Characterization of a yeast artificial chromosome contig spanning the Huntington's disease gene candidate region

Huntington's Disease: Lessons from and for Molecular Neuroscience

The past 2 decades have witnessed an explosion in molecular neurogenetics and neurobiology. The aggres sive application of new techniques to the dominantly inherited disorder, Huntington's disease, defined the standard for the positional cloning of human genetic diseases. A parallel effort from neurobiologists and clinicians has set the stage for the development of potential new therapies for the disease. Along the winding road to finding the gene, many lessons were learned by clinicians and scientists alike. The next decade of research offers new challenges and rewards for those involved with this disease. The Neuroscientist 1:51- 58, 1995

Mouse models of Huntington disease: variations on a theme

An accepted prerequisite for clinical trials of a compound in humans is the successful alleviation of the disease in animal models. For some diseases, however, successful translation of drug effects from mouse models to the bedside has been limited. One question is whether the current models accurately reproduce the human disease. Here, we examine the mouse models that are available for therapeutic testing in Huntington disease (HD), a late-onset neurodegenerative disorder for which there is no effective treatment. The current mouse models show different degrees of similarity to the human condition. Significant phenotypic differences are seen in mouse models that express either truncated or full-length human, or full-length mouse, mutant huntingtin (mHTT). These differences in phenotypic expression may be attributable to the influences of protein context, mouse strain and a difference in regulatory sequences between the mouse Htt and human HTT genes.

The molecular genetics of Huntington disease — a history

The Huntington disease gene was mapped to human chromosome 4p in 1983 and 10 years later the pathogenic mutation was identified as a CAG-repeat expansion. Our current understanding of the molecular pathogenesis of Huntington disease could never have been achieved without the recent progress in the field of molecular genetics. We are now equipped with powerful genetic models that continue to uncover new aspects of the pathogenesis of Huntington disease and will be instrumental for the development of therapeutic approaches for this disease.

Identification of a deletion hotspot on distal mouse chromosome 4 by YAC fingerprinting

Using repetitive elements as probes, genomic DNA fingerprints of four randomly selected yeast artificial chromosome (YAC) clones (two human and two mouse-derived YAC) were analyzed to determine the mutation level following X-ray exposure. Because the repetitive probes were derived from the mammalian host DNA, most of the fingerprint bands originated from the artificial chromosomes and not from the yeast genome. For none of the YAC clones was the mutation frequency elevated following X-ray exposure. However, for one mouse-derived YAC, the mutation level was unusually high (7%; 42 mutants of 607 clones analyzed), whereas for the other three YACs, the mutation level was nearly 0%. Surprisingly, 40 of the 42 mutations were deletions occurring only at three of the 20 mouse specific fingerprint bands. One of the frequently deleted fragments was cloned, sequenced and mapped to distal mouse chromosome 4, which has been repeatedly reported to be the most unstable region of the whole mouse genome, associated with various tumors. Deletion mapping of six YAC mutants revealed this fragment to be completely deleted in four YACs. In the other two mutants, recombination occurred within the fragment, in each case initiated at the same LINE-1 element. In conclusion, the presented YAC fingerprint is a useful tool for detecting and characterizing unstable regions in mammalian genomes.

The third member of the transforming acidic coiled coil-containing gene family, TACC3, maps in 4p16, close to translocation breakpoints in multiple myeloma, and is upregulated in various cancer cell lines

We have recently identified a novel gene, TACC1 (transforming acidic coiled coil-containing gene 1), which is located close to FGFR1 within a region amplified in breast cancer on human chromosome 8p11. The coiled coil domain of this gene identified a series of cDNAs in the expressed sequence tag database, which suggested the existence of a family of TACC genes comprising at least three family members. We have now characterized the human and mouse TACC3 cDNAs, and demonstrate that this gene is upregulated in various cancer cell lines, and at Embryonic Day 15 in mice, suggesting that the TACC3 protein is involved in the control of cell growth and differentiation. The TACC3 gene maps telomeric to the FGFR3 gene in 4p16.3, close to a region disrupted by translocation breakpoints associated with multiple myeloma. Thus, TACC1, TACC2, and TACC3 map close to the corresponding FGFR1, FGFR2, and FGFR3 genes. The phylogenetic relationship among the three TACC genes is similar to that of the three FGFR family members. These relationships suggest that the FGFR and TACC genes arose from a physically linked ancestral gene pair. Subsequently, this gene pair has undergone two successive rounds of gene duplication to give rise to the three FGFR/TACC gene pairs on chromosomes 4, 8, and 10.

