The gene map of the Norway rat (Rattus norvegicus) and comparative mapping with mouse and man

Rat Genome Assemblies, Annotation, and Variant Repository

The first and only published version of the rat reference genome sequence was RGSC3.1, accomplished by the Rat Genome Sequencing Project Consortium. Here we present the history of the community effort in the correction of sequence errors and filling missing gaps in the process of refining and providing researchers with a high-quality rat reference sequence. The genome assembly improvements, addition of different evidence resources over time, such as RNA-Seq data, and software development methodologies had a positive impact on the gene model annotations. Over the years we observed a great increase in the numbers of genes, protein coding sequences, predicted transcripts and transcript features. Before the sequencing of the rat genome was possible, first biochemical and next genomic markers like RAPD, AFLP, RFLP, and SSLP were fundamental in research studies involving cross-breeding between different rat strains, in finding the level of polymorphism, linkage mapping, and phylogeny. Linkage maps provide information on recombination rates, give insight into intra- and interspecies gene rearrangements, and help to identify Mendelian loci and Quantitative Trait Loci (QTL). In the 1990s many reports were published on the construction of rat linkage maps that incorporated increasing numbers of markers and facilitated the localization of disease loci. Current genetic monitoring and linkage mapping relies on single nucleotide polymorphisms (SNPs). The Rat Genome Database collects information on genetic variation from the worldwide community of rat researchers and provides tools for searching and retrieving these data. As of today we show details about almost 605 million variants coming from many studies in our Variant Visualizer tool.

The Rat: A Model Used in Biomedical Research

The laboratory rat, Rattus norvegicus, has been used in biomedical research for more than 150 years, and in many cases remains the model of choice for studies of physiology, behavior, and complex human disease. This book provides detailed information on a number of methodologies that can be used in rat. This chapter gives an introduction to rat as a species and as a biomedical model, providing historical information, a brief introduction to the current state of rat research, and a perspective on the future of rat as a model for human disease.

Hippocampal long-term depression in freely behaving mice requires the activation of beta-adrenergic receptors

In the intact mouse hippocampus patterned afferent stimulation does not lead to long-term depression (LTD) at Schaffer collateral (Sc)-CA1 synapses, but the same synapses express robust LTD (<24 h) if test-pulse or patterned afferent experience is coupled with novel spatial learning. This suggests that the failure of sole afferent stimulation to elicit LTD relates to the absence of neuromodulatory input related to increased arousal or novelty during learning. Locus coeruleus (LC) firing increases during novel experience, and in rats patterned stimulation of the LC together with test-pulse stimulation of Sc-CA1 synapses leads to robust LTD in vivo. This effect is mediated by beta-adrenergic receptors. Here, we explored if activation of beta-adrenergic receptors supports the expression of LTD in freely behaving mice. We also explored if beta-adrenergic receptors contribute to endogenous LTD that is expressed following spatial learning. Patterned stimulation of Sc-CA1 synapses at 3 Hz (200 pulses) resulted in short-term depression (STD). Pretreatment with isoproterenol, an agonist of beta-adrenergic receptors, resulted in robust LTD (<24 h). Test-pulse stimulation under control conditions elicited field potentials that were stable for the 24-h monitoring period. Coupling of test-pulses with a novel spatial object recognition task resulted in robust endogenous LTD (<24 h). Pretreatment with propranolol, a beta-adrenergic receptor antagonist, completely prevented endogenous LTD that was enabled by learning and prevented object recognition learning itself. These data indicate that the absence of LTD in freely behaving mice, under standard recording conditions, does not reflect an inability of mice to express LTD, rather it is due to the absence of a noradrenalin tonus. Our data also support that spatial object recognition requires beta-adrenergic receptor activation. Furthermore, LTD that is enabled by novel spatial learning critically depends on activation of beta-adrenergic receptors that are presumably activated by noradrenalin released by the LC in response to the novel experience.

