Overlapping Yeast Artificial Chromosome Research Articles

Refinement within single yeast artificial chromosome clones of a minimal region commonly deleted on the short arm of chromosome 7 in Wilms tumours.

Cytogenetic and molecular data indicate an involvement of genes mapped to the proximal portion of the short arm of chromosome 7 (7p) in Wilms tumours (WTs). We have analysed 38 WTs using a panel of eight microsatellite markers mapped to proximal 7p. Loss of heterozygosity (LOH) in tumour, compared with matched constitutional DNA, was identified in eight cases. To define better the minimal region commonly deleted in these tumours, they were analysed with nine additional markers, mapped within the region of interest. One tumour (case 30) showed LOH for only one marker (D7S510), while maintaining heterozygosity for the two immediately flanking loci (D7S555 and D7S668). This result was confirmed by fluorescence in situ hybridisation analysis, which showed that in the majority (65%) of nuclei from tumour 30 hybridising with a bacterial artificial chromosome clone containing the D7S510 locus, only one signal was visible. Noticeably, both markers defining the limits of the observed deleted region are simultaneously present within two distinct overlapping yeast artificial chromosome (YAC) clones mapped to chromosome bands 7p13-p14. This suggests that the maximum length of the missing DNA fragment was approximately 1.3 Mb, corresponding to the length of the smaller of the two YAC clones. In all other cases that showed LOH, the deletion encompassed the 7p13-p14 region. For this reason, we speculate that the identified interval contains a gene whose inactivation is important for the development of at least a fraction of WTs.

Regional insertional mutagenesis of genes on Arabidopsis thaliana chromosome V using the Ac/Ds transposon in combination with a cDNA scanning method.

For regional insertional mutagenesis of Arabidopsis thaliana genes, we combined a cDNA scanning method (Hayashida et al. Gene 1995; 165:155-161) and an Ac/Ds transposon designed for local mutagenesis, and evaluated this approach with two overlapping yeast artificial chromosome (YAC) clones, CIC7E11 and CIC8B11, on A. thaliana chromosome 5. We applied a previously developed novel cDNA selection method using DNA latex particles (cDNA scanning method) to the two YAC clones and constructed two sub-libraries in which cDNAs for genes on each YAC DNA were concentrated. From each sub-library we isolated cDNAs for genes on each YAC DNA, partially sequenced them, and produced expressed sequence tags (ESTs). In total, 113 non-redundant groups of cDNAs were obtained. Forty-four per cent of these EST clones were novel, and 34% had significant homology to functional proteins from various organisms. In parallel, we transposed Ds from a donor Ds-GUS-T-DNA line, Ds4391-20, already mapped to the CIC7E11/8B11 region. We obtained Ds-transposed lines and recovered their Ds-flanking genomic DNAs by thermal asymmetric interlaced (TAIL) polymerase chain reaction (PCR). Dot-blot analysis indicated that 20% of the lines contained transposed Ds in the CIC7E11/8B11 region, suggesting that this Ac/Ds transposon system is effective for regional insertional mutagenesis. To isolate Ds insertion mutants in the genes identified from the CIC7E11/8B11 region, we carried out PCR screening from 800 Ds-containing lines using Ds-specific and gene-specific primers that were designed from the 113 cDNA sequences identified by the cDNA scanning method. We found that 49 lines contain Ds insertion mutations, and that five lines contain Ds mutations in genes that are mapped to the sequenced CIC7E11/8B11 genomic DNA region. These results indicate that combining the cDNA scanning method and the Ac/Ds transposon gives a powerful tool for regional insertional mutagenesis not only in Arabidopsis but also in other plants or crops whose genomes are not sequenced.

Molecular characterization of a novel amplicon at 1q21-q22 frequently observed in human sarcomas.

