A new era in mammalian gene mapping: somatic cell genetics and recombinant DNA methodologies

A 50 year history of technologies that drove discovery in eukaryotic transcription regulation

Transcription regulation is critical to organism development and homeostasis. Control of expression of the 20,000 genes in human cells requires many hundreds of proteins acting through sophisticated multistep mechanisms. In this Historical Perspective, I highlight the progress that has been made in elucidating eukaryotic transcriptional mechanisms through an array of disciplines and approaches, and how this concerted effort has been driven by the development of new technologies.

Of model pets and cancer models: an introduction to mouse models of cancer

The extraordinary endeavor to faithfully model human disorders in mice began in the early 1900s, and in the century since has delivered fundamental advances in our understanding and treatment of human disease. Although it could not be appreciated at the time, 99% of mouse protein-coding genes have an equivalent homolog in the human genome, despite the striking differences in appearance between mouse and man. This remarkable genetic similarity, together with our ability to finely engineer the murine genome, has made the mouse the ideal animal in which to model and analyze human biology and disease. Here we describe this remarkable shared journey between human and mouse, and envisage the next generation of mouse models, which will no doubt prove increasingly sophisticated and even more faithful to human disease. We also address the strategic use of mice in the fight against cancer, and the role they will play in the development of therapies to eradicate this disease.

Horizontal transmission of malignancy: in-vivo fusion of human lymphomas with hamster stroma produces tumors retaining human genes and lymphoid pathology

We report the in-vivo fusion of two Hodgkin lymphomas with golden hamster cheek pouch cells, resulting in serially-transplanted (over 5-6 years) GW-532 and GW-584 heterosynkaryon tumor cells displaying both human and hamster DNA (by FISH), lymphoma-like morphology, aggressive metastasis, and retention of 7 human genes (CD74, CXCR4, CD19, CD20, CD71, CD79b, and VIM) out of 24 tested by PCR. The prevalence of B-cell restricted genes (CD19, CD20, and CD79b) suggests that this uniform population may be the clonal initiating (malignant) cells of Hodgkin lymphoma, despite their not showing translation to their respective proteins by immunohistochemical analysis. This is believed to be the first report of in-vivo cell-cell fusion of human lymphoma and rodent host cells, and may be a method to disclose genes regulating both organoid and metastasis signatures, suggesting that the horizontal transfer of tumor DNA to adjacent stromal cells may be implicated in tumor heterogeneity and progression. The B-cell gene signature of the hybrid xenografts suggests that Hodgkin lymphoma, or its initiating cells, is a B-cell malignancy.

First steps: bovine genomics in historical perspective

The vision of Morris Soller was instrumental in launching the field of bovine genomics. This study is a review of the early years of bovine gene mapping leading up to the sequencing and assembly of the bovine genome in 2009. A historical perspective of parasexual, linkage and physical mapping is provided with a focus on the contribution of these maps to the eventual assignment and orientation of genes and sequence to cattle chromosomes.

The bovine gene map

The present status of the bovine gene map as well as some of the methods and strategies important for future efforts in completing the gene map of cattle are reviewed.

Primer on medical genomics part II: Background principles and methods in molecular genetics

The nucleus of every human cell contains the full complement of the human genome, which consists of approximately 30,000 to 70,000 named and unnamed genes and many intergenic DNA sequences. The double-helical DNA molecule in a human cell, associated with special proteins, is highly compacted into 22 pairs of autosomal chromosomes and an additional pair of sex chromosomes. The entire cellular DNA consists of approximately 3 billion base pairs, of which only 1% is thought to encode a functional protein or a polypeptide. Genetic information is expressed and regulated through a complex system of DNA transcription, RNA processing, RNA translation, and posttranslational and cotranslational modification of proteins. Advances in molecular biology techniques have allowed accurate and rapid characterization of DNA sequences as well as identification and quantification of cellular RNA and protein. Global analytic methods and human genetic mapping are expected to accelerate the process of identification and localization of disease genes. In this second part of an educational series in medical genomics, selected principles and methods in molecular biology are recapped, with the intent to prepare the reader for forthcoming articles with a more direct focus on aspects of the subject matter.

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.

