Radiation hybrids: irradiation and fusion gene transfer

Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.

Delayed Encounter of Parental Genomes Can Lead to Aneuploidy in Saccharomyces cerevisiae

We have investigated an extreme deviation from the norm of genome unification that occurs during mating in the yeast, Saccharomyces cerevisiae This deviation is encountered when yeast that carry a mutation of the spindle pole body protein, Kar1, are mated with wildtype cells. In this case, nuclear fusion is delayed and the genotypes of a fraction of zygotic progeny suggest that chromosomes have "transferred" between the parental nuclei in zygotes. This classic, yet bizarre, occurrence is routinely used to generate aneuploid (disomic) yeast. [kar1 × wt] zygotes, like [wt × wt] zygotes, initially have a single spindle pole body per nucleus. Unlike [wt × wt] zygotes, in [kar1 × wt] zygotes, the number of spindle pole bodies per nucleus then can increase before nuclear fusion. When such nuclei fuse, the spindle pole bodies do not coalesce efficiently, and subsets of spindle pole bodies and centromeres can enter buds. The genotypes of corresponding biparental progeny show evidence of extensive haplotype-biased chromosome loss, and can also include heterotypic chromosomal markers. They thus allow rationalization of chromosome "transfer" as being due to an unanticipated yet plausible mechanism. Perturbation of the unification of genomes likely contributes to infertility in other organisms.

V-fusion: a convenient, nontoxic method for cell fusion

Cell-to-cell fusion (cell fusion) is a fundamental biological process that also has been used as a versatile experimental tool to dissect a variety of cellular mechanisms, including the consequences of cell fusion itself, and to produce cells with desired properties, such as hybridomas and reprogrammed progenitors. However, current methods of cell fusion are not satisfactory because of their toxicity, inefficiency, or lack of flexibility. We describe a simple, versatile, scalable, and nontoxic approach that we call V-fusion, as it is based on the ability of the vesicular stomatitis virus G protein (VSV-G), a viral fusogen of broad tropism, to become rapidly and reversibly activated. We suggest that this approach will benefit a broad array of studies that investigate consequences of cell fusion or use cell fusion as an experimental tool.

Application of radiation hybrid in gene mapping

Radiation hybrid (RH) mapping technique was exploited to determine chromosome locations of 26 human novel full length cDNAs recently cloned. All these cDNA clones were isolated from human cord blood CD (+) (34) cells and may be related to regulation of hematopoiesis. 23 genes were successfully mapped to chromosomal positions, while RH analyses were not possible in the remaining 3 cases. RH technique is indeed a powerful tool for mapping novel cDNA sequences due to its rapidity, precision, convenience and reproducibility.

Mapping and expression analysis of chicken NDRG1 and NDRG3 genes

N-myc downstream-regulated genes 1 and 3 (NDRG1 and NDRG3) are members of the alpha/beta hydrolase superfamily. Phylogenetic analysis of the family demonstrated that human NDRG1 and 3 belong to a subfamily. The mapping and gene expression patterns of these genes represent one step toward further investigation into their possible roles in the chicken (Gallus gallus). To map these genes in the chicken chromosome, a 6000 rads chicken-hamster radiation hybrid panel (ChickRH6) was used. Primers were designed according to the published human sequences for amplification of those two genes. We compared the corresponding human mRNA sequences with the predicted coding sequences of the chicken NDRG1 and 3 genes and found that the assembled contigs shared a high percentage of similarity with the human genes. PCR of samples from ChickRH6 revealed that the locations of NDRG1 and 3 are linked to the markers MYC (58 cRs away, LOD score 4.52) and SEQ0265 (10 cRs away, LOD score 17.81), respectively. This result adds two new markers to the chicken RH map, and it reinforces that the RH technique is indeed a powerful tool for mapping genes due to its rapidity, precision, convenience, and reproducibility. In addition, we detected the gene expression and distribution of chicken NDRG1 and 3 in seven tissues, including heart, liver, spleen, lung, muscle, brain, and thymus, by RT-PCR, and found that NDRG1 is relatively ubiquitously expressed in all the tested tissues and highly expressed in heart and liver, whereas NDRG3 is high in heart, muscle, and brain.