In a recent comparative genomic hybridization (CGH) study of a panel of sarcomas, we detected recurrent amplification of 1q21-q22 in soft tissue and bone tumours. Amplification of this region had not previously been associated with sarcoma development, but occasional amplification of CACY/S100A6 and MUC1 in 1q21 had been reported for melanoma and breast carcinoma respectively. Initial screening by Southern blot analysis showed amplification of S100A6, FLG and SPRR3 in several sarcomas and, in a first attempt to characterize the 1q21-q22 amplicon in more detail, we have now investigated the amplification status of these and 11 other markers in the region in 35 sarcoma samples. FLG was the most frequently amplified gene, and the markers located in the same 4.5-Mb region as FLG showed a higher incidence of amplification than the more distal ones. However, for most of the 14 markers, amplification levels were low, and only APOA2 and the anonymous marker D1S3620 showed high-level amplifications (> tenfold increases) in one sample each. We used fluorescence in situ hybridization (FISH) to determine the amplification patterns of two overlapping yeast artificial chromosomes (YACs) covering the region between D1S3620 and FLG (789f2 and 764a1), as well as two more distally located YACs in nine selected samples. Six samples had amplification of the YAC containing D1S3620 and, in three, 764a1 was also included. Five of these tumours showed normal copies of the more distal YACs; thus, it seems likely that an important gene may be located within 789f2, or very close. Two samples had high copy numbers of the most distal YACs. Taken together, FISH and molecular analyses indicate complex amplification patterns in 1q21-q22 with at least two amplicons: one located near D1S3620/789f2 and one more distal.

The Human Genome Project: from mapping to sequencing.

Until recently, the "human genome" programs were mainly directed towards the development of maps to identify disease genes. The genetic map comprises about 8000 highly informative second generation markers of the microsatellite type. The density of markers is now sufficient to localize a gene for a monogenic disease with a precision of 1 to 2 million base pairs easily, and to define intervals which contain susceptibility genes for multifactorial disorders. A third generation map based on single nucleotide polymorphisms that can be genotyped using DNA chip technology is in progress. The physical map, based on sets of overlapping yeast artificial chromosomes ordered using sequence-tagged sites, covers over 90% of the genome. However, this physical map cannot serve as a support for sequencing because of the numerous rearrangements that occur in yeast artificial chromosomes. An international network of laboratories has mapped a set of more than 30,000 expressed sequences from cDNAs using whole genome radiation hybrids that enable integration of genes within existing maps. The human genome program is now progressively shifting to massive sequencing, although sequence ready maps are not available for the major part of the human genome. Similarly, our capacity to interpret the available genomic sequence remains limited.

Cloning of a breakpoint cluster region on chromosome 14 in uterine leiomyoma

A recurrent reciprocal chromosomal translocation, t(12;14)(q15;q24) is frequently observed in uterine leiomyoma. Chromosome 12 breakpoints have been shown to occur in a region of approximately 150 kb that contains the gene for a high mobility group protein (HMGI-C). The breakpoint region on chromosome 14 has not been precisely defined. We have generated a contig of overlapping yeast artificial chromosome (YAC) clones approximately 3 Mb in size. Fluorescence in situ hybridization (FISH) analysis showed that this contig spanned the t(12;14) breakpoints in three uterine leiomyomas and that the breakpoints in these tumors occurred within a 1 Mb region. A 30 kb cosmid spanning one of the breakpoints was isolated to set the stage for identifying regions on chromosome 14 that may cause this region to be a preferential site for chromosomal translocation.

Sequence ready-or not?