Contribution of zebrafish-mouse cell hybrids to the mapping of the zebrafish genome

The zebrafish, Danio rerio, is becoming an increasingly popular model for the study of vertebrate development. Indeed, the biology of the fish offers great advantages for such studies. The life cycle of the zebrafish is relatively short (2-3 months) and the embryos develop outside the mother, facilitating the visualization of any mutated phenotype. At present, more than 1000 embryonic mutations have been reported. However, until recently, there was no physical or genetic map for this organism. In an effort to generate such a map, we have produced and characterized a panel of zebrafish-mouse cell hybrids. We have used whole-cell fusion to transfer zebrafish chromosomes from two different zebrafish cell lines into mouse recipient cells, thus generating more than 100 hybrids. Using fluorescence in situ hybridization and polymerase chain reaction analysis, we have determined the zebrafish chromosome composition of these hybrids. Here we report that elements from the 25 linkage groups of the zebrafish genome are present in our hybrids. These hybrids could identify the chromosomal location of genes affected in zebrafish mutants.

Identification of disease genes by positional cloning

Positional cloning or reverse genetics is a combination of techniques that has been extraordinarily successful in finding the genes that cause many inherited disorders, including some that affect the cardiovascular system. This approach consists of finding a DNA marker that cosegregates with the disorder and then using the tools of molecular biology to examine systematically the DNA in the vicinity of such a marker until the gene is identified. In addition to the availability of preclinical diagnostic tests for individuals at risk, the identification of such genes might also provide the basis for targeted drug design. In the longer term, with the emerging technologies for the delivery of genes into cells, finding the genes that cause inherited disorders raises the possibility of eventual therapeutic intervention.

Mapping the bovine genome: methodological aspects and strategy

The mapping of genes that control traits of economic importance will ultimately lead to the unravelling of the molecular basis of genetic variation. The main prerequisite for mapping of the unknown genes is a sufficient number of highly polymorphic marker loci which are evenly distributed along the chromosomes. The establishment of such a marker map in cattle and other species is based on methods used in human gene mapping. Comparative mapping facilitates saturation of the chromosomes with markers by utilizing the high degree of conservation of synteny among mammalian species. Comparative mapping will also allow access to the detailed mapping data and to extensive sequence information expected from the human genome initiative.

Synteny mapping in the bovine: genes from human chromosome 5

In an effort to generate a more complete bovine syntenic map of Type I comparative anchor loci, seven homologs to genes found on HSA5 were mapped using a panel of bovine x rodent hybrid somatic cells. Five HSA5 genes, CSF2, RPS14, PDGFRB, FGFA, and CSF1R, were assigned to bovine syntenic group U22 (chromosome 7), while two others, C9 and HGMCR, mapped to U10 and U5, respectively. Previous studies had assigned the HSA5 marker SPARC to bovine syntenic group U22. The mapping of genes spanning the length of HSA5 in cattle and also in mouse permits syntenic comparisons between prototypic genomes of three mammalian orders, providing insight into the evolutionary history of this region of the ancestral mammalian genome.

Molecular and classical cytogenetic analyses demonstrate an apomorphic reciprocal chromosomal translocation in Gorilla gorilla

The existence of an apomorphic reciprocal chromosomal translocation in the gorilla lineage has been asserted or denied by various cytogeneticists. We employed a new molecular cytogenetic strategy (chromosomal in situ suppression hybridization) combined with high-resolution banding, replication sequence analysis, and fluorochrome staining to demonstrate that a reciprocal translocation between ancestral chromosomes homologous to human chromosome 5 and 17 has indeed occurred.

Homologies in human and Macaca fuscata chromosomes revealed by in situ suppression hybridization with human chromosome specific DNA libraries

We established chromosomal homologies between all chromosomes of the human karyotype and that of an old world monkey (Macaca fuscata) by chromosomal in situ suppression (CISS) hybridization with human chromosome specific DNA libraries. Except for the human chromosome 2 library and limited cross-hybridization of X and Y chromosome libraries all human DNA libraries hybridized to single GTG-banded macaque chromosomes. Only three macaque chromosomes (2, 7, 13) were each hybridized by two separate human libraries (7 and 21, 14 and 15, 20 and 22 respectively). Thus, an unequivocally high degree of synteny between human and macaque chromosomes has been maintained for more than 20 million years. As previously suggested, both Papionini (macaques, baboons, mandrills and cercocebus monkeys, all of which have nearly identical karyotypes) and humans are chromosomally conservative. The results suggest, that CISS hybridization can be expected to become an indispensable tool in comparative chromosome and gene mapping and will help clarify chromosomal phylogenies with speed and accuracy.