Radiation hybrid (RH) and HAPPY mapping in plants

Radiation hybrid (RH) and HAPPY mapping are two technologies used in animal systems that have attracted the attention of the plant genetics community because they bridge the resolution gap between meiotic and BAC-based physical mapping that would facilitate the analysis of plant species lacking substantial genomics resources. Research has shown that the essence of these approaches can be applied and that a variety of strategies can be used to produce mapping panels. Mapping panels composed of live plants, protoplast fusion cultures, and sub-genomic DNA samples have been described. The resolution achievable by RH mapping panels involving live-plant derivatives of a monosomic maize (Zea mays) chromosome 9 addition in allohexaploid oat (Avena sativa), a monosomic chromosome 1D addition in allotetraploid durum wheat (Triticum turgidum), and interspecific hybrids between two tetraploid cotton species (G. hirsutum and G. barbadense), has been estimated to range from 0.6 to 6 Mb. On the other hand, a more comprehensive evaluation of one panel from durum wheat suggests that a higher mapping resolution (approximately 200 kb) is possible. In cases involving RH mapping panels based on barley (Hordeum vulgare)-tobacco (Nicotiana tabacum) protoplast fusions or a HAPPY mapping panel based on genomic DNA from Arabidopsis thaliana, the potential mapping resolution appears to be higher (50 to 200 kb). Despite these encouraging results, the application of either RH or HAPPY mapping in plants is still in the experimental phase and additional work is clearly needed before these methods are more routinely utilized.

Cell-to-cell fusion as a link between viruses and cancer

The ability to fuse cells is shared by many viruses, including common human pathogens and several endogenous viruses. Here we will discuss how cell fusion can link viruses to cancer, what types of cancers it can affect, how the existence of this link can be tested and how the hypotheses that we propose might affect the search for human oncogenic viruses. In particular, we will focus on the ability of cell fusion that is caused by viruses to induce chromosomal instability, a common affliction of cancer cells that has been thought to underlie the malignant properties of cancerous tumours.

Development of a deer mouse whole-genome radiation hybrid panel and comparative mapping of Mus chromosome 11 loci

A 5000-rad whole-genome radiation hybrid cell panel (BW5000) was developed for mapping the deer mouse (Peromyscus maniculatus bairdii) genome. The panel consists of 103 cell lines and has an estimated marker retention frequency of 63.9% (range, 28%-88%) based on PCR typing of 30 Type I (coding gene) and 25 Type II (microsatellite) markers. Using the composite Mus map, Type I markers were selected from six Mus chromosomes, 22 of which are on Mus Chr 11. Fifteen of the Mus Chr 11 markers were simultaneously mapped on an interspecific (P. maniculatus x P. polionotus) backcross panel to test the utility of the radiation hybrid panel, create a framework map, and help establish gene order. The radiation hybrids have effectively detected linkage in the deer mouse genome between markers as far apart as 6.7 cM and resolved markers that are, in the Mus genome, as close as 0.2 Mb. Combined results from both panels have indicated a high degree of gene order conservation of the telomeric 64 cM of Mus Chr 11 in the deer mouse genome. The remaining centromeric portion also shows gene order conservation with the deer mouse but as a separate linkage group. This indicates a translocation of that portion of Mus Chr 11 in P. maniculatus and is consistent with rearrangement breakpoints observed between Mus and other mammalian genomes, including rat and human. Furthermore, this separate linkage group is likely to reside in a chromosomal region of inversion polymorphism between P. maniculatus and P. polionotus.

Application of spectral karyotyping to the analysis of the human chromosome complement of interspecies somatic cell hybrids

Mouse-human somatic cell hybrids have been extensively used in the molecular genetic dissection of human disease-related chromosome rearrangements because of their ability to selectively and randomly eliminate human chromosomes. This technology allows the isolation of structural chromosome abnormalities, which then allows determination of the precise molecular address of chromosome breakpoints associated with deletions and translocations, down to the nucleotides involved. The main confounding problem with the analysis of somatic cell hybrids is determining the exact chromosome complement unequivocally and quickly. Spectral karyotyping can identify each of the individual human chromosomes in a normal metaphase spread, as well as structural chromosome rearrangements-although, because of potential cross-hybridization between the human probe and mouse DNA sequences during the hybridization reaction, it has not been determined whether the same analysis will selectively identify human chromosomes on a mouse background. We show (to our knowledge, for the first time) that, under modified conditions of chromosomal in situ suppression hybridization, the standard spectral karyotyping probe does not cross-react with mouse chromosomes and can be used to identify subtle structurally rearranged chromosomes in hybrid cells. This analysis allows for the rapid and unequivocal identification of the human chromosome complement in these hybrids, as well as structural chromosome rearrangements that occur between mouse and human chromosomes that might otherwise confound the analysis.