En route to the goal of the Human Genome Project (HGP) of obtaining the complete sequence of the human genome by the year 2005, several milestones have been reached (Collins and Galas 1993). First was the construction of a genetic linkage map with an average resolution of 1 cM (Dib et al. 1996). Second was the construction of a physical map with an average marker spacing of <150 kb (Hudson et al. 1995). These are laudable achievements; however, they only represent the completion of the initial phase of generating a sequenceready physical map of the human genome that will provide the necessary templates for large-scale sequencing. The current physical map is composed of two main resources. The first is physical maps made up of overlapping cloned fragments of human DNA. These clone contigs have been largely constructed using sequence-tagged site (STS) content mapping methods (Green and Olson 1990). The most comprehensive human genome physical maps are largely composed of overlapping yeast artificial chromosome [(YAC) Burke et al. 1992] clones [see http: / /wwwgenome.wi.mit.edu (Cohen et al. 1993; Chumakov et al. 1995; Hudson et al. 1995)]. Unfortunately, YAC clones are not suitable substrates for large-scale sequencing of the human genome. This is largely due to the high rate of chimaerism, the high frequency of deletions and rearrangements observed in these clones, and the difficulty of obtaining purified YAC DNA. The second physical map resource that is widely used is the whole-genome radiation hybrid (RH) map (Hudson et al. 1995; Schuler et al. 1996; Stewart et al. 1997). This map provides many additional ordered and binned markers and has been integrated with the YAC map. It is important to realize that although the average STS spacing is approximately one every 150 kb, the distribution is not random. A large number of these markers have been derived for positional cloning projects or from expressed sequence tags (ESTs), which may enrich marker density in disease regions or gene-rich regions, respectively. The combined maps provide much of the basis for the current effort to generate a sequence-ready map of the human genome. A sequence-ready map must meet certain criteria. Obviously, it must be composed of clones that are suitable sequence templates. Experience with sequencing the yeast and Caenorhabditis elegans genomes has shown that bacterial clones are an excellent choice. The primary clones being used are bacterial artificial chromosomes [(BACs) Shizuya et al. 1992], P1-derived artificial chromosomes [(PACs) Ioannou et al. 1994], and cosmids (Wahl et al. 1987). The clones corresponding to the STSs from a target region are typically isolated from arrayed libraries using PCR or hybridization strategies (see Fig. 1). An alternate approach is to subclone YAC clones into cosmids directly (Wong et al. 1997). Once the appropriate clones have been identified, the next step is to assemble these clones into an ordered contig. Clones are subjected to restriction endonuclease digestion, and fragments are separated by gel electrophoresis (Marra et al. 1997; Wong et al. 1997). Overlapping clones are then identified by shared restriction pattern or ‘‘fingerprint’’ similarities (see Fig. 2). It is a critical requirement for a sequence-ready map that the contigs have sufficient depth so that all restriction fragments can be validated by several overlapping clones. That is, if restriction fragment inconsistencies are observed, enough clones must be examined to establish the correct fragment pattern from the anomalous one. This is further complicated by the presence of polymorphisms. The BAC and PAC libraries being used for assembling sequence-ready maps of the human genome have two, and often more, haplotypes. Experience has shown that 6to

High-Resolution Physical Map of the Immunoglobulin λ Variant Gene Cluster Assembled by Quantitative DNA Fiber Mapping

Quantitative DNA fiber mapping (QDFM) allows rapid construction of near-kilobase-resolution physical maps by hybridizing specific probes to individual stretched DNA molecules. We evaluated the utility of QDFM for the large-scale physical mapping of a rather unstable, repeat-rich 850-kb region encompassing the immunoglobulin λ variant (IGLV) gene segments. We mapped a minimal tiling path composed of 32 cosmid clones to three partially overlapping yeast artificial chromosome (YAC) clones and determined the physical size of each clone, the extent of overlap between clones, and contig orientation, as well as the sizes of gaps between adjacent contigs. Regions of germline DNA for which we had no YAC coverage were characterized by cosmid to cosmid hybridizations. Compared to other methods commonly used for physical map assembly, QDFM is a rapid, versatile technique delivering unambiguous data necessary for map closure and preparation of sequence-ready minimal tiling paths.