Blood pressure and heart rate QTL in mice of the B6/D2 lineage: sex differences and environmental influences

A quantitative trait locus (QTL) approach was used to define the genetic architecture underlying variation in systolic blood pressure (SBP) and heart rate (HR), measured indirectly on seven occasions by the tail cuff procedure. The tests were conducted in 395 F(2) adult mice (197 males, 198 females) derived from a cross of the C57BL/6J (B6) and DBA/2J (D2) strains and in 22 BXD recombinant-inbred (RI) strains. Interval mapping of F(2) data for the first 5 days of measurement nominated one statistically significant and one suggestive QTL for SBP on chromosomes (Chr) 4 and 14, respectively, and two statistically significant QTL for HR on Chr 1 (which was specific to female mice) and Chr 5. New suggestive QTL emerged for SBP on Chr 3 (female-specific) and 8 and for HR on Chr 11 for measurements recorded several weeks after mice had undergone stressful blood sampling procedures. The two statistically significant HR QTL were confirmed by analyses of BXD RI strain means. Male and female F(2) mice did not differ in SBP or HR but RI strain analyses showed pronounced strain-by-sex interactions and a negative genetic correlation between the two measures in both sexes. Evidence for a role for mitochondrial DNA was found for both HR and SBP. QTL for HR and SBP may differ in males and females and may be sensitive to different environmental contexts.

Rat gene mapping in the post-genome sequencing era: the continued utility of cell hybrids to localize rat genes (Cks2, Ephb4, Fabp5, Il13ra1, Rpl10, Ssr4)

Finding the position of a gene is now easily done when the genome sequence is available: the gene position is generally found by a simple query of genomic databases such as those available at the Ensembl browser or the NCBI. We were interested in determining the position of 125 cancer-related rat genes and we found that the position of most of these genes (110) could indeed be identified in this manner. However, in 15 cases, the gene position was not available in these databases, or the results were ambiguous. We then explored a more specialized database, namely the Rat Genome Database, and experimentally mapped these genes using standard and radiation cell hybrids. The 15 genes in question could be localized unambiguously. In four cases, the radiation cell hybrids were indispensable: the sequence of these four genes could not be found in the rat genome sequence. On the basis of the sample we examined, it thus appears that a classical gene mapping method is still required to localize about 3% of the rat genes, as if 3% of the rat gene sequences were lacking in the current rat genome sequence.

Chromosome evolution of MMU16 and RNO11: conserved synteny associated with gene order rearrangements explicable by intrachromosomal recombinations and neocentromere emergence

Comparative mapping between the rat and mouse genomes has shown that some chromosomes are entirely or almost entirely conserved with respect to gene content. Such is the case of rat chromosome 11 (RNO11) and mouse chromosome 16 (MMU16). We determined to what extent such an extensive conservation of synteny is associated with a conserved gene order. Therefore, we regionally localized several genes on RNO11. The comparison of the gene map of RNO11 and MMU16 unambiguously shows that the gene order has not been conserved in the Murinae lineage, thereby implying the occurrence of intrachromosomal evolutionary rearrangements. The transition from one chromosome configuration to the other one can be explained either by two intrachromosomal recombinations or by a single intrachromosomal recombination accompanied by neocentromere emergence.

Utilizing alpha-fetoprotein expression to enhance oncolytic viral therapy in hepatocellular carcinoma

OBJECTIVE

To determine whether alpha-fetoprotein (AFP)-regulated ribonucleotide reductase (RR) production would promote more vigorous and specific viral killing in AFP-expressing hepatocellular carcinoma (HCC).

BACKGROUND

AFP is expressed in over 70% of primary HCC but not in normal adult liver. AFP production by HCC can be exploited to target viral killing of tumor cells. G207 is an oncolytic herpes virus lacking UL39, the gene encoding RR. RR is an enzyme required for viral DNA synthesis and cytotoxicity.

METHODS

Enzyme-linked immunosorbent assay (ELISA) was performed for AFP levels on Hep3B and PLC5 human HCC cells. An AFP-albumin enhancer-promoter complex (AFP-alb) was constructed in a luciferase vector to assess function. AFP-alb was cloned upstream of UL39 (AFP-alb/UL39) and transfected into HCC cells for G207 cytotoxicity assays. Viral plaque forming assays evaluated G207 replication. Hep3B flank tumors, with and without AFP-alb/UL39 transfection, were established in athymic mice (n = 28) and treated with G207.