Use of radiation hybrid panels to map genetic loci

The mapping of genetic loci within organisms has been accelerated by the advent of Radiation Hybrid (RH) panels. These panels are available for humans and non-humans including mice, baboon, rat, and canine. This article contains a general protocol for the use of the Genebridge 4 whole genome RH panel to map a human locus. This protocol may also be adjusted to suit the other RH panels currently available.

Identification and cellular localization of human PFTAIRE1

We isolated a novel member of putative Cdc2-related serine/threonine protein kinases from a Hela cell cDNA library. The cDNA encodes a protein of 469 amino acids, sharing 95% identities with the mouse PFTAIRE1 throughout the entire protein sequence. This gene was designated human PFTAIRE1. The gene was located at human chromosome 7q21.13 with radiation hybrid polyermase chain reaction (RH-PCR) analysis. By Northern blotting analysis, an approximately 6 kb transcript is detected with varied levels of expression of the hPFTAIRE1 in 16 human tissues. The hPFTAIRE1 was highly expressed in brain, pancreas, kidney, heart, testis and ovary. The transcript was also detected at lower level in other tissues, except in spleen and thymus where the transcript was hardly detected. The protein was fused to the C-terminus of a green fluorescent protein (GFP) and ectopically expressed in Hela cells. The florescence microscope results indicated that the hPFTAIRE1 exhibits cytoplasmic distribution.

Genetic analysis of inherited hypertension in the rat

Blood pressure is a quantitative trait that has a strong genetic component in humans and rats. Several selectively bred strains of rats with divergent blood pressures serve as an animal model for genetic dissection of the causes of inherited hypertension. The goal is to identify the genetic loci controlling blood pressure, i.e., the so-called quantitative trait loci (QTL). The theoretical basis for such genetic dissection and recent progress in understanding genetic hypertension are reviewed. The usual paradigm is to produce segregating populations derived from a hypertensive and normotensive strain and to seek linkage of blood pressure to genetic markers using recently developed statistical techniques for QTL analysis. This has yielded candidate QTL regions on almost every rat chromosome, and also some interactions between QTL have been defined. These statistically defined QTL regions are much too large to practice positional cloning to identify the genes involved. Most investigators are, therefore, fine mapping the QTL using congenic strains to substitute small segments of chromosome from one strain into another. Although impressive progress has been made, this process is slow due to the extensive breeding that is required. At this point, no blood pressure QTL have met stringent criteria for identification, but this should be an attainable goal given the recently developed genomic resources for the rat. Similar experiments are ongoing to look for genes that influence cardiac hypertrophy, stroke, and renal failure and that are independent of the genes for hypertension.

Radiation hybrid mapping of the zebrafish genome

The zebrafish is an excellent genetic system for the study of vertebrate development and disease. In an effort to provide a rapid and robust tool for zebrafish gene mapping, a panel of radiation hybrids (RH) was produced by fusion of irradiated zebrafish AB9 cells with mouse B78 cells. The overall retention of zebrafish sequences in the 93 RH cell lines that constitute the LN54 panel is 22%. Characterization of the LN54 panel with 849 simple sequence length polymorphism markers, 84 cloned genes and 122 expressed sequence tags allowed the production of an RH map whose total size was 11,501 centiRays. From this value, we estimated the average breakpoint frequency of the LN54 RH panel to correspond to 1 centiRay = 148 kilobase. Placement of a group of 235 unbiased markers on the RH map suggests that the map generated for the LN54 panel, at present, covers 88% of the zebrafish genome. Comparison of marker positions in RH and meiotic maps indicated a 96% concordance. Mapping expressed sequence tags and cloned genes by using the LN54 panel should prove to be a valuable method for the identification of candidate genes for specific mutations in zebrafish.