A High-Resolution PAC and BAC Map of the SCA2 Region

The spinocerebellar ataxia type 2 (SCA2) gene has been localized to chromosome 12q24.1. To characterize this region and to aid in the identification of the SCA2 gene, we have constructed a 3.9-Mb physical map, which covers markers D12S1328 and D12S1329 known to flank the gene. The map comprises a contig of 84 overlapping yeast artificial chromosomes (YACs), P1 artificial chromosomes (PACs), and bacterial artificial chromosomes (BACs) onto which we placed 82 PCR markers. We localized eight genes and expressed sequence tags on this map, many of which had not been precisely mapped before. In contrast to YACs, which showed a high degree of chimerism and deletions in this region, PACs and BACs were stable. Only 1 in 65 PACs contained a small deletion, and 2 in 18 BACs were chimeric. The high-resolution physical map, which was used in the identification of the SCA2 gene, will be useful for the positional cloning of other disease genes mapped to this region.

A novel murine P-450 gene, Cyp4a14, is part of a cluster of Cyp4a and Cyp4b, but not of CYP4F, genes in mouse and humans.

Genomic clones for Cyp4a12 and a novel member of the murine Cyp4a gene family were isolated. The novel gene, designated Cyp4a14, has a GC rich sequence immediately 5' of the transcription start site, and is similar to the rat CYP4A2 and CYP4A3 genes. The Cyp4a14 gene spans approximately 13 kb, and contains 12 exons; sequence similarity to the rat CYP4A2 gene sequence falls off 300 bp upstream from the start site. In view of the known sex-specific expression of the rat CYP4A2 gene, the expression and inducibility of Cyp4a14 was examined. The gene was highly inducible in the liver when mice were treated with the peroxisome proliferator, methylclofenapate; induction levels were low in control animals and no sex differences in expression were observed. By contrast, the Cyp4a12 RNA was highly expressed in liver and kidney of control male mice but was expressed at very low levels in liver and kidney of female mice. Testosterone treatment increased the level of this RNA in female liver slightly, and to a greater extent in the kidney of female mice. In agreement with studies on the cognate RNA, expression of Cyp4a12 protein was male-specific in the liver of control mice and extremely high inducibility of Cyp4a10 protein, with no sex differences, was also demonstrated. In view of the overlapping patterns of inducibility of the three Cyp4a genes, we investigated whether the three genes were co-localized in the genome. Two overlapping yeast artificial chromosome (YAC) clones were isolated, and the three Cyp4a genes were shown to be present on a single YAC of 220 kb. The Cyp4a genes are adjacent to the Cyp4b1 gene, with Cyp4a12 most distant from Cyp4b1. The clustering of these two gene subfamilies in the mouse was replicated in the human, where the CYPA411 and CYP4B1 genes were present in a single YAC clone of 440 kb. However, the human CYP4F2 gene was mapped to chromosome 19. Phylogenetic analysis of the CYP4 gene families demonstrated that CYP4A and CYP4B are more closely related than CYP4F.

Generation of novel human MHC class II mutant B-cell lines by integrating YAC DNA into a cell line homozygously deleted for the MHC class II region.

The human B lymphoblastoid cell line (LCL) 721.174 sustains a large homozygous deletion in the major histocompatibility complex (MHC) class II region that results in an absence of DQ and DR molecules as well as a deficiency in the assembly and transport of class I molecules to the cell surface. The deleted genes include the transporters associated with antigen processing TAP1 and TAP2, DMA and DMB which are involved in editing class II bound peptides, and four genes whose roles in antigen processing are unclear; the low mass polypeptide genes LMP2 and LMP7, and DNA and DOB. To study this region we have integrated into 721.174 two overlapping yeast artificial chromosome (YAC) clones which cover the interval LMP2-DRA inclusive. Three clones (11.2A1.1, 4D1D10.1 and 4D1D10.2), containing complete copies of the transfected YAC, produced varying levels of mRNA from the LMP, TAP, DQ and DR genes and corresponding levels of LMP and TAP protein. Class I cell surface expression was restored in 11.2A1.1 and 4D1D10.1, as was DR expression in both 4D1D10 transfectants. These studies demonstrate the feasibility of introducing large groups of functional genes back into human lymphoblastoid cells sustaining deletions, with full restoration of biological function. The procedure could be exploited in order to restore all but one gene covered by the deletion, effectively producing a single gene defect. This could be used to introduce copies of genes engineered to contain mutations and to study cis regulatory elements at some distance from the chosen loci.