RESULTS

Hep3B had 5-fold higher AFP levels than PLC5 (P < 0.00001). AFP-alb increased luciferase expression 72-fold in Hep3B (P < 0.001) and 3-fold in PLC5 (P < 0.001). AFP-alb/UL39 transfection increased G207 cytotoxicity 93% in Hep3B (P < 0.0005), with no significant increase in PLC5. Peak viral titers were 46-fold higher in Hep3B transfected with AFP-alb/UL39 versus mock-transfected cells (P < 0.01), with no significant change in PLC5. Flanks tumors transfected with AFP-alb/UL39 and treated with G207 demonstrated a 76% volume reduction versus mock-transfected tumors infected with G207 (P < 0.0001).

CONCLUSIONS

AFP-driven RR production by hepatoma cells significantly enhances herpes viral cytotoxicity and specificity in vitro and reduces tumor burden in vivo.

Trisomy 8 and urogenital malformation in the ACI-rat

ACI-rats are considered as a model for studying urogenital abnormalities. In order to recognise cytogenetic changes related to these abnormalities 50 male ACI/Seg rats were examined by means of gross macroscopic, histological, and karyotypical investigations. In six of the examined animals (12%) unilateral agenesis of the kidney and ipsilateral hypoplasia of the testes and seminal vesicles were observed. Isochromosome 8 and trisomy 8 (i8, +8) were observed in 26.5% of karyotypes from the animals with kidney agenesis. Chromosome heteromorphisms such as 1p+, 3p+, 11p+, 12p+ were found in animals with and without apparent pathology. Because of the similarity between the phenotypical changes found in ACI-rats and in patients with familial renal agenesis (Potter's syndrome) and hereditary renal agenesis and aplasia (HRA), rat and human chromosomes associated with manifested renal malformations were examined by comparative cytogenetics and gene mapping.

Mapping of glutathione transferase (GST) genes in the rat

Glutathione transferases (GST) make up a large group of related enzymes in mammalian tissues. The enzyme molecules are dimeric and at least 13 different subunits occur in the rat. Each subunit appears to be coded for by a distinct gene, and thus there is a large GST gene family in the rat. Recently, there have been several reports of the mapping of rat GST genes. In the present communication we confirm the previous assignments and extend the data with the mapping to rat chromosome 2 of a previously unmapped GST gene (Gstm1), and with the regional mapping of seven Gstp genes. These mappings provide further evidence for conservation of syntenic gene relationships among mammals. The human homologs of Gstm1 map to chromosome 1, and belong to a group of 9 genes that show conserved synteny on rat chromosome 2. The corresponding murine genes in most cases map to mouse chromosome 3. Similarly, the human homolog of Gstp maps to chromosome 11, and is one of 10 genes that exhibit conserved synteny on rat chromosome 1. The corresponding mouse genes map to mouse chromosome 7. Previously only one gene on rat chromosome 8 had a human homolog on chromosome 6, and rat Gsta1 is the second instance. Based on these mappings it appears that a new group of genes will exhibit conserved synteny on rat chromosome 8, human chromosome 6 and mouse chromosome 9. Interestingly, each of the three groups of conserved synteny seems to span the region across the centromeres of the human chromosomes.

A candidate chimeric mammalian mRNA transcript is derived from distinct chromosomes and is associated with nonconsensus splice junction motifs

The process of creating chimeric mRNA transcripts derived from separately transcribed genes via known spliceosome mechanisms is termed trans-splicing, and has been primarily described in lower eukaryotes. Isolation of cDNA clones containing sequences from distinct genes has raised the possibility of trans-splicing across distinct genes in mammalian systems; however, the possibility of cloning artifacts or splicing via nonspliceosome mechanisms has been difficult to rule out. In most cases, the absence of corresponding genomic clones has limited assessment of splice donor and acceptance sites and associated intronic elements that would be expected to participate in spliceosome-based reactions. We have previously reported a cDNA clone encoding the rat Leukocyte Common Antigen-Related (LAR) tyrosine phosphatase receptor that contains an alternative 3' UTR. In the present study Northern, RT-PCR and RNase protection assays verified the existence of developmentally regulated 3' UTR alternative splicing of LAR transcripts in vivo. FISH and radiation hybrid mapping demonstrated that loci encoding LAR and its alternative 3' UTR are present on distinct chromosomes, raising the possibility that alternatively spliced transcripts resulted from trans-splicing. Exon/intron analysis of corresponding genomic clones revealed nonconsensus splice junctions along with elements known to promote both cis- and trans-splicing. Verification in a mammalian in vivo system of chimeric transcripts derived from distinct genes along with identification of atypical nonconsensus-associated genomic elements points to the novel possibilities of atypical spliceosome-based trans-splicing or nonconventional, nonspliceosome-based mechanisms leading to chimeric transcripts.