Detection of DNA abnormalities by arbitrarily primed PCR fingerprinting: amplification of the MDM2 gene in a mediastinum fibrosarcoma

Arbitrarily primed PCR (AP-PCR) fingerprinting method is easy and useful for analysis of genetic alterations in anonymous chromosomal regions. We applied this technology to analysis of DNA from human primary cancers and found amplification of a DNA fragment in a mediastinum fibrosarcoma. PCR-based analysis of radiation hybrid panels following cloning and nucleotide sequence determination of the fragment revealed that it was derived from a region of chromosome 12q13-q15. In this region, the MDM2 and IFNG genes were noted as known genes that could be involved in human carcinogenesis. Southern blot analysis of genomic DNA of the tumor revealed the amplification of the MDM2 gene together with the fragment locus, but not the IFNG gene. Our results demonstrated that detection of DNA alterations by AP-PCR fingerprinting without any previous knowledge of the genes and subsequent analysis of radiation hybrid panels could lead to easy identification of candidates for genes involved in carcinogenesis.

Transchromosomal mouse embryonic stem cell lines and chimeric mice that contain freely segregating segments of human chromosome 21

At least 8% of all human conceptions have major chromosome abnormalities and the frequency of chromosomal syndromes in newborns is >0.5%. Despite these disorders making a large contribution to human morbidity and mortality, we have little understanding of their aetiology and little molecular data on the importance of gene dosage to mammalian cells. Trisomy 21, which results in Down syndrome (DS), is the most frequent aneuploidy in humans (1 in 600 live births, up to 1 in 150 pregnancies world-wide) and is the most common known genetic cause of mental retardation. To investigate the molecular genetics of DS, we report here the creation of mice that carry different human chromosome 21 (Hsa21) fragments as a freely segregating extra chromosome. To produce these 'transchromosomal' animals, we placed a selectable marker into Hsa21 and transferred the chromosome from a human somatic cell line into mouse embryonic stem (ES) cells using irradiation microcell-mediated chromosome transfer (XMMCT). 'Transchromosomal' ES cells containing different Hsa21 regions ranging in size from approximately 50 to approximately 0.2 Mb have been used to create chimeric mice. These mice maintain Hsa21 sequences and express Hsa21 genes in multiple tissues. This novel use of the XMMCT protocol is applicable to investigations requiring the transfer of large chromosomal regions into ES or other cells and, in particular, the modelling of DS and other human aneuploidy syndromes.

Comparative genomics and host resistance against infectious diseases

The large size and complexity of the human genome have limited the identification and functional characterization of components of the innate immune system that play a critical role in front-line defense against invading microorganisms. However, advances in genome analysis (including the development of comprehensive sets of informative genetic markers, improved physical mapping methods, and novel techniques for transcript identification) have reduced the obstacles to discovery of novel host resistance genes. Study of the genomic organization and content of widely divergent vertebrate species has shown a remarkable degree of evolutionary conservation and enables meaningful cross-species comparison and analysis of newly discovered genes. Application of comparative genomics to host resistance will rapidly expand our understanding of human immune defense by facilitating the translation of knowledge acquired through the study of model organisms. We review the rationale and resources for comparative genomic analysis and describe three examples of host resistance genes successfully identified by this approach.

Estimation of distances and map construction using radiation hybrids

A method of estimating distances between pairs of genetic markers is described that directly uses their observed joint frequency distribution in a panel of radiation hybrids (RHs). The distance measure is based on the strength of association between marker pairs, which is high for close markers and decays with distance. These distances are then submitted to a previous method that generates linear coordinates for the markers directly from the intermarker distance matrix. This method of map building from RH data is simpler than others, because it uses only the observed joint frequency distributions of markers in the panel, and does not attempt to model unobserved quantities such as the retention of different sized fragments that contain the markers. It also incorporates directly the observed variation in retention of different markers, without needing a model for differential fragment retention dependent on chromosomal location, which is generally not known. Only small, precise distances are used in map construction, thereby reducing any effects of different fragment retention frequencies and local variations in X-ray sensitivity. The method is tested by simulation, and known marker distances and locations are successfully recovered from RH raw data. The method is also applied to publicly available data sets related to the recent transcript map of the human genome.