Substantial narrowing of the Niemann-Pick C candidate interval by yeast artificial chromosome complementation.

Niemann-Pick disease type C (NP-C) is an autosomal recessive lipidosis linked to chromosome 18q11-12, characterized by lysosomal accumulation of unesterified cholesterol and delayed induction of cholesterol-mediated homeostatic responses. This cellular phenotype is identifiable cytologically by filipin staining and biochemically by measurement of low-density lipoprotein-derived cholesterol esterification. The mutant Chinese hamster ovary cell line (CT60), which displays the NP-C cellular phenotype, was used as the recipient for a complementation assay after somatic cell fusions with normal and NP-C murine cells suggested that this Chinese hamster ovary cell line carries an alteration(s) in the hamster homolog(s) of NP-C. To narrow rapidly the candidate interval for NP-C, three overlapping yeast artificial chromosomes (YACs) spanning the 1 centimorgan human NP-C interval were introduced stably into CT60 cells and analyzed for correction of the cellular phenotype. Only YAC 911D5 complemented the NP-C phenotype, as evidenced by cytological and biochemical analyses, whereas no complementation was obtained from the other two YACs within the interval or from a YAC derived from chromosome 7. Fluorescent in situ hybridization indicated that YAC 911D5 was integrated at a single site per CT60 genome. These data substantially narrow the NP-C critical interval and should greatly simplify the identification of the gene responsible in mouse and man. This is the first demonstration of YAC complementation as a valuable adjunct strategy for positional cloning of a human gene.

A 2-Mb YAC Contig and Physical Map of the Natural Killer Gene Complex on Mouse Chromosome 6

We have constructed a physical map of a >2-Mb region on mouse chromosome 6 that contains the natural killer gene complex (NKC). The map comprises a contig of 14 overlapping yeast artificial chromosomes onto which we positioned 25 NKC markers. NKC genetically linked genes encode >17 proteins that directly control innate NK cell-mediated tumor lysis and disease resistance. Herein we show thatNkrp1genes are clustered in a region flanked byA2mandCd69genes and that mostLy49genes are clustered in a distal region ∼1 Mb distant. Importantly, syntenic intervals of mouse chromosome 6 and human chromosome 12p that include the NKC are conserved. NKC species conservation suggests that the human NKC may contain orthologues for the mouse viral disease resistance genes,Cmv1andRmp1.The high-resolution NKC map will facilitate investigation of NKC gene regulation and identification of phenotypically defined gene products that confer NK cell defense against viral pathogens.

Characterization of a YAC contig containing the NBCCS locus and a novel Kruppel-type zinc finger sequence on chromosome segment 9q22.3

Gorlin's syndrome or nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant disorder characterized by a familial or hereditary predisposition to basal cell carcinomas (generally multiple and of early onset), odontogenic keratocysts (jaw cysts), palmar and plantar pits, a wide variety of developmental defects, as well as cancers such as medulloblastomas and ovarian fibromas. The gene for NBCCS has been mapped to human chromosome region 9q22.1-q31 by linkage analysis and by cytogenetic evidence of deletions in this region in patients with the syndrome. This is supported by loss of heterozygosity in tumors of polymorphic marker loci flanked by D9S197 and D9S180. We have utilized sequence tagged site (STS) mapping and somatic cell hybrid panel analysis to construct two overlapping yeast artificial chromosome (YAC) contigs spanning this region of the genome. We used the YAC contigs to identify a new zinc finger gene containing a highly informative microsatellite locus.