Active role of a human genomic insert in replication of a yeast artificial chromosome

Yeast artificial chromosomes (YACs) are a common tool for cloning eukaryotic DNA. The manner by which large pieces of foreign DNA are assimilated by yeast cells into a functional chromosome is poorly understood, as is the reason why some of them are stably maintained and some are not. We examined the replication of a stable YAC containing a 240-kb insert of DNA from the human T-cell receptor beta locus. The human insert contains multiple sites that serve as origins of replication. The activity of these origins appears to require the yeast ARS consensus sequence and, as with yeast origins, additional flanking sequences. In addition, the origins in the human insert exhibit a spacing, a range of activation efficiencies, and a variation in times of activation during S phase similar to those found for normal yeast chromosomes. We propose that an appropriate combination of replication origin density, activation times, and initiation efficiencies is necessary for the successful maintenance of YAC inserts.

A distamycin A-inducible fragile site, FRA8E, located in the region of the hereditary multiple exostoses gene, is not involved in HPV16 DNA integration and amplification

The rare fragile site is a specific point on a chromosome that is expressed as an isochromatid gap or break under certain conditions of cell culture and is inherited in a Mendelian codominant fashion. Five folate-sensitive fragile sites were cloned, and the molecular basis of fragile site mutation was shown to be a new class of mutation, called dynamic mutation, resulting from an allelic expansion of (CCG)n repeats. The mechanism responsible for other types of rare fragile sites, i.e., distamycin A-inducible and BrdU-requiring, is unknown, although cytogenetic studies suggested that these fragile sites play a mechanistic role in breakage and recombination and may also be integration and modification sites of foreign viral DNA genomes. A distamycin A-inducible fragile site, FRA8E, is mapped to 8q24.1 in which various loci implicated in genomic instability are located. Here we identified a YAC clone spanning both FRA8E and the hereditary multiple exostosis (EXT1) gene, using fluorescence in situ hybridization (FISH) analysis of a yeast artificial chromosome (YAC) contig. By using P1 clones as probes, the FRA8E locus was further localized to a 400-kb region including the EXT1 gene. Furthermore, the integration and amplification site of human papillomavirus 16 DNA in the ASCC (argyrophil small cell carcinoma) cells were shown not to coincide with FRA8E, but to be involved in an extensively broad genomic region of 8q24.1, including the c-myc gene.

Exon trapping and sequence-based methods of gene finding in transcript mapping of human 4p16.3

We have applied exon amplification, GRAIL2 exon prediction and EST database searching to a 2 Mb segment of chromosome 4p16.3. Experimental and computational methods of identifying exons were comparable in efficiency and apparent false positive rate, but were complementary in gene identification, revealing distinct overlapping sets of expressed sequences. EST searching was most powerful when we considered only those ESTs that show evidence of splicing relative to the genomic sequence. The combination of the three gene finding methods produced a transcription map of 30 loci in this segment of 4p16.3 that includes known human genes, homologs of loci identified in rodents and several anonymous transcripts, including a putative novel DNA polymerase and a gene related to Drosophila ash1. While most of the genes in the region have been found, our data suggest that even with the entire DNA sequence available, complete saturation of the transcript map will require additional, focused experimental effort.

The structure of the human multiple exostoses 2 gene and characterization of homologs in mouse and Caenorhabditis elegans

Hereditary multiple exostoses (EXT) is an autosomal dominant disorder characterized by multiple cartilage-capped outgrowths from the epiphyses of long bones. In some cases, these osteochondromas progress to malignant chondrosarcomas. Alterations in at least three genes (EXT1, EXT2, and EXT3) can cause this disorder. Two of these have been isolated (EXT1 and EXT2) and encode related members of a putative tumor suppressor family. We report here the genomic structure of the human EXT2 gene consisting of 14 exons (plus 2 alternative exons) covering an estimated 108 kb of chromosome 11p11-13. We have derived the DNA sequences at all exon/intron boundaries throughout this gene-information that is important for the detailed study of mutations in EXT2. We have also characterized the mouse EXT2 cDNA and have mapped the mouse locus to chromosome 2 between D2Mit15 and Pax6. This mouse homolog should enable transgenic knockout experiments to be initiated to further elucidate gene function. Interestingly, sequence comparisons reveal that the human and mouse EXT genes have at least two homologs in the invertebrate Caenorhabditis elegans, indicating that they do not function exclusively as regulators of bone growth. This observation opens the way for a functional analysis of these genes in nematodes and other lower organisms.