A first-generation whole genome-radiation hybrid map spanning the mouse genome

We have assembled a first-generation anchor map of the mouse genome using a panel of 94 whole-genome-radiation hybrids (WG-RHs) and 271 sequence-tagged sites (STSs). This is the first genome-wide RH anchor map of a model organism. All of the STSs have been previously localized on the genetic map and are located 8.8 Mb apart on average. This mouse WG-RH panel, known as T31, has an average retention frequency of 27.6% and an estimated potential resolution of 145 kb, making it a powerful resource for efficient large-scale expressed sequence tag mapping. [All of the mapping data for the maps presented here have been deposited at the Research Genetics, Inc., web site and can be freely accessed and downloaded at http://www.resgen.com/.]

A radiation hybrid framework map of bovine chromosome 13

In this paper we present a 5000-rad radiation hybrid framework map of bovine chromosome 13 (BTA13) containing 13 loci, including five conserved genes and eight polymorphic microsatellites. All framework markers are ordered with odds greater than 1000:1. Furthermore, we present a comprehensive map of BTA13 integrating 11 genes and 16 microsatellites. The proposed order is in general agreement with the recently published medium-density linkage maps. A model of five blocks of genes with conserved order between human, mouse and cattle is presented.

A minichromosome carrying a pigmentation gene and brook trout DNA sequences in transgenic rainbow trout

We describe the transmission of an introduced minichromosome of brook trout (Salvelinus fontinalis) origin, carrying a pigmentation gene, through three generations in rainbow trout (Oncorhynchus mykiss). The minichromosome was originally introduced into gynogenetic albino rainbow trout using gamma-irradiated brook trout sperm. In the third generation, the presence of the minichromosome was correlated with pigmentation. A brook trout specific interspersed repeat DNA sequence, Fok I, was also correlated with pigmentation in these individuals. This system, the first clearly documented example of induced chromosome mediated gene transfer at the organismal level, could have applications in studies of gene mapping, development, gene regulation, and chromosome function.

Identification of a novel breast-cancer-anti-estrogen-resistance (BCAR2) locus by cell-fusion-mediated gene transfer in human breast-cancer cells

Development of anti-estrogen resistance limits the benefit of endocrine therapy of breast cancer. The mechanistic basis for resistance to the anti-estrogen tamoxifen may involve (epi)genetic alterations within tumor cells. We have initiated a random search for genes allowing estrogen-dependent ZR-75-1 human breast-cancer cells to proliferate in the presence of tamoxifen. The strategy was based on insertion mutagenesis of ZR-75-1 cells using defective retrovirus and subsequent identification of common integration sites. As an alternative approach to identify integration loci involved in anti-estrogen resistance, we have applied cell fusion. Integration regions from lethally irradiated, tamoxifen-resistant cells were transferred to hygromycin B-resistant ZR-75-1 cells. Somatic cell hybrids were established by selection for resistance to G418 (encoded by the integrated virus) and hygromycin B. Individual integration loci were thus separated among different cell hybrids and tested for their role in anti-estrogen resistance. Analysis of a panel of 29 somatic-cell hybrids revealed that tamoxifen resistance co-segregated with only 1 of the 2 integration loci present in the tamoxifen-resistant donor cell line. This locus was further identified as a common integration site in our panel of tamoxifen-resistant cell clones. Our results designate this integration site as the second breast-cancer-anti-estrogen-resistance locus (BCAR2), which most likely contains a gene responsible for the anti-estrogen-resistant phenotype in close proximity to the integrated virus. Our data also imply that individual genes can alter the estrogen dependency of human breast-cancer cells in a dominant manner in vitro.