Identification of three 11p11.2 candidate liver tumor suppressors through analysis of known human genes

We have previously mapped a liver tumor suppressor locus to human chromosome 11p11.2-p12 using a functional model of tumor suppression. Using this model system, we have employed a candidate gene approach to identify potential liver tumor suppressor genes. Thirty-eight known genes have been positioned in human 11p11.2-p12 by the Human Genome Project. Here we show that four of these genes (guanine nucleotide binding protein gamma 3; mitochondrial carrier homolog 2; p53-induced protein (PIG11), and pRDI-BF1-rIZ1 domain containing 11) localized to the minimal liver tumor suppressor region within 11p11.2-p12. In fact, all of these genes mapped to human 11p11.2, allowing refinement of the liver tumor suppressor region to this cytogenetic band. Three of the four genes (mitochondrial carrier homolog 2, PIG11, and pRDI-BF1-rIZ1 domain containing 11) were uniformly expressed by an index panel of suppressed microcell hybrid cell lines, identifying them as candidate liver tumor suppressor genes. In a preliminary analysis of four human hepatocellular carcinoma cell lines (HepG2, Hep3B, SNU398, and SNU449), the transcript for PIG11 was lost or significantly decreased in two of these cell lines (HepG2 and Hep3B), suggesting the potential involvement of PIG11 in some human hepatocellular carcinomas. The results of this study extended our previous knowledge of genes located in the minimal liver tumor suppressor region of human 11p11.2 and identified several candidate liver tumor suppressor genes from this region. Further characterization of these candidates will provide new insight into the role of human 11p11.2 in the molecular pathogenesis of human liver cancer.

Identification of candidate liver tumor suppressor genes from human 11p11.2-p12

We have previously described a functional model for identification of human liver tumor suppressor genes in which human chromosome 11 was introduced into rat liver epithelial tumor cell lines via microcell-mediated chromosome transfer, producing microcell hybrid (MCH) cell lines that exhibit suppression of tumorigenicity in vivo. Chromosome deletion mapping studies identified a 950-kb region of 11p11.2-p12 that was retained in all suppressed MCH cell lines, suggesting that this region may harbor one or more genes with liver tumor suppressor function. In this study, we generated a comprehensive transcription map of the 11p11.2-p12 liver tumor suppressor region through examination of 142 expressed sequence tag (EST) markers among a group of suppressed MCH cell lines. Of 142 ESTs examined, 19 were localized within the 11p11.2-p12 liver tumor suppressor region. RT-PCR analysis of gene expression for these 19 ESTs among an index panel of suppressed MCH cell lines (n = 3) identified 11 potential candidate liver tumor suppressor genes. Examination of candidate gene expression among six additional suppressed MCH cell lines reduced the number of potential candidate genes to three (stSG30184, stSG10014, and stSG29748). Northern blot analysis of suppressed MCH cell lines and derived tumor cell lines suggested stSG30184 as the best candidate liver tumor suppressor gene. The 3.7 kb stSG30184 transcript was expressed by all suppressed MCH cell lines, but expression was extinguished coordinately with reexpression of tumorigenicity by these cells, consistent with a tumor suppressor gene. Subsequent characterization of this EST indicates that it is a novel transcript with expression in a broad range of tissue types. Further characterization of the genes identified in this study will provide a greater understanding of their role in the molecular pathogenesis of neoplastic liver disease.

High-density marker loss of heterozygosity analysis of rat chromosome 10 in endometrial adenocarcinoma

Endometrial cancer is a disease with serious impact on the human population, but not much is known about genetic factors involved in this complex disease. Female BDII rats are genetically predisposed to spontaneous endometrial carcinoma, and the BDII inbred strain provides an experimental animal model for endometrial carcinoma development. In the present study, BDII females were crossed with males from two nonsusceptible inbred rat strains. Endometrial adenocarcinomas (EACs) developed in a proportion of the F1 and F2 progeny. We screened 18 EAC solid tumors and 9 EAC cell cultures for loss of heterozygosity (LOH) using fluorescent-PCR-based marker allelotyping methodology with 47 microsatellite markers covering the proximal part of rat chromosome 10 (RNO10). Conclusive evidence was obtained for LOH/deletion involving about 56 cM in the proximal part of RNO10 in DNA from six out of seven informative tumor cell cultures. Analysis of the solid tumors confirmed the presence of LOH in this part of RNO10 in 14 of 17 informative tumors. However, from the studies in the solid tumors it appeared that in fact three separate segments in the proximal part of RNO10 were affected. These three LOH/deletion regions were located approximately in cytogenetic bands 10q11-12, 10q22, and 10q24.