Mapping of murine YACs containing the genes Cea2 and Cea4 after B1-PCR amplification and FISH-analysis

PCR with primers specific for the murine B1 consensus sequence allows amplification of DNA from murine sources. We have used B1-PCR for amplifying yeast artificial chromosome (YAC) DNA which can be used to localize single YACs by fluorescence in situ hybridization. The genes for the pregnancy-specific glycoproteins Cea2 and Cea4, both belonging to the large carcinoembryonic antigen gene family, were localized by chromosomal in situ suppression hybridization of three YAC clones to murine chromosome 7A2-A3. This was facilitated by the use of the mouse lymphoma cell line WMP/WMP which contains nine pairs of Robertsonian fusion chromosomes.

Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q telomeres

Large terminal fragments of human chromosomes 2p, 6p, 8q, 12q, and 18q were cloned using yeast artificial chromosomes (YACs). RecA-assisted restriction endonuclease (RARE) cleavage analysis of genomic DNA samples from II unrelated individuals using YAC-derived probes confirmed the telomeric localizations of the half-YACs studied. The cloned fragments provide telomeric closure of maps for the respective chromosome arms and will supply the reagents needed for analyzing and sequencing these distal subtelomeric regions.

Repetitive sequence fingerprinting in the long range mapping of mammalian genomes

This review presents some properties of interspersed repeats, particularly human and mouse repeats, and shows how these have been utilized in long-range genome mapping. The link between the distribution of such repeats and their relationship with genome organization is discussed.

Construction of a human DNA library in a circular centromere-based yeast plasmid

The construction of a human DNA library in a centromere-based circular yeast plasmid is described. The vector contains the yeast CEN3 sequence, the URA3 gene for propagation in yeast and a hygromycin-resistance gene (HyR) for selection in mammalian cells. The library consists of 64,000 members with an average insert size of 150 kb, with some members containing inserts of > 1 Mb. We calculate that the library contains three human genome equivalents of DNA. Clones can be identified by a PCR-based screening of DNA pools from individual colonies that have been stored in microtiter wells.

Techniques in mammalian genome mapping

Increasing emphasis is being given to genomic cloning using Escherichia coli vectors of intermediate insert capacity, such as bacteriophage P1, P1-derived artificial chromosomes and the F factor based bacterial artificial chromosomes. These vectors are being used in addition to yeast artifical chromosomes (YACs) in recognition of the difficulties encountered with YAC stability and with handling of YAC DNAs (problems that will not easily be overcome). Nonetheless, YACs remain the most practical cloning system for global contig building. Efforts are currently under way to produce YAC contigs that represent the human and mouse genomes, and these will increasingly exploit extensive anchoring to detailed genetic maps. Intermediate capacity clone collections based on YAC contigs will follow, enabling the compilation of mapped gene catalogues. In this way, the era of big gene hunts will draw to a close.

Genomic organization of the human alpha-adducin gene and its alternately spliced isoforms

The cDNA for the human alpha-adducin gene has been cloned, and different alternately spliced forms have been identified. We report the complete genomic organization of the human alpha-adducin gene and these alternately spliced forms. The human alpha-adducin gene, spanning approximately 85 kb, consists of 16 exons ranging in size from 34 to 1892 bp. One of the spliced forms of the human alpha-adducin gene results from alternate use of the 5' splice donor site for exon 10, while another results in a truncated protein following insertion of 34 bp comprising exon 15, followed by a premature stop codon. This alternate spliced form of alpha-adducin is predicted to result in an altered carboxyl terminus that would eliminate a protein kinase and calmodulin binding site. Seven nucleotide substitutions and 4 insertion/deletions were also identified. The 5' region of the human alpha-adducin gene contains one Sp1 site, two AP2 sites, and two CAAT boxes. No TATA box was apparent, consistent with features of a housekeeping gene. We have mapped another cDNA within the first intron of the human alpha-adducin gene, suggesting overlapping genes in this 4p16.3 genomic region.

The role of recombination and RAD52 in mutation of chromosomal DNA transformed into yeast

While transformation is a prominent tool for genetic analysis and genome manipulation in many organisms, transforming DNA has often been found to be unstable relative to established molecules. We determined the potential for transformation-associated mutations in a 360 kb yeast chromosome III composed primarily of unique DNA. Wild-type and rad52 Saccharomyces cerevisiae strains were transformed with either a homologous chromosome III or a diverged chromosome III from S. carlsbergensis. The host strain chromosome III had a conditional centromere allowing it to be lost on galactose medium so that recessive mutations in the transformed chromosome could be identified. Following transformation of a RAD+ strain with the homologous chromosome, there were frequent changes in the incoming chromosome, including large deletions and mutations that do not lead to detectable changes in chromosome size. Based on results with the diverged chromosome, interchromosomal recombinational interactions were the source of many of the changes. Even though rad52 exhibits elevated mitotic mutation rates, the percentage of transformed diverged chromosomes incapable of substituting for the resident chromosome was not increased in rad52 compared to the wild-type strain, indicating that the mutator phenotype does not extend to transforming chromosomal DNA. Based on these results and our previous observation that the incidence of large mutations is reduced during the cloning of mammalian DNA into a rad52 as compared to a RAD+ strain, a rad52 host is well-suited for cloning DNA segments in which gene function must be maintained.