Estimating physical distances from radiation hybrid mapping data

Radiation hybrid mapping has become an established tool for building physical maps. It represents a powerful way of constructing YAC contigs and high-resolution maps for positional cloning experiments. Ideally, radiation hybrids should not only provide support for the true order of the markers, but also accurate estimates of the physical distances between them. Statistical analysis of radiation hybrids has proved difficult because of the number of parameters (representing the fragment retention probabilities) that must be estimated, and simplifying assumptions are needed to analyze large numbers of markers simultaneously. The ramifications of these assumptions for the calculation of physical distances are investigated. A simple two-locus model is presented to demonstrate that variation in marker retention can lead to distortions in the estimates of distance. Multilocus simulations show that, when marker retention is constant across the chromosome, good estimates of physical distance can be derived using simple models of retention. However, further simulations exploring variable retention schemes demonstrate that significant errors in the estimates of map distances can occur. Ways of minimizing these distortions are discussed.

Generation of a panel of radiation-reduced hybrids containing human 11q22-23 fragments bearing a HPRT selective marker: identification of hybrids carrying various subregions around the ataxia-telangiectasia locus

A human-mouse monochromosomal hybrid that contains a human t(X;11) translocated chromosome carrying pter-->q23 segment of chromosome 11 was used to construct a panel of radiation-reduced hybrids. The hypoxhanthine phosphoribosyltransferase (HPRT) gene located close to the translocation breakpoint was used as a marker to select for the hybrids that preferentially retain the 11q22-23 region. Twenty-three HAT-resistant hybrids were isolated and screened by polymerase chain reaction (PCR) for the retention of 31 loci on 11q22-23 region. Among the 14 hybrids that had breakpoints within the 11q22-23 region, 6 hybrids contained fragments that extend either from centromere or telomere to the 5-Mb region spanned by GRIA4 and FDX, carrying various breakpoints within the region. This subpanel could be a potential resource to analyze the ataxia-telangiectasia disease locus and its neighboring region.

A radiation hybrid map spanning the entire human X chromosome integrating YACs, genes, and STS markers

We present a radiation hybrid (RH) map of human Chromosome (Chr) X, using 50 markers on 72 radiation hybrids. The markers, obtained from the consensus map, form a grid spanning the entire chromosome. To check the RH map, the marker order was determined by analysis of presence or absence of retained human DNA fragments in the RHs; the comparison with the consensus showed a similar order. Any STSs, microsatellites, genes, and clones can be positioned and ordered relative to the marker grid. This approach integrates genetic, physical, and large-scale clone mapping and is used to link YAC contigs containing data from various experimental sources.

Hybrid selection as a method of increasing mapping power for radiation hybrids

Radiation hybrids have become a widely used tool for physical mapping. A drawback of the technique is that large numbers of hybrids are required to construct robust, high-resolution maps. The information contained within a panel of radiation hybrids is limited by the frequency of retention of chromosomal fragments from the donor cell line. In almost all experiments to date, the retention frequency has been below the optimal level; therefore, many hybrids are needed to produce high-quality maps. Because of the labor-intensive nature of large-scale mapping projects, it is important to make panels as small as possible. One method that has been adopted is to produce initially a large number of hybrids that are all typed with a few loci. Those hybrids showing satisfactorily high retention are admitted to the final panel and the rest are discarded. In this way, a panel of radiation hybrids with higher than expected retention can be created. Methods for conducting such a selection regime are discussed. To investigate the potential advantages of selecting hybrids based on their retention frequency, simulations were run under a variety of conditions. As expected panels with high retention (40%) provided better mapping resources than panels with lower (20%) retention. Beginning with an initial panel of 200 hybrids, comparisons of a random sample of 100 hybrids and the set of those 100 hybrids showing the highest marker retention demonstrated that selection may not be always the best strategy despite the increase in mean retention it yields. The selection of hybrids containing large numbers of fragments leads to an overestimation of the frequency of radiation-induced breaks. When breaks occur with high frequency (for example, when high radiation doses are used), the selection of hybrids leads to a loss of linkage and hence an inability to order the markers. As such, the merits of screening hybrids depends on both the radiation dose and the desired map resolution.