Syntenic conservation between humans and cattle. I. Human chromosome 9

Bovine X hamster hybrid somatic cells have been used to investigate the syntenic relationship of nine loci in the bovine that have homologous loci on human chromosome 9. Six loci, ALDH1, ALDOB, C5, GGTB2, GSN, and ITIL, were assigned to the previously identified bovine syntenic group U18 represented by ACO1, whereas the other three loci, ABL, ASS, and GRP78, mapped to a new, previously unidentified autosomal syntenic group. Additionally, a secondary locus, ABLL, which cross-hybridized with the ABL probe, was mapped to bovine syntenic group U1 with the HSA 1 loci PGD and ENO1. The results predict that ACO1 will map proximal to ALDH1; GRP78 distal to ITIL and C5; GSN proximal to AK1, ABL, and ASS on HSA 9; GRP78 to MMU 2; and ITIL and GSN to MMU 4.

Syntenic conservation between humans and cattle. II. Human chromosome 12

Bovine X hamster and bovine X mouse hybrid somatic cells have been used to investigate the syntenic relationship of nine loci in the bovine that have homologous loci on human chromosome 12. Eight loci, including A2M, GLI, HOX3, IFNG, INT1, KRAS2, NKNB, and PAH, were assigned to the previously identified bovine syntenic group U3 represented by GAPD. However, a single locus from the q-terminus of HSA 12, ALDH2, mapped to a new, previously unidentified autosomal syntenic group. These results indicate the existence of a very large ancestral syntenic group spanning from the p-terminus to q24 of HSA 12 and containing over 4% of the mammalian genome. Additionally, the results predict that ALDH2 is distal to PAH and IFNG on HSA 12, the type II keratin gene complex will reside between q11 and q21 of HSA 12, A2M will map to MMU 6, and LALBA and GLI will map to MMU 15.

Dynamic changes of microtubule and actin structures in CV-1 cells during electrofusion

To study the involvement of the cytoskeletal system in the fusion of animal cells, we examined the dynamic changes of cytoskeletal proteins during the various stages of cell fusion. CV-1 cells were fused by applying a radio-frequency electrical pulse. Structural changes of microtubules (MTs) and F-actin were monitored simultaneously by double-label fluorescence microscopy. It was observed that in a few minutes after the initiation of cell fusion, MT bundles began to extend into the cytoplasmic bridges which were formed by fusing the membranes of neighboring cells. Later, a network of parallel MT bundles appeared between the adjacent nuclei of the fusing cells; such MT bundles may provide the mechanical links that are responsible for nuclear aggregation. The structural changes of F-actin during cell fusion were more complicated. We observed many different patterns of actin distribution in the fusing cells, including some giant, ring-shaped structures. Reorganization of actin is unlikely to be involved in the nuclear aggregation process. Instead, actin bundles condensed at the cell edges may help to widen the cytoplasmic bridges to allow merging of cellular contents between the fusing cells.

Frontiers in mammalian cell culture

For the past 60 years, fundamental discoveries in eukaryotic biology using mammalian cell cultures have been significant but modest relative to the enormous potential. Combined with advances in technologies of cell and molecular biology, mammalian cell culture technology is becoming a major, if not essential tool, for fundamental discovery in eukaryotic biology. Reconstruction of the milieu for cells has progressed from simple salt solutions supporting brief survival of tissues outside the body to synthesis of the complete set of structurally defined nutrients, hormones and elements of the extracellular matrix needed to reconstruct complex tissues from cells. The isolation of specific cell types in completely defined environments reveals the true complexity of the mammalian cell and its environment as a dynamic interactive physiological unit. Cell cultures provide the tool for detection and dissection of the mechanism of action of cellular regulators and the genes that determine individual aspects of cell behavior. The technology underpins advances in virology, somatic cell genetics, endocrinology, carcinogenesis, toxicology, pharmacology, hematopoiesis and immunology, and is becoming a major tool in developmental biology, complex tissue physiology and production of unique mammalian cell-derived biologicals in industry.

Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources

Current efforts to map the human genome are focused on individual chromosomes or smaller regions and frequently rely on the use of somatic cell hybrids. We report the application of the polymerase chain reaction to direct amplification of human DNA from hybrid cells containing regions of the human genome in rodent cell backgrounds using primers directed to the human Alu repeat element. We demonstrate Alu-directed amplification of a fragment of the human HPRT gene from both hybrid cell and cloned DNA and identify through sequence analysis the Alu repeats involved in this amplification. We also demonstrate the application of this technique to identify the chromosomal locations of large fragments of the human X chromosome cloned in a yeast artificial chromosome and the general applicability of the method to the preparation of DNA probes from cloned human sequences. The technique allows rapid gene mapping and provides a simple method for the isolation and analysis of specific chromosomal regions.