Recombination during transformation as a source of chimeric mammalian artificial chromosomes in yeast (YACs)

Mammalian DNAs cloned as artificial chromosomes in yeast (YACs) frequently are chimeras formed between noncontiguous DNAs. Using pairs of human and mouse YACs we examined the contribution of recombination during transformation or subsequent mitotic growth to chimeric YAC formation. The DNA from pairs of yeast strains containing homologous or heterologous YACs was transformed into a third strain under conditions typical for the development of YAC libraries. One YAC was selected and the presence of the second was then determined. Co-penetration of large molecules, as deduced from co-transformation of markers identifying the different YACs, was > 50%. In approximately half the cells receiving two homologous YACs, the YACs had undergone recombination. Co-transformation depends on recombination since it was reduced nearly 10-fold when the YACs were heterologous. While mitotic recombination between homologous YACs is nearly 100-fold higher than for yeast chromosomes, the level is still much lower than observed during transformation. To investigate the role of commonly occurring Alu repeats in chimera formation, spheroplasts were transformed with various human YACs and an unselected DNA fragment containing an Alu at one end and a telomere at the other. When unbroken YACs were used, between 1 and 6% of the selected YACs could incorporate the fragment as compared to 49% when the YACs were broken. We propose that Alu's or other commonly occurring repeats could be an important source of chimeric YACs. Since the frequency of chimeras formed between YACs or a YAC and an Alu-containing fragment was reduced when a rad52 mutant was the recipient and since intra-YAC deletions are reduced, rad52 and possibly other recombination-deficient mutants are expected to be useful for YAC library development.

Fluorescence in situ hybridisation of multiple probes on a single microscope slide

We report a method to analyse multiple samples by fluorescence in situ hybridisation on a single glass microscope slide. Wells were formed in which independent hybridisation reactions could proceed by sealing a silicon rubber gasket to the slide. In the largest format tested, different probes were hybridised simultaneously by applying them directly from a 96-well microtitre dish which was inverted on a glass plate. This technique will increase the rate of analysis of multiple probes against a standard set of chromosomes and could also be used to analyse different karyotypes using a panel of probes such as single chromosome paints during a single operation. It should be useful for both chromosomal mapping projects and screening for chromosome abnormalities in clinical diagnostic laboratories.

Characterization of four human YAC libraries for clone size, chimerism and X chromosome sequence representation

Four collections of human X-specific YACs, derived from human cells containing supernumerary X chromosomes or from somatic cell hybrids containing only X human DNA were characterized. In each collection, 80-85% of YAC strains contained a single X YAC. Five thousand YACs from the various libraries were sized, and cocloning was assessed in subsets by the fraction of YAC insert-ends with non-X sequences. Cocloning was substantial, ranging up to 50% for different collections; and in agreement with previous indications, in all libraries the larger the YACs, the higher the level of cocloning. In libraries made from human-hamster hybrid cells, expected numbers of clones were recovered by STS-based screening; but unexpectedly, the two collections from cells with 4 or 5 X chromosomes yielded numbers of YACs corresponding to an apparent content of only about two X equivalents. Thus it is possible that the DNA of inactive X chromosomes is poorly cloned into YACs, speculatively perhaps because of its specialized chromatin structure.

Synteny conservation of the Huntington's disease gene and surrounding loci on mouse Chromosome 5

The mouse homologs of the Huntington's disease (HD) gene and 17 other human Chromosome (Chr) 4 loci (including six previously unmapped) were localized by use of an interspecific cross. All loci mapped in a continuous linkage group on mouse Chr 5, distal to En2 and I16, whose human counterparts are located on Chr 7. The relative order of the loci on human Chr 4 and mouse Chr 5 was maintained, except for a break between D5H4S115E and Idua/rd, with relocation of the latter to the opposite end of the map. The mouse HD homolog (Hdh) mapped within a cluster of seven genes that were completely linked in our data set. In human these loci span a approximately 1.8 Mb stretch of human 4p16.3 that has been entirely cloned. To date, there is no phenotypic correspondence between human and mouse mutations mapping to this region of synteny conservation.