Automated construction of high-density comparative maps between rat, human, and mouse

Animal models have been used primarily as surrogates for humans, having similar disease-based phenotypes. Genomic organization also tends to be conserved between species, leading to the generation of comparative genome maps. The emergence of radiation hybrid (RH) maps, coupled with the large numbers of available Expressed Sequence Tags (ESTs), has revolutionized the way comparative maps can be built. We used publicly available rat, mouse, and human data to identify genes and ESTs with interspecies sequence identity (homology), identified their UniGene relationships, and incorporated their RH map positions to build integrated comparative maps with >2100 homologous UniGenes mapped in more than one species (approximately 6% of all mammalian genes). The generation of these maps is iterative and labor intensive; therefore, we developed a series of computer tools (not described here) based on our algorithm that identifies anchors between species and produces printable and on-line clickable comparative maps that link to a wide variety of useful tools and databases. The maps were constructed using sequence-based comparisons, thus creating "hooks" for further sequence-based annotation of human, mouse, and rat sequences. Currently, this map enables investigators to link the physiology of the rat with the genetics of the mouse and the clinical significance of the human.

Mouse chromosome 19 and distal rat chromosome 1: a chromosome segment conserved in evolution

Through a combination of radiation hybrid mapping and studies by FISH and zoo-FISH we have made a comparative investigation of the distal portion of rat chromosome 1 (RNO1) and the entire mouse chromosome 19 (MMU19). It was found that homologous segments of RNO1 and MMU19 are similar in banding morphology and in length as determined by several different methods, and that the gene order of the 46 genes studied appears to be conserved across the homologous segments in the two species. High-resolution zoo-FISH techniques showed that MMU19 probes highlight only a continuous segment on RNO1 (1q43-qter), with no detectable signals on other rat chromosomes. We conclude that these data suggest the evolutionary conservation of a chromosomal segment from a common rodent ancestor. This segment now constitutes the entire MMU19 and a large segment distally on RNO1q in the mouse and rat, respectively.

A high-resolution consensus linkage map of the rat, integrating radiation hybrid and genetic maps

We have constructed a high-resolution consensus genetic map of the rat in a single large intercross, which integrates 747 framework markers and 687 positions of our whole-genome radiation hybrid (RH) map of the rat. We selected 136 new gene markers from the GenBank database and assigned them either genetically or physically to rat chromosomes to evaluate the accuracy of the integrated linkage-RH maps in the localization of new markers and to enrich existing comparative mapping data. These markers and 631 D-Got- markers, which are physically mapped but still uncharacterized for evidence of polymorphism, were tested for allele variations in a panel of 16 rat strains commonly used in genetic studies. The consensus linkage map constructed in the GK x BN cross now comprises 1620 markers of various origins, defining 840 resolved genetic positions with an average spacing of 2.2 cM between adjacent loci, and includes 407 gene markers. This whole-genome genetic map will contribute to the advancement of genetic studies in the rat by incorporating gene/EST maps, physical mapping information, and sequence data generated in rat and other mammalian species into genetic intervals harboring disease susceptibility loci identified in rat models of human genetic disorders.

Distant enhancers stimulate the albumin promoter through complex proximal binding sites