Molecular genetics of congenital adrenal hyperplasia

Congenital adrenal hyperplasia results from a deficiency in any of the five enzymes necessary to synthesize cortisol from cholesterol: cholesterol desmolase (P450scc), 3 beta-hydroxysteroid dehydrogenase (3 beta-HSD), 17-hydroxylase (P450c17), 21-hydroxylase (P450c21) and 11-hydroxylase (P450c11). P450scc and P450c11 are structurally-related mitochondrial cytochrome P450 enzymes, whereas P450c17 and P450c21 are microsomal enzymes. The P450scc gene, CYP11A, is located on chromosome 15, and the P450c17 gene, CYP17, is on chromosome 10. The P450c21 gene, CYP21B, and a pseudogene, CYP21A, are located in the HLA major histocompatibility complex on chromosome 6p, while the P450c11 gene, CYP11B, is on chromosome 8q along with a second related gene of unknown function. Thus, despite common regulation by ACTH, there is no clustering of the genes for steroidogenic enzymes. CYP11A and CYP11B have an identical intron-exon organization, and CYP17 and CYP21B have similar gene structures, but the two pairs of genes encoding mitochondrial and microsomal P450 enzymes resemble each other poorly. More than 90% of cases of congenital adrenal hyperplasia result from 21-hydroxylase deficiency, and most of the remainder are caused by 11-hydroxylase deficiency. About one-quarter of 21-hydroxylase deficiency alleles are associated with a deletion of all or part of CYP21B. Most of the remaining mutant alleles result from transfers of deleterious mutations from the CYP21A pseudogene to CYP21B, a process termed gene conversion. These mechanisms provide an explanation for the relatively high frequency of 21-hydroxylase deficiency. The clinical severity of various forms of 21-hydroxylase deficiency may be roughly correlated with particular mutations.

Hitch-hiking from HRAS1 to the WAGR locus with CMGT markers

The clinical association of Wilms' tumour with aniridia, genitourinary abnormalities and mental retardation (WAGR syndrome) is characterised cytogenetically by variable length, constitutional deletion of the short arm of chromosome 11, which always includes at least part of band 11p13. HRAS1-selected chromosome mediated gene transfer (CMGT) generated a transformant, E65-6, in which the only human genes retained map either to band 11p13 or, with HRAS1, in the region 11p15.4-pter. Human recombinants isolated from E65-6 were mapped to a panel of five WAGR deletion hybrids and two clinically related translocations. We show that E65-6 is enriched congruent to 400-fold for 11p15.4-pter markers and congruent to 200-fold for 11p13 markers. 'Hitch-hiking' from HRAS1 with CMGT markers has allowed us to define seven discrete intervals which subtend band 11p13. Both associated translocations co-locate within the smallest region of overlap for the WAGR locus, which has been redefined by identifying a new interval closer than FSHB.

HRAS1-selected chromosome transfer generates markers that colocalize aniridia- and genitourinary dysplasia-associated translocation breakpoints and the Wilms tumor gene within band 11p13

We show that chromosome-mediated gene transfer can provide an enriched source of DNA markers for predetermined, subchromosomal regions of the human genome. Forty-four human DNA recombinants isolated from a HRAS1-selected chromosome-mediated gene transformant map exclusively to chromosome 11, with several sublocalizing to the Wilms tumor region at 11p13. We present a detailed molecular map of the deletion chromosomes 11 from five WAGR (Wilms tumor/aniridia/genitourinary abnormalities/mental retardation) syndrome patients, three of which are at the limits of cytogenetic resolution but shown here to be molecularly distinguishable and overlapping. We can define ten distinct regions of the short arm of chromosome 11, five of which subdivide band 11p13. We also map two independent 11p13 translocation breakpoints to within the smallest region of overlap defined by the WAGR deletions. The first comes from a patient with familial aniridia, and the second from a patient with Potter facies and genitourinary dysplasia. The close similarities in map location and affected cell lineage for Wilms tumor and genitourinary dysplasia suggest that they may be alternative manifestations of mutation at the same locus.