High resolution localization of recombination hot spots using sperm typing

We have applied sperm DNA typing to determine the distribution of crossover events within a one megabase region of the short arm of human chromosome 4 near the locus for Huntington disease. A total of 29 recombinants were detected among 602 sperm typed after whole genome amplification. These recombinants were typed for seven polymorphic markers. The 280 kilobase D4S10-D4S126 interval was found to undergo recombination at a 6-9-fold greater rate per unit of physical distance than the adjacent 720 kb D4S126-D4S127 interval. Sperm typing has the potential to dissect mammalian recombination hot spots to the point where DNA sequence analysis may reveal the molecular basis for hyperrecombination.

Island rescue PCR: a rapid and efficient method for isolating transcribed sequences from yeast artificial chromosomes and cosmids

The identification of transcripts from large genomic regions cloned in yeast artificial chromosomes (YACs) or cosmids continues to be a critical and often rate-limiting step in positional cloning of human disease genes. We have developed a PCR-based method for rapid and efficient generation of probes from YACs or cosmids that can be used for cDNA library screening. The method, which we call island rescue PCR (IRP), is based upon the observation that the 5' ends of many genes are associated with (G+C)-rich regions called CpG islands. In IRP, the YAC of interest is digested with a restriction enzyme that recognizes sequences of high CpG content, and vectorette linkers are ligated to the cleaved ends. The PCR is used to amplify the region extending from the cleaved restriction enzyme site to the nearest SINE (Alu) repeat. In many cases this product contains sequences from the 5' end of the associated gene. cDNA clones isolated with these products are then verified by mapping them back to the original YAC. The method allows rapid screening of > 500 kb of human genomic insert in one experiment, is tolerant of contaminating yeast sequences, and can also be applied to cosmid pools. In a control experiment, the method was able to identify cDNA clones for the neurofibromatosis type 1 (NF1) gene using a probe generated from a YAC in the region. Application of IRP has yielded nine other genes from YACs isolated from chromosome locations 4p16.3 and 17q21.

Towards cloning the familial breast-ovarian cancer gene on chromosome 17

The past year has seen a great deal of excitement in the field of breast cancer genetics. Since linkage of the familial breast-ovarian cancer gene (BRCA1) to chromosome 17, the critical region has been narrowed to 1.0-1.5 Mb by recombination studies, a detailed physical map has been constructed and much of the region has been cloned in yeast artificial chromosome, bacteriophage P1 and cosmid vectors. The focus now lies on identifying the genes housed within the BRCA1 region and scanning them for oncogenic mutations.

Rapid restriction analysis of YAC clones

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Yeast artificial chromosome cloning

Yeast artificial chromosome (YAC) cloning systems enable the cloning of DNA stretches of 50 to well over 2000 kb. This makes it possible to study large intact regions of DNA in detail, by restriction mapping the YAC to produce a physical map and by examining the YAC for coding sequences or genes. YACs are important for their ability to clone the complete sequences of large genes or gene complexes that exceed the size limit for cloning in conventional bacterial cloning vectors like plasmids (up to 10 kb), bacteriophage (15 kb), and cosmids (50 kb). A major advantage of cloning in yeast, a eukaryote, is that many sequences that are unstable, underrepresented, or absent when cloned into prokaryotic systems, remain stable and intact in YAC clones. It is possible to reintroduce YACs intact into mammalian cells where the introduced mammalian genes are expressed and used to study the functions of genes in the context of flanking sequences. The correct protein processing mechanisms are present in the mammalian cells to ensure that a viable protein product is produced.

A new bacteriophage P1-derived vector for the propagation of large human DNA fragments

We have designed a P1 vector (pCYPAC-1) for the introduction of recombinant DNA into E. coli using electroporation procedures. The new cloning system, P1-derived artificial chromosomes (PACs), was used to establish an initial 15,000 clone library with an average insert size of 130-150 kilobase pairs (kb). No chimaerism has been observed in 34 clones, by fluorescence in situ hybridization. Similarly, no insert instability has been observed after extended culturing, for 20 clones. We conclude that the PAC cloning system will be useful in the mapping and detailed analysis of complex genomes.

Gene mapping of the mammalian genome: the CEPH and Genethon initiative

Over the past four years, the CEPH (Jean Dausset Foundation) has expanded its linkage mapping effort to include physical mapping and, in 1990, co-founded the Genethon to ensure that a combined physical and genetic map of the entire human genome would be achieved. The Genethon has applied methods developed at CEPH on an industrial scale to accomplish the colossal task of constructing an integrated map. It is the role of such an integrated map to accelerate the search for the genes responsible for inherited diseases, and the results of the past 12 months encourage our optimism that this goal will be realized rapidly. These discoveries are providing not only an approach to the diagnosis of genetically based disease but also some of the first breakthroughs in the area of gene therapy.