Genetic mechanisms of estrogen-independence in breast cancer

Endocrine therapy is effective in the treatment of breast cancer. Adjuvant treatment with tamoxifen reduces tumor recurrence and achieves increased survival. In metastatic disease, tamoxifen treatment accomplishes objective responses in +/- 50% of the patients with estrogen receptor-positive primary tumors. However, the response duration is limited due to the inevitable development of metastases resistant to tamoxifen. The mechanisms leading to tamoxifen resistance are largely unknown. We have set out to identify genetic pathways in the tumor cells causing failure of tamoxifen therapy. We selected an estrogen-dependent human breast cancer cell line (ZR-75-1) and demonstrated that genetic and epigenetic alterations can change the hormone-response phenotype of these cells. Subsequently, we applied insertional mutagenesis with defective retroviruses to these ZR-75-1 breast cancer cells. Integration of a retrovirus in the cellular DNA alters the genome structure and may modify the expression of genes in its surroundings. As a result of the altered gene expression, the biological phenotype of the infected cell may be changed. The infected ZR-75-1 cells were subjected to tamoxifen selection and a panel of tamoxifen-resistant cell lines has been established. Screening for a common integration site for the retrovirus has provided, so far, compelling evidence for the involvement of at least one genetic locus (BCAR 1) in breast cancer antiestrogen resistance in vitro.

Pairwise analysis of radiation hybrid mapping data

Two point lod scores are widely used in pedigree analysis as they provide a fast and efficient method of establishing linkage. Groups of markers that lie in close proximity to one another can be formed by admitting any locus that is linked to at least one existing member of the group with lod score greater than some predetermined value. It seems natural to extend this technique to Radiation Hybrid Mapping both for constructing groups of tightly linked loci that may then be analysed using more powerful statistics and as a method of ordering in its own right. A general extension of two point analysis is derived and the problems associated with radiation hybrid data are discussed. In particular, the additional parameters representing the probabilities of different fragments being retained (which have no parallel in classical linkage analysis) lead to a range of estimators of the breakage probability, O, which have equal and maximal likelihood. Ways of circumventing this problem are discussed along with the potential errors they introduce. Importantly the ambiguity in estimation of theta is not carried through to the lod score as this depends only on the maximum value of the likelihood and not on the particular value of theta at which it occurs. Thus even though two point analysis fails to provide robust estimates of either breakage probabilities or the distance between loci, it represents a simple and effective method of constructing linkage groups that may be analysed with more powerful statistical methods. This is particularly important given the large number of microsatellites, ESTs and candidate genes currently being typed on radiation hybrids.

Regional assignment of human ESTs by whole-genome radiation hybrid mapping

The UK HGMP Resource Centre's collection of human partial cDNA sequences (ESTs) have been examined for suitability for mapping by PCR on a panel of somatic cell hybrids. The chromosomal assignments of 92 ESTs were determined with a monochromosomal hybrid panel, and a subset of 45 were linked to genetic markers with a panel of whole-genome radiation hybrids (WG-RHs). These results demonstrate the potential of WG-RHs to construct a transcript map of the human genome.

SINE sequences detect DNA fingerprints in salmonid fishes

DNA probes homologous to two previously described salmonid short interspersed nuclear elements (SINEs) detected DNA fingerprint patterns in 14 species of salmonid fishes. The probes showed more homology to some species than to others and little homology to three nonsalmonid fishes. The DNA fingerprint patterns derived from the SINE probes are individual-specific and inherited in a Mendelian manner. Probes derived from different regions of the same SINE detect only partially overlapping banding patterns, reflecting a more complex SINE structure than has been previously reported. Like the human Alu sequence, the SINEs found in salmonids could provide useful genetic markers and primer sites for PCR-based techniques. These elements may be more desirable for some applications than traditional DNA fingerprinting probes that detect tandemly repeated arrays.

Human repeat-mediated integration of selectable markers into somatic cell hybrids

We describe a strategy to introduce preferentially the dominant selectable marker neoR into the human chromosome within a monochromosome hybrid cell line. Integration of a construct containing the marker is mediated by human-specific repeat elements that promote multilocus human-specific integration with a single targeting vector. We tested two classes of repeat elements: the Alu family of SINE repeats and the Line1 repeat family. We show that Alu sequences alone are insufficient to direct human-specific integration but when used in combination with a Line1 element, or when only Line1 elements are included, integration of the vector into the human component of a monochromosome somatic cell hybrid is favored. The vectors also carry sequences that facilitate mapping and selective cloning of the targeted region. This strategy provides a means to generate selectable human subchromosomal fragments that can be used for localization of genes through positional cloning and, more important, for the identification of functional units through DNA transfer.