Confirmation of assignment of the human alpha 1-crystallin gene (CRYA1) to chromosome 21 with regional localization to q22.3

The crystallins are highly conserved structural proteins universally found in the eye lens of all vertebrate species. In mammals, three immunologically distinct classes are present, alpha-, beta-, and gamma-crystallins, and each class represents a multigene family. The alpha-crystallin gene family consists of alpha 1-crystallin (CRYA1) and alpha 2-crystallin (CRYA2) genes (previously designated alpha A- and alpha B-crystallin, respectively), which show extensive sequence homology. We constructed a synthetic oligonucleotide probe of 25 bases corresponding to a specific region of the human alpha 1-crystallin gene sequence. This 25-mer probe bears little sequence homology to human alpha 2-crystallin gene and does not cross-hybridize to alpha 2-crystallin sequences in Southern blot analysis. Using this unique synthetic probe, we have demonstrated the identity of the alpha 1-crystallin gene in human genomic DNA. In addition, we have also confirmed its chromosomal location on human chromosome 21. Finally, we have regionally localized the gene to q22.3 by using both Southern blot analysis of a panel of cell hybrids containing different parts of human chromosome 21, and in situ hybridization to metaphase chromosomes. The use of synthetic oligonucleotide probes specific for individual genes should be useful in identifying and mapping members of multigene families.

A fission yeast chromosome can replicate autonomously in mouse cells

To test the functional capacity of a fission yeast chromosome in mouse cells, a strain of the fission yeast Schizosaccharomyces pombe, ED628 Int5, was constructed. A plasmid bearing the SV2NEO gene, which can confer G418 resistance to mouse cells, was integrated at the ura4 locus on S. pombe chromosome III. S. pombe Int5 chromosomes were introduced into mouse C127 cells by PEG-facilitated protoplast fusion. Here we describe two independent G418-resistant cell lines with distinct growth characteristics, F1.1 and F7.1, and examine the structure of material derived from S. pombe Int5 chromosome III in these lines. F1.1 is shown to contain a single rearranged block of chromatin from S. pombe chromosome III integrated into a mouse chromosome, maintained in the absence of selection. In contrast, the data for F7.1 are consistent with the presence of linear, unintegrated copies of S. pombe chromosome III, which are apparently intact and maintained in an unstable but autonomous state. The unstable maintenance of this chromosome may be due to defective centromere function leading to missegregation at mitosis or to over- or underreplication.

HRAS1-selected, chromosome-mediated transformants vary in phenotype in vitro and tumorigenic potential in vivo

Transfection of mouse C127 cells with mitotic chromosomes isolated from a human EJ bladder carcinoma cell line gave rise, at high frequency, to foci of transformed cells. Independent, HRAS1-selected chromosome-mediated transformants displayed distinctive cellular morphologies in monolayer culture and colony-forming abilities in low-melting-point agarose. Subcutaneous inoculation of neonatally thymectomized, Ara-C-protected, total-body-irradiated CBA mice was used to compare the tumorigenic potential of each transformant. Significant quantitative and qualitative differences in tumorigenicity were found between transformants which correlated with differences in malignant phenotype observed in vitro. The sensitivity of the tumorigenicity assay is such that rare transformation events can be selected directly in vivo.

Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition

The DNA immediately flanking the 164-base-pair U1 RNA coding region is highly conserved among the approximately 30 human U1 genes. The U1 multigene family also contains many U1 pseudogenes (designated class I) with striking although imperfect flanking homology to the true U1 genes. Using cosmid vectors, we now have cloned, characterized, and partially sequenced three 35-kilobase (kb) regions of the human genome spanning U1 homologies. Two clones contain one true U1 gene each, and the third bears two class I pseudogenes 9 kb apart in the opposite orientation. We show by genomic blotting and by direct DNA sequence determination that the conserved sequences surrounding U1 genes are much more extensive than previously estimated: nearly perfect sequence homology between many true U1 genes extends for at least 24 kb upstream and at least 20 kb downstream from the U1 coding region. In addition, the sequences of the two new pseudogenes provide evidence that class I U1 pseudogenes are more closely related to each other than to true genes. Finally, it is demonstrated elsewhere (Lindgren et al., Mol. Cell. Biol. 5:2190-2196, 1985) that both true U1 genes and class I U1 pseudogenes map to chromosome 1, but in separate clusters located far apart on opposite sides of the centromere. Taken together, these results suggest a model for the evolution of the U1 multigene family. We speculate that the contemporary family of true U1 genes was derived from a more ancient family of U1 genes (now class I U1 pseudogenes) by gene amplification and transposition. Gene amplification provides the simplest explanation for the clustering of both U1 genes and class I pseudogenes and for the conservation of at least 44 kb of DNA flanking the U1 coding region in a large fraction of the 30 true U1 genes.