A 4.5-megabase yeast artificial chromosome contig from human chromosome 13q14.3 ordering 9 polymorphic microsatellites (22 sequence-tagged sites) tightly linked to the Wilson disease locus

We have previously performed a genetic analysis of multiply affected families to map a locus responsible for Wilson disease (WND) to a 0.3-centimorgan (cM) region within chromosome 13q14.3, between D13S31 and D13S59. Here we describe the construction of a contig of approximately 4.5 Mb, which spans this region and extends from D13S25 to D13S59. This contig consists of 28 genomic yeast artificial chromosome (YAC) clones. Five critical crossover events have been defined in this interval in two unaffected (Centre d'Etudes du Polymorphisme Humain) and three WND families. The combination of sequence tagged site content mapping of YACs with both polymorphic and nonpolymorphic markers and recombination breakpoint mapping resulted in the following order of polymorphic markers: centromere-RB1-D13S25-AFM205vh2-D13S31-D13S22 7-D13S228-AFM238vc3-D13S133- AFM084xc5-D13S137-D13S169, D13S155-D13S59-telomere. The recombination/physical distance ratio varies from approximately 3000 kb per cM in the region between D13S31 and D13S25 to 6000 kb per cM in the region between D13S31 and D13S59. Three WND families exhibiting recombination between the disease locus and D13S31 or D13S59 were genotyped for additional markers in this region and further refined the location of the WND gene to between D13S155 and D13S133. Nine of the markers in this region of < 1 cM are polymorphic microsatellites (seven have observed heterozygosities of 70% or above) that will be extremely useful in prenatal and preclinical diagnosis of this disease. This physical map is an essential step in the isolation of the WND gene and is a framework for the identification of candidate genes.

Molecular cloning of BRCA1: a gene for early onset familial breast and ovarian cancer

Molecular analyses allow one to determine genetic lesions occurring early in the development of tumors. With positional cloning approaches we are searching for a gene involved in the development of early onset familial breast and ovarian cancer that maps to human chromosome 17q21 and is termed BRCA1. This involves localizing the region genetically within families with multiply affected members, capturing the region identified by genetic analyses in YACs (yeast artificial chromosomes), converting those YACs to smaller manipulable pieces (such as cosmids), and searching for genes via a variety of approaches such as direct screening of cDNA libraries with genomic clones, direct selection by hybridization, "exon trapping", and CpG island rescue. Once identified, candidate genes will be screened for mutations in affected family members in whom breast cancer segregates with the locus on 17q21. The frequency of this gene has been calculated to be 0.0033; from this the incidence of carriers, i.e. those carrying such a predisposition, is one in 150 women. The isolation of BRCA1 and the elucidation of the mutations resulting in breast and ovarian cancer predisposition will allow identification of women who have inherited germ-line mutations in BRCA1. In families known to harbor a germ-line BRCA1 mutation, diagnosis of affected members will be rapid. It is possible that one will also be able to detect alterations of the second copy of this gene early in tumor development in individuals carrying a germ-line mutation. It is not yet known how frequently somatic BRCA1 mutations predispose to breast and ovarian carcinoma in the general female population. If, as in other genetic diseases, new germ-line mutations occur in some women and thus contribute to the development of breast cancer, it may be feasible to screen women in the general population for predisposing mutations. In addition, if acquired genetic mutations of the BRCA1 gene are involved as early events in the development of non-familial forms of the disease, early detection of possible breast carcinoma may become feasible in biopsy of breast tissue.

Widespread distribution of cells containing human DNA in embryos derived from mouse eggs injected with human chromosome fragments

The possibility that metaphase chromosomes can serve as a source of genetic material for making transgenic mice was suggested by our previous finding of the incorporation of human satellite DNA into mouse embryos that were injected with microdissected human centromeric fragments. In the present study, we further examined whether this chromosome transfer method can be used to generate transgenic mice containing a portion of human chromosome 4 spanning the Huntington's disease (HD) gene. For this purpose, we used an improved method of metaphase chromosome preparation that may minimize the potential for DNA damage. Using metaphase chromosomes prepared in this manner, chromosome fragments spanning the region of chromosome 4 containing the HD gene were microdissected, retrieved, and injected into fertilized mouse eggs. The injected eggs exhibited good viability and developed with a high efficiency when implanted into foster mothers. To determine whether the human DNA from the injected chromosome fragment had been incorporated into the mouse genome, embryos were harvested at 12.5 days of gestation (dg) and analyzed by in situ hybridization using a human Alu repetitive DNA probe. This analysis showed that most of the embryos contained cells with human Alu repeats. However, all of the embryos were mosaic, and the level of mosaicism was such that we were not able to determine the precise chromosomal origin of the human DNA insert. We discuss the possible basis for the mosaicism and the potential value of such mosaic animals for studying Huntington's disease.