Localisation of a human homologue of the Drosophila mnb and rat Dyrk genes to chromosome 21q22.2.

Exon trapping was used to identify portions of human chromosome 21-encoded genes. More than 600 potential exons on the chromosome have been cloned and characterised to date. A BLAST search of databases revealed that three of these trapped "exons", hmc18a08, hmc18f10 and hmc27g09, showed strong homology to different regions of the Drosophila mnb (Genbank X70794) and rat Dyrk (Genbank X79769) genes, indicating that these three exons may be portions of a human homologue of these genes (we termed this gene MNB for minibrain). With amplification by the polymerase chain reaction and hybridisation analysis we have mapped the human MNB gene on overlapping yeast artificial chromosomes 336G11 and 806A11 of chromosome 21q22.2 between markers D21S65 and ERG. The Drosophila mnb (minibrain) gene, which encodes a member of the protein kinase family, is involved in postembryonic neurogenesis. The Dyrk gene, which encodes a dual specificity protein kinase, is a rat homologue of the Drosophila mnb gene. The kinase activity is dependent on tyrosine residues in the catalytic domain, and it has been speculated that the protein is involved in control of the cell cycle. Altered expression of the human MNB gene may be involved in the pathogenesis of certain phenotypes of Down syndrome, including mental retardation.

A Yeast Artificial Chromosome Contig andNotI Restriction Map That Spans the Tumor Suppressor Gene(s) Locus, 11q22.2–q23.3

Human chromosome 11q22–q23 is a pathologically important region in which a high level of loss of heterozygosity has been reported for breast, ovary, cervical, colon, and lung carcinomas, malignant melanomas, and hematologic malignancies. This strongly indicates that one or more tumor suppressor genes reside within the deleted region. In this report, we report the development of a contig map that covers most of the deleted regions found in these malignancies. The map comprises a contig of 66 overlapping yeast artificial chromosomes (YACs) and spans a region of 17 Mb from thePGRgene at 11q22.2 to theMLLgene at q23.3. In the process of screening the YACs, 50 new sequence-tagged site markers were developed from the termini of the YAC inserts. These markers were used for chromosome walking, and the data were then integrated into the contig map.NotI restriction mapping of these YACs revealed the presence of at least 26NotI sites in the region. Using 22 of them, aNotI restriction map of the region fromPGRto D11S939 was developed. This YAC contig will provide efficient tools for identification of the putative tumor suppressor gene(s).

Mitochondrial glycerol-3-phosphate dehydrogenase. Cloning of an alternatively spliced human islet-cell cDNA, tissue distribution, physical mapping, and identification of a polymorphic genetic marker.

Pancreatic beta-cell mitochondrial glycerol-3-phosphate dehydrogenase (mGPDH) plays a major role in glucose-induced insulin secretion. Decreased activity of this enzyme has thus been proposed to play a role in the pathogenesis of NIDDM. Cloning of human insulinoma mGPDH cDNAs disclosed the existence of two variant transcripts with different 5' ends. Reverse transcription polymerase chain reaction (PCR) confirmed the presence of both mGPDH mRNAs in purified native human pancreatic islets and other tissues. A major 6.5-Kb mGPDH transcript was detected by Northern blot analysis in RNA from human and rat pancreatic islets, with distinctly lower levels in other human tissues, indicating that previously reported high mGPDH enzymatic activity in beta-cells is determined by high transcript levels. The mGPDH gene was mapped to chromosome 2 by PCR analysis of genomic DNA from human/rodent somatic cell hybrids, and five independent overlapping yeast artificial chromosome (YAC) clones containing the mGPDH sequence were identified from the Centre d'Etude du Polymorphisme Humain YAC library. Analysis of these YAC clones identified a highly polymorphic chromosome 2q21-q33 dinucleotide repeat genetic marker (D2S141) physically linked to the mGPDH gene. These studies provide the means to investigate the role of the human mGPDH gene in the pathogenesis of NIDDM and illustrate the value of a novel strategy to identify genetic markers for diabetes candidate genes.