Detection of restriction fragment length polymorphisms at the centromeres of human chromosomes by using chromosome-specific alpha satellite DNA probes: implications for development of centromere-based genetic linkage maps

We describe a general strategy for the detection of high-frequency restriction fragment length polymorphisms in the centromeric regions of human chromosomes by molecular analysis of alpha satellite DNA, a diverse family of tandemly repeated DNA located near the centromeres of all human chromosomes. To illustrate this strategy, cloned alpha satellite repeats isolated from two human chromosomes, 17 and X, have been used under high-stringency conditions that take advantage of the chromosome-specific organization of this divergent repeated DNA family. Multiple high-frequency restriction fragment length polymorphisms are described for the centromeric region of both chromosome 17 and X chromosome. Mendelian inheritance of the variants is demonstrated. The X-linked alpha satellite polymorphisms in particular are highly informative and constitute a virtually unique centromeric DNA marker for each X chromosome examined. Since the strategy we describe is a general one, the alpha satellite family of DNA should provide a rich source of molecular variation in the human genome and should contribute to the development of centromere-based genetic linkage maps of human chromosomes.

Gene mapping and physical arrangements of human chromatin in transformed, hybrid cells: fluorescent and autoradiographic in situ hybridization compared

We compare a fluorescent in situ hybridization technique, using N-acetoxy-2-acetylaminofluorene (N-ACO-AAF) modified DNA adducts, with 3H-labeled DNA in situ hybridization for visualizing human transgenomes in HRAS1-selected, chromosome-mediated gene transfer (CMGT), and mapping chromosomal SV40 in an SV40-transformed, human-mouse hybrid cell line. We demonstrate that individual HRAS1-CMGTs may contain multiple fragments of human chromatin. We deduce that the CMGT process can involve interstitial loss of mouse chromatin. We conclude that the N-ACO-AAF technique gives finer resolution than 3H-labeled in situ hybridization. However, 3H-labeling is more sensitive and has allowed us to sublocalize SV40 in C121 to the region 7q31-35.

Interrelationships between recent developments in molecular genetics and cytogenetics and animal breeding

Animal breeding traditionally has entailed devising means to apply quantitative and population genetic theory to increase productive capacity of livestock. A highly developed and successful industry has been built on foundations established by academic animal breeders. Recent developments in related sciences such as reproductive biology, molecular biology, cellular biology, and cytogenetics offer prospects for the emergence of a number of methodologies that might usefully be applied to animal breeding. Scientists engaged in development of the newer technologies are not wholly familiar with the livestock industry, its breeding structure, its objectives, its institutions or its peculiarities. Animal breeders, however, are not fully cognizant of the scientific advances being made in related fields, their potential for development and application or their limitations, and therefore, animal breeders have not seriously thought about how they might be integrated most usefully and efficaciously into the animal breeding enterprise. A collaboration is needed in which the laboratory scientists produce new ideas, products, and methods and the animal breeders--using system analysis, simulation procedures, and laboratory animal and livestock breeding tests--help make rational choices, partially direct work of the laboratory scientists, help the industry integrate new methods, and monitor the extent of success of adapted innovations.

The suitability of restriction fragment length polymorphisms as genetic markers in maize

Strain identification in Zea mays by restriction fragment length polymorphism should be feasible due to the high degree of polymorphism found at many loci. The polymorphism in maize is apparently higher than that currently known for any other organism. Five randomly selected maize inbred lines were examined by Southern filter hybridization with probes of cloned low copy sequences. Typically, several alleles could be distinguished among the inbred lines with any one probe and an appropriately selected restriction enzyme. Despite considerable polymorphism at the DNA level, 16 RFLP markers in three inbred lines of maize were examined for six to 11 generations and found be stable. Mapping of RFLP markers in maize can be accelerated by the use of B-A translocation stocks, which enable localization of a marker to chromosome arm in one generation. The use of recombinant inbred lines in further refinement of the map is discussed.