Gene expression in response to retinoic acid in novel human chromosome 21 monochromosomal cell hybrids

To access a wide a variety of expressed sequence from human chromosome 21 we have placed this chromosome into undifferentiated P19 mouse embryonic carcinoma cells. Cell lines resulting from these experiments have a range of morphologies and a wide variety of karyotypes. We have studied the retinoic acid response of five cell lines, compared to P19 cells, by observing three markers of retinoic acid induced P19 differentiation--cell morphology, RAR alpha and Wnt1 transcription. We see an 'early' retinoic acid response effect, however this response breaks down by the time the 'late' gene. Wnt1 would be transcribed in P19 cells. A highly responsive cell line will be useful for cloning expressed sequences from human chromosome 21 which are produced by early genes in retinoic acid inducible pathways, such as those involved in neurogenesis.

Established epigenetic modifications determine the expression of developmentally regulated globin genes in somatic cell hybrids

Somatic cell hybrids generated from transgenic mouse cells have been used to examine the developmental regulation of human gamma-to-beta-globin gene switching. In hybrids between mouse erythroleukemia (MEL) cells and transgenic erythroblasts taken at various stages of development, there was regulated expression of the human fetal gamma and adult beta genes, reproducing the in vivo pattern prior to fusion. Hybrids formed from embryonic blood cells produced predominantly gamma mRNA, whereas beta gene expression was observed in adult hybrids and a complete range of intermediate patterns was found in fetal liver hybrids. The adult environment of the MEL cells, therefore, did not appear to influence selective transcription from this gene complex. Irradiation of the embryonic erythroid cells prior to fusion resulted in hybrids containing only small fragments of donor chromosomes, but the pattern of gene expression did not differ from that of unirradiated hybrids. This finding suggests that continued expression of trans-acting factors from the donor erythroblasts is not necessary for continued expression of the human gamma gene in MEL cells. These results contrast with the lack of developmental regulation of the cluster after transfection of naked DNA into MEL cells and suggest that epigenetic processes established during normal development result in the gene cluster adopting a developmental stage-specific, stable conformation which is maintained through multiple rounds of replication and transcription in the MEL cell hybrids. On prolonged culture, hybrids that initially expressed only the gamma transgene switched to beta gene expression. The time period of switching, from approximately 10 to > 40 weeks, was similar to that seen previously in human fetal erythroblast x MEL cell hybrids but in this case bore no relationship to the time of in vivo switching. It seems unlikely, therefore, that switching in these hybrids is regulated by a developmental clock.

Irradiation and fusion gene transfer

Irradiation and fusion gene transfer (IFGT) is a technique that spans the gap between the limitations of molecular methods and somatic-cell genetics, allowing the separation of DNA fragments between 0.25 and 30 Mb in size. In conjunction with genetic linkage analysis and physical mapping techniques, IFGT provides a very useful addition to methods for cloning disease loci, and mapping chromosomes and entire genomes.

Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene

Induction of testis development in mammals requires the presence of the Y-chromosome gene SRY. This gene must exert its effect by interacting with other genes in the sex-determination pathway. Cloning of a translocation chromosome breakpoint from a sex-reversed patient with campomelic dysplasia, followed by mutation analysis of an adjacent gene, indicates that SOX9, an SRY-related gene, is involved in both bone formation and control of testis development.

A method for constructing radiation hybrid maps of whole genomes

In radiation hybrid mapping, chromosomes in human-rodent hybrid cells are fragmented by X-rays and fragments rescued by fusion of the donor cell to a recipient rodent cell. The co-retention frequencies of markers in 100-200 hybrids are used to map individual chromosomes, but mapping the whole genome in this way is impractical. We have reverted to the original protocols of Goss and Harris and have produced a panel of 44 hybrids using irradiated human fibroblasts as donors. This panel has been used to make a map of human chromosome 14 containing 40 ordered markers. The map integrates previously published maps and localizes nine new markers. We suggest that the construction of a high resolution map of the whole human genome is feasible with a single panel of 100-200 hybrids.