Construction of a yeast artificial chromosome contig spanning the spinal muscular atrophy disease gene region

The childhood spinal muscular atrophies (SMAs) are the most common, serious neuromuscular disorders of childhood second to Duchenne muscular dystrophy. A single locus for these disorders has been mapped by recombination events to a region of 0.7 centimorgan (range, 0.1-2.1 centimorgans) between loci D5S435 and MAP1B on chromosome 5q11.2-13.3. By using PCR amplification to screen yeast artificial chromosome (YAC) DNA pools and the PCR-vectorette method to amplify YAC ends, a YAC contig was constructed across the disease gene region. Nine walk steps identified 32 YACs, including a minimum of seven overlapping YAC clones (average size, 460 kb) that span the SMA region. The contig is characterized by a collection of 30 YAC-end sequence tag sites together with seven genetic markers. The entire YAC contig spans a minimum of 3.2 Mb; the SMA locus is confined to roughly half of this region. Microsatellite markers generated along the YAC contig segregate with the SMA locus in all families where the flanking markers (D5S435 and MAP1B) recombine. Construction of a YAC contig across the disease gene region is an essential step in isolation of the SMA-encoding gene.

A cosmid contig and high resolution restriction map of the 2 megabase region containing the Huntington's disease gene

The quest for the mutation responsible for Huntington's disease (HD) has required an exceptionally detailed analysis of a large part of 4p16.3 by molecular genetic techniques, making this stretch of 2.2 megabases one of the best characterized regions of the human genome. Here we describe the construction of a cosmid and P1 clone contig spanning the region containing the HD gene, and the establishment of a detailed, high resolution restriction map. This ordered clone library has allowed the identification of several genes from the region, and has played a vital role in the recent identification of the Huntington's disease gene. The restriction map provides the framework for the detailed analysis of a region extremely rich in coding sequences. This study also exemplifies many of the strategies to be used in the analysis of larger regions of the human genome.

Identification of an Alu retrotransposition event in close proximity to a strong candidate gene for Huntington's disease

Huntington's disease (HD) is a late-onset autosomal dominant neuropsychiatric disorder presenting in mid-adult life with personality disturbance and involuntary movements, cognitive and affective disturbance, and inexorable progression to death. The underlying genetic defect has been mapped to chromosomal band 4p16.3 (refs 2, 3). Analysis of specific recombination events in some families with HD has further refined the location of the HD defect to a 2.2 megabase DNA interval. Using a direct complementary DNA selection strategy we have identified at least seven transcriptional units within the minimal region believed to contain the HD gene. Screening with one of the cDNA clones identified an Alu insertion in genomic DNA from two persons with HD which showed complete cosegregation with the disease in these families but was not found in 1,000 control chromosomes. Two genes including the previously identified alpha-adducin gene and another that encodes for a 12-kilobase transcript, map in close proximity to the Alu insertion site. The 12-kilobase transcript should be regarded as a strong candidate for the HD gene.

Age at onset in Huntington's disease and methylation at D4S95

Age at onset in Huntington's disease (HD) is variable and is influenced by parental sex, paternal age, and genetic background. Several recent models have tried to explain this variable expressivity by invoking parental imprinting and related aspects of epigenetic inheritance. Some of these mechanisms may result in variable DNA methylation at or near the HD gene. We show here that methylation at D4S95, a locus tightly linked to the HD gene, is highly variable. A comparison between patients with early onset HD, late onset HD, and normal controls showed no significant correlation between methylation and age at onset. However, we found a significant association of the age of the patient with demethylation at D4S95. Older persons tend to have lower levels of methylation at this locus. This observation is of interest with regard to studies that show an effect of paternal age, or more generally of 'ageing genes', on age at onset in HD.

Magnetic bead capture of expressed sequences encoded within large genomic segments

Magnetic bead capture utilizes biotin-streptavidin magnetic bead technology to isolate cDNAs rapidly from large genomic intervals, giving several thousand-fold enrichment of the selected cDNAs. The technique can allow parallel analysis of several large genomic segments of varying complexities and can be applied to the isolation of expressed sequences from various tissue sources.

