et al., 1998). The human extracellular matrix gene 1 (ECM1) also maps to 1q21 but outside the EDC region and the encompassing 6 Mb YAC contig (Smits et al., 1997).
Physical Mapping
Twelve new contig maps have been reported since the last workshop, with seven of these being presented at this meeting. Of note in this report are four new contigs from the Epidermal Differentiation Complex at 1q21, and the appearance of three sequence-ready bacterial clone contigs.
The Epidermal Differentiation Complex (EDC) at 1q21 contains an astoundingly large and still growing number of related genes which play an indispensable role in terminal differentiation of the human epidermis. To further exploit this important region, the European Commission is funding a network of nine laboratories, four of which presented results of last year's collaborative work at this meeting.
Commencing from the previously established 6 Mb contig of YACs covering the EDC and its flanking regions (Marenholz et al., 1996), Lioumi and colleagues (1998 and this workshop) have refined the physical map of 1q21 by generating 400 YAC derivatives. Accordingly, map resolution has been increased about 15 fold and the transcriptional map of the region has been extended by precisely localizing the EDC genes and positioning 20 ESTs reported to map between D1S442 and D1S305. The ESTs are arranged in two distinct clusters that were confirmed by isolating PACs and chromosome 1-specific cosmids. Two of the ESTs correspond to the genes for YL1 and selenium-binding protein (hSBP), both of which have potential tumor suppressor activity. The established order of markers and ESTs in the region is shown in Table 5.
To supply a starting resource for the large scale genomic sequencing of this region, South and colleagues (this workshop) constructed a 2.6 Mb sequence-ready contig of bacterial clones in 1q21 consisting of 55 PAC clones, 2 BAC clones, 28 cosmid clones, and one gap. The main contig, however, is continuous for 2.4 Mb and encompasses 26 of the 28 genes in the EDC, resolving these genes and various STS markers to the level of EcoRI restriction fragments. A full NotI and SalI restriction map along with a partial EcoRI restriction map has also been completed.
Mischke and colleagues (this workshop) used four of the YACs from the 6 Mb contig as hybridization probes for a gridded human keratinocyte cDNA library and reported the assignment of 16 additional transcribed sequences to 1q21. Eight genes represent novel, previously undetected transcripts of human keratinocytes, whereas the other eight correspond to already known genes including ADAR/DRADA (double-stranded RNA adenosine-deaminase); PRS31 (26S proteasome regulatory subunit p31; gene name pending); PS MB4 (proteasome beta-type subunit HsN3, thereby narrowing the map position reported by McCusker et al., 1997); TPM3 (alpha-tropomyosin 3); HAX-1 (HS-1 binding protein, gene name pending); LAMRL (laminin-binding protein like gene, gene name pending); NOTCH2-like (neurogenic locus notch protein homolog); and PIP5KI (phosphatidylinositol phosphate 5-kinase; gene name pending).
In summary, and as South and colleagues pointed out at this workshop, one would hypothesize that this region on chromosome 1q21 appears to be extremely gene rich, perhaps approaching the gene density of the major histocompatibility complex (MHC) on chromosome 6p, which yields a gene density of at least 55 genes/ Mb (Newell et al., 1996). In accord with that notion, Zhao & Elder (1997) have identified three additional cDNAs in the EDC by positional cloning that so far have not been identified by the European 1q21 consortium. In addition, a wealth of additional mapping results from 1q21 and a valuable tool for the analysis of this region can be found on the Chromosome 1 Home Page, where an updated release (2.0) of the "Characterization of chromosome 1q21 ESTs" was posted by Dr. Hans L. Vos on August 21, 1997.
The detailed characterization of the role of all the newly identified 1q21 genes in epidermal differentiation or in tumors frequently associated with this region of chromosome 1 is still emerging. However, FISH and molecular analyses of the amplification status of 14 markers of the region in thirty-six sarcoma samples have already indicated complex amplification patterns in such tumors, as reported at this workshop by Meza-Zepeda and colleagues.
Other contigs in 1q21 have either not yet been experimentally linked to the physical map and YAC contigs of the EDC or to each other, including the previously established contigs in 1q21 surrounding the FCGR1 genes (Maresco et al., 1996), the pycnodysostosis locus (Polymeropoulos et al., 1995; Gelb et al., 1996), and the EPH-related kinases (Cerretti et al., 1996). Likewise, the glucocerebrosidase (Gaucher disease) locus on chromosome 1q21 should be considered, for which Winfield and colleagues (1997) reported the identification of three additional, contiguous genes: propin1, sharing homology to a rat secretory carrier membrane protein 37 (SCAMP37); cote1, a gene of unknown function; and a protein kinase (clk2).
This workshop marked the first year for the presentation of sequence-ready bacterial clone (SRBC) contigs. Although the mapping and sequencing efforts at the Sanger Centre at this time are focused on the short arm of chromosome 1, three regions of the long arm were targeted for early sequence analysis based on their high gene density or on the availability of an existing SRBC contig. SRBC contigs were presented at the workshop by A. South at 1q21 (described above), H. Williams at 1q23-q25, and B. Schutte at 1q32-q41 (Table 5). The SRBC contig presented by H. Williams currently includes 624 PAC clones in 10 contigs containing 145 STSs and spans an estimated 4.8 Mb. The SRBC contig presented by B. Schutte originally included 14 BAC clones in a single contig containing 45 STSs that spans the 600 Kb critical region for the Van der Woude (VWS) syndrome gene. Recently, these reagents were used to find more STSs over this region and to identify an additional 97 PAC clones to the SRBC contig in this region. Eight of these clones were targeted for sequence analysis and are a various stages of completeness. Detailed information on these contigs, including clone names, sizes, and sequence or stage of sequence analysis, is available at the Sanger Centre’s Web site using "Webace" (see next section).
Gene structures
The genomic structure of 14 genes from 1q were reported since the last workshop (Table 6). Of significance is the fact that in the previous workshop, none of the reported gene structures were derived from Sanger sequence. In this report, the structure of almost half of the reported genes (TNR, VWS1, VWS17, VWS14, IRF6, VWS2) was determined solely or aided by analysis of genomic sequence generated by the Sanger Centre. This trend will undoubtedly increase and demonstrates the impact of the sequence generated by the Sanger Centre on genomic research on chromosome 1.