Mapping genes in domesticated animals

Gene maps are constructed by the synthesis of data obtained by different methods which include family analyses, somatic cell hybridization, direct mapping of DNA segments by Southern blot analysis, and in situ hybridization to fixed metaphase chromosomes. Gene mapping has already contributed significantly to a better understanding of the mammalian genome, in particular the human genome, but the gene maps of economically important domestic species are not well-characterized. The application of somatic cell genetics and recombinant DNA methodologies now allows rapid progress to be made in the construction of detailed gene maps for domestic animals. Such gene maps will serve as tools for selection in applied animal breeding and for the analysis of polygenic traits.

Gene transfer into mouse embryos

Gene transfer into the murine genome was accomplished nearly a decade ago by use of chimeras and teratocarcinomas; however, the low frequencies of transfer into the germ line and other difficulties stemming from mosaicism and karyotypic abnormalities in chimeric mice have limited the general usefulness of this procedure in achieving transformation in mammalian embryos. The introduction of cloned genes into teratocarcinoma cells, selection for a mutant phenotype, and transfer of those cells into mouse embryos holds some promise as a technique to employ mouse chimeras for gene transfer into mice. Infection with animal viruses and retroviral vectors provides another way to introduce exogenous DNA into mouse embryos. Infection with Mo-MuLV has been utilized to characterize the relationship between sites of integration and gene function in developing and adult mice. Gene transfer by microinjection of cloned recombinant DNA has been used by many laboratories for the transfer of DNAs into mouse embryos. The factors affecting transformation frequencies and sites of integration are unknown at present, although it seems that integration is not strictly mediated by homology-dependent events. Many genes have been introduced into mouse embryos by these procedures and many of these are expressed at high levels in appropriate tissues. No realistic possibility exists at the present time for the utilization of embryo gene transfer in the medical field for the correction of genetic defects for several reasons. First, in order to effectively provide "gene therapy" it would be necessary to determine the genotype of each recipient egg, a technical impossibility. The genetic diseases that would be amenable to germ line intervention are recessive diseases and there would be only a 25% chance of any one embryo derived from heterozygous parents being a homozygous recessive. Moreover, it would be impossible to distinguish the normal from abnormal embryos. Second, the frequencies of transformation are so low as to exclude work on human beings on ethical grounds. Third, the parameters effecting chromosomal integration sites and gene expression have not been fully characterized. Until it becomes experimentally possible to target the newly introduced DNA into expressable chromosomal sites and actively replace or supplement defective genes, the possibility of gene therapy through manipulation of embryos is remote. Yet, efforts to provide gene therapy in somatic tissues have been promising, leading to expression of a modified phenotype (Anderson, 1984). In contrast to embryo gene therapy, gene therapy in somatic tissues would not lead to germ line propagation of the manipulated genotype.(ABSTRACT TRUNCATED AT 400 WORDS)

The role of cytochemistry in human genetic research

The role of cytochemistry in human genetics is reviewed. In basic research, autoradiography and cytochemical staining procedures for DNA, RNA, proteins and other cell constituents have contributed to the understanding of the way DNA is localized, duplicated and translated. The development of new "banding techniques" for the identification of human chromosomes and parts of these together with somatic cell hybridization procedures have significantly contributed to the mapping of the human genome. Cytochemical methods have also been of great help in the elucidation of the responsible molecular defects in Mendelian disorders based on a single gene mutation. The combination of immunological methods and electron-microscopical cytochemistry now enables different posttranslational processing defects to be related to various subcellular compartments. Cytochemistry is also likely to be of importance for the direct demonstration of gene mutations using recombinant DNA technology. Examples are given of contributions of cytochemical methods to the early diagnosis and prevention of congenital disorders. The main examples are the early diagnosis of patients with a chromosomal aberration and of carriers with a balanced translocation. Early genetic counseling of couples at risk forms the basis for prevention of subsequent affected children. Cytochemistry also contributes to the early detection of heterozygotes of X-linked mutations. Finally, autoradiography and ultramicrochemical procedures have been of great help in improving the prenatal diagnosis of genetic metabolic diseases.