Genetic and physical mapping of the biglycan gene on the mouse X chromosome

A human cDNA for biglycan (BGN) has recently been mapped to proximal Xq28. We have mapped the murine locus, Bgn, approximately 50 kb distal to DXPas8, using a combination of genetic mapping in an interspecific backcross of B6CBA-Aw-J/A-Bpa x Mus spretus and physical mapping using pulsed field gel electrophoresis and analysis of murine yeast artificial chromosomes (YACs) containing both DXPas8 and Bgn. Our mapping studies also appear to exclude Bgn as a candidate gene for the bare patches (Bpa) mutation and for the homologous human disorder X-linked dominant chondrodysplasia punctata (CDPX2).

Generation of high-density DNA markers from yeast artificial chromosome DNA by single unique primer-polymerase chain reaction

We have developed a method for the whole sequence amplification of yeast artificial chromosome (YAC) DNA excised from preparative pulsed-field gel electrophoresis using single unique primer-polymerase chain reaction procedures. We used seven contiguous YAC clones, which span 2 Mbp of the Huntington disease gene region on 4p16.3, to amplify the YAC DNAs. The average size of the amplified DNA was approximately 300 bp long, and 12 DNA markers located on the YAC clones positively hybridized with these amplified products, implying that the sequences of the YAC clones were comprehensively amplified by our procedures. These amplified YAC DNAs greatly facilitate the characterization of YAC clones, leading to the detailed analysis of the defined chromosomal region.

Cloning of the α–adducin gene from the Huntington's disease candidate region of chromosome 4 by exon amplification

We have applied the technique of exon amplification to the isolation of genes from the chromosome 4p16.3 Huntington's disease (HD) candidate region. Exons recovered from cosmid Y24 identified cDNA clones corresponding to the alpha-subunit of adducin, a calmodulin-binding protein that is thought to promote assembly of spectrin-actin complexes in the formation of the membrane cytoskeleton, alpha-adducin is widely expressed and, at least in brain, is encoded by alternatively spliced mRNAs. The alpha-adducin gene maps immediately telomeric to D4S95, in a region likely to contain the HD defect, and must be scrutinized to establish whether it is the site of the HD mutation.

New insights into the clinical features, pathogenesis and molecular genetics of Huntington disease

Traditionally, a clinical diagnosis of Huntington disease (HD) presents no problems in patients with a positive family history, consistent with autosomal dominant inheritance, chorea or other extrapyramidal motor signs, and progressive mental decline. However, due to the slowly progressive nature of the disease and the slow evolution of signs and symptoms, it is often difficult to determine when at risk individuals are showing early signs. Moreover, the clinical recognition of both early and late-onset cases, and of choreic patients in whom a family history is lacking, presents special diagnostic challenges. In recent years, much progress has been made in the recognition of early clinical signs of the disease. Factors which have contributed to this understanding include the longitudinal study of large cohorts of at-risk individuals, particularly in Venezuela, the data from predictive testing programs, and the application of positron emission tomography (PET)-scanning to individuals without overt chorea. We are now able to identify persons at risk as being affected before they display overt and obvious involuntary movements.

Mapping the whole human genome by fingerprinting yeast artificial chromosomes

Physical mapping of the human genome has until now been envisioned through single chromosome strategies. We demonstrate that by using large insert yeast artificial chromosomes (YACs) a whole genome approach becomes feasible. YACs (22,000) of 810 kb mean size (5 genome equivalents) have been fingerprinted to obtain individual patterns of restriction fragments detected by a LINE-1 (L1) probe. More than 1000 contigs were assembled. Ten randomly chosen contigs were validated by metaphase chromosome fluorescence in situ hybridization, as well as by analyzing the inter-Alu PCR patterns of their constituent YACs. We estimate that 15% to 20% of the human genome, mainly the L1-rich regions, is already covered with contigs larger than 3 Mb.

Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3

The sequences of three cosmids (90 kilobases) from the Huntington's disease region in chromosome 4p16.3 have been determined. A 30,837 base overlap of DNA sequenced from two individuals was found to contain 72 DNA sequence polymorphisms, an average of 2.3 polymorphisms per kilobase (kb). The assembled 58 kb contig contains 62 Alu repeats, and eleven predicted exons representing at least three expressed genes that encode previously unidentified proteins. Each of these genes is associated with a CpG island. The structure of one of the new genes, hda1-1, has been determined by characterizing cDNAs from a placental library. This gene is expressed in a variety of tissues and may encode a novel housekeeping gene.