The telomeric and centromeric ends of HLA class I: MCD maps of YAC derived cosmids and sequence analysis of 740 kb of genomic DNA.

We previously isolated and characterized a set of overlapping yeast artificial chromosome (YAC) clones spanning 2.4 Mb, including the entire MHC class I region, as a first step towards a detailed genetic analysis. We report here the genomic sequence of the two ends of HLA class I. The centromeric portion of HLA class I, extending from TNF to HLA-C was determined using two different sources of genomic DNA. As a first source, we sequenced cosmids (provided by T. Spies) derived from a total human DNA library which were mapped with conventional restriction digestion and fingerprinting. A second more generalizable approach was used to obtain cosmids for the remainder of the region. The new technology of Multiple-Complete-Digest (MCD) mapping, developed in Maynard Olson's laboratory, was used to map cosmids derived from YACs. This technique involves screening deep cosmid libraries derived from selected YACs and subjecting the cosmids to complete digestion with restriction enzymes, followed by computational assembly into completed maps. This method was also used to obtain material for sequence from three overlapping YACs covering a contiguous region from HLA-G to a point 330 kb telomeric. Among the plethora of new genetic information is a detailed picture of the organization of new multigene families contained within the telomeric end and of members of families spread throughout HLA class I. A clear relationship between the telomeric and centromeric ends of HLA class I has been defined, suggesting that large portions of these regions derived from a common ancestor. Our results demonstrate genomic sequencing to be one of the most effective and efficient means of identifying new genes, yielding information about genomic structure, regulation, and offering new insights into the meaning of physical relationships among functionally interacting genes.

Integrated Physical, Genetic, and Genic Map Covering 3 Mb Around the Human NGF Gene (NGFB) at 1p13

We have characterized 11 overlapping yeast artificial chromosomes (YACs) in the 1p13 region, 8 of them containing the human nerve growth factor (NGF) gene (HGMW-approved symbol NGFB). Sequence-tagged sites (STSs) corresponding to YAC extremities have been designed and used for chromosome assignment on a panel of monochromosomic somatic cell hybrids to check for YAC chimerism, in parallel with analyses by fluorescencein situhybridization. Determination of end STS content and restriction mapping of the YACs led to the construction of a 3-Mb YAC contig. Four microsatellite markers from the Généthon collection and seven genes known to map to the 1p13 region have been ordered on the contig around the NGF gene. A new gene transcript from the Genexpress catalog has been localized on the contig. This work provides an integrated physical, genetic, and genic map of this chromosome 1 region. It constitutes a basis for determining the structure of the NGF gene and for further characterizing its genic environment.

A second-generation YAC contig map of human chromosome 12.

Human chromosome 12 constitutes approximately 4.5% of the human genome and has an estimated size of 135 million base pairs (Mb). We have started to construct a high-resolution physical map of chromosome 12 as overlapping yeast artificial chromosomes (YACs), using as a foundation the first-generation physical map of this chromosome covers nearly 102 Mb of DNA and includes 426 highly polymorphic, monomorphic and gene-based markers. We also mapped 119 of the YACs, most of which are part of the physical map, by cytogenetic methods. Thus the map integrates genetic, physical and cytogenetic data and provides information about the organization of this chromosome and will help in the localization and cloning of disease-related genes. The strategy used here to generate the chromosome-12 map could be applied for the rapid construction of physical and expression maps for other human chromosomes.

Structure and Organization of the Human Glucose Phosphate Isomerase Gene (GPI)

Two overlapping yeast artificial chromosome clones containing the human glucose 6-phosphate isomerase gene (GPI) have been isolated. PCR and direct sequencing were used to determine the exon/intron structure of the gene. The gene spans in excess of 40 kb and consists of 18 exons ranging in size from 44 to 153 bp. All splice sites conform to the GT/AG rule.