Characterization of a set of X-linked sequences and of a panel of somatic cell hybrids useful for the regional mapping of the human X chromosome

We have characterized 19 DNA fragments originating from the human X chromosome. Most of them have been isolated from an X chromosome genomic library (Davies et al. 1981) using a systematic screening procedure. These DNA probes have been used to search for restriction fragment length polymorphisms (RFLP). The frequency of restriction polymorphisms (1 per 350 bp analysed) was lower than expected from data obtained with autosomal fragments. The various probes have been mapped within 12 subchromosomal regions using a panel of human-rodent hybrid cell lines. The validity of the panel was established by hybridization experiments performed with 27 X-specific DNA probes, which yielded information on the relative position of translocation breakpoints on the X chromosome. The DNAs from the various hybrid lines are blotted onto a reusable support which allows one to quickly map any new X-specific DNA fragment. The probes already isolated should be of use to map unbalanced X chromosome aberrations or to characterize new somatic cell hybrid lines. The probes which detect RFLPs define new genetic markers which will help to construct a detailed linkage map of the human X chromosome, and might also serve for the diagnosis of carriers or prenatal diagnosis.

Detection of species specific chromosomes in somatic cell hybrids

We describe an in situ hybridization technique which allows rapid identification of species-specific chromosomes in somatic cell hybrid lines. Chromosome preparations from rodent-human hybrid lines are hybridized to biotinylated total human DNA which is subsequently detected by a series of immunocytochemical reactions which culminate in a peroxidase reaction visible by light microscopy. This technique not only allows identification of intact human chromosomes but also fragmented and rearranged human chromosomal segments. We have detected as little as 1 X 10(7) bp of human DNA inserted into a mouse chromosome using this procedure and estimate that the sensitivity of the technique would allow detection of sequences 5- to 10-fold smaller. The usefulness of the technique for screening hybrid cell gene mapping panels is discussed.

Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition

The DNA immediately flanking the 164-base-pair U1 RNA coding region is highly conserved among the approximately 30 human U1 genes. The U1 multigene family also contains many U1 pseudogenes (designated class I) with striking although imperfect flanking homology to the true U1 genes. Using cosmid vectors, we now have cloned, characterized, and partially sequenced three 35-kilobase (kb) regions of the human genome spanning U1 homologies. Two clones contain one true U1 gene each, and the third bears two class I pseudogenes 9 kb apart in the opposite orientation. We show by genomic blotting and by direct DNA sequence determination that the conserved sequences surrounding U1 genes are much more extensive than previously estimated: nearly perfect sequence homology between many true U1 genes extends for at least 24 kb upstream and at least 20 kb downstream from the U1 coding region. In addition, the sequences of the two new pseudogenes provide evidence that class I U1 pseudogenes are more closely related to each other than to true genes. Finally, it is demonstrated elsewhere (Lindgren et al., Mol. Cell. Biol. 5:2190-2196, 1985) that both true U1 genes and class I U1 pseudogenes map to chromosome 1, but in separate clusters located far apart on opposite sides of the centromere. Taken together, these results suggest a model for the evolution of the U1 multigene family. We speculate that the contemporary family of true U1 genes was derived from a more ancient family of U1 genes (now class I U1 pseudogenes) by gene amplification and transposition. Gene amplification provides the simplest explanation for the clustering of both U1 genes and class I pseudogenes and for the conservation of at least 44 kb of DNA flanking the U1 coding region in a large fraction of the 30 true U1 genes.

Rapid and quantitative detection of unique sequence donor DNA in extracts of cultured mammalian cells: an aid to chromosome mapping

A rapid and highly sensitive method for screening the human DNA content of hybrid or transfected mammalian cells is described. Transfectants containing as little as 200 kb of otherwise undefined human DNA can be readily detected in a background of mouse chromatin. At the highest stringency, single-copy sequences can be detected. Large numbers of independent gene-transfer products are easily screened, making the method ideally suited to the identification of rare, but otherwise unselectable, events. The method does not rely upon the expression of the gene sequence of interest; the sole proviso is the availability of an appropriate DNA probe for the chromosomal region or locus of interest.

Isolation and regional mapping of random X sequences from distal human X chromosome

Chromosome-mediated gene transfer (CMGT) lines were shown to be convenient donors of genomic sequences from specific regions of the genome adjacent to selectable markers. Two libraries were prepared from CMGT lines carrying sequences spanning the long arm of the human X chromosome from HPRT (Xq26) to G6PD (Xq28). A series of 22 CMGT lines sharing the same selectable marker (HPRT) were used in conjunction with five standard translocation hybrids to provide fine-resolution regional mapping of the nonrepetitive X specific probes isolated from the libraries. The order of three human recombinant sequences with respect to known X-linked markers is: PGK (Xq13), 05-02 (DXS78); HPRT (Xq26), 07-03 (DXS79); surface antigen S11 (Xq27), 07-14 (DXS80); and G6PD (Xq28).