The albumin-alpha-fetoprotein locus epitomizes the main features of transcriptional regulation of fetal and adult hepatocyte-specific genes: developmentally regulated promoters and strong distant enhancers. Full enhancer activity required only a proximal albumin-promoter region containing the TATA box, hepatic nuclear factor 1 (HNF1), and nuclear factor Y (NF-Y) sites. Deletion of the HNF1 site abrogated enhancer and promoter activity, whereas methylation of the site reduced all activity by about 3-fold. Deletion of the NF-Y site attenuated activity by about half, but much of the activity could be replaced by juxtaposition of an upstream region (designated distal element IV). Gel shift and competition analysis demonstrated that binding of architectural factors overlapped NF-Y binding. Moreover, a mutation that eliminated NF-Y binding but only minimally perturbed the surrounding region did not affect enhancer function. In plasmids with a second promoter, the enhancers simultaneously stimulated both albumin and alpha-fetoprotein promoters with minimal competition, but surprisingly some mutations in the albumin promoter attenuated expression from both promoters, whereas another uncoupled their expression. With single promoters, the function of the proximal promoter region was controlled by three parameters in the following hierarchy: HNF1 binding > local architecture > NF-Y binding, but integrated two-promoter function had a much greater dependence on NF-Y.

Inheritance of ventilatory behavior in rodent models

Studies in mice and rats support the hypothesis that ventilation and its components (frequency and tidal volume) are determined to a significant extent by genetic mechanisms. The question can no longer be 'is there a genetic effect?' but rather 'how strong is the genetic component?' and 'what genes are involved?' The computational analyses of selectively bred animals now offer powerful tools to begin to dissect the genetic factors that track with ventilatory traits. Control of the conditions in the colony and in the laboratory are keys to reducing the environmental 'noise' and increasing the likelihood of detecting gene loci that correlate quantitatively with phenotype values before and during the response to chemosensory challenges. Knowing the chromosomal location of genes for ventilation will then permit the identification of proteins systems responsible for the structural and functional components for respiration.

Genomewide assessment of genetic alterations in DMBA-induced rat sarcomas: cytogenetic, CGH, and allelotype analyses reveal recurrent DNA copy number changes in rat chromosomes 1, 2, 4, and 7

Rat sarcomas, induced by subcutaneous injections of 7,12-dimethylbenz[a]anthracene (DMBA), were studied with the objective of identifying critical chromosome regions associated with tumorigenesis. We employed three genomewide screening techniques-cytogenetics, CGH, and allelotyping-in 19 DMBA-induced sarcomas in F1 (BN/Han x LE/Mol) rats. The most conspicuous finding in the cytogenetic analysis was a high incidence of trisomy for rat chromosome 2 (RNO2). Signs of gene amplification (hsr) were also seen in several tumors. The CGH analysis revealed that gains in copy number were much more common than losses. The gains mostly affected RNO2 (10/19), RNO12q (7/19), and RNO19q (5/19), as well as the proximal part of RNO4 (8/19) and the distal part of RNO7 (7/19). Reduction in copy number was seen in RNO17 (2/19). For the allelotyping, we used 318 polymorphic microsatellite marker loci covering the entire genome. We identified regions of allelic imbalance affecting most of the rat chromosomes. The highest incidences of recurrent allelic imbalance were observed at loci in certain regions in RNO1, 2, 4, and 7 and at lower incidences in parts of RNO12, 16, 18, and 19. The combined results suggested that genetic alterations detected in RNO2 and RNO12 usually corresponded to complete or partial trisomy, whereas those in RNO1 and RNO7 seemed to involve regional deletions and/or gains. Furthermore, we could confirm that copy number gains occur proximally in RNO4, where a previous study showed amplification of the Met oncogene in a subset of these tumors.

An integrated rat genome map based on genetic and cytogenetic data

In this study we combined three major rat genome maps, by adding 66 markers to the Kyoto Laboratory Animal Science map (KLAS map), and constructed an integrated map. The resultant integrated map consists of 5,682 redundant markers, spanning a genetic length of 2,028 cM. Eighty genetic markers were anchored to the cytogenetic map, fixing all the genetic maps in the physically correct orientation. This map encapsulates the progress in rat mapping studies in past years and offers useful information for QTL analysis. The map figures are available at http:/(/)www.anim.med.kyoto-u.ac.jp/.

Detailed comparative gene map of rat chromosome 1 with mouse and human genomes and physical mapping of an evolutionary chromosomal breakpoint

We report the localization of 92 new gene-based markers assigned to rat chromosome 1 by linkage or radiation hybrid mapping. The markers were chosen to enrich gene mapping data in a region of the rat chromosome known to contain several of the principal quantitative trait loci in rodent models of human multifactorial disease. The composite map reported here provides map information on a total of 139 known genes, including 80 that have been localized in mouse and 109 that have been localized in human, and integrates the gene-based markers with anonymous microsatellites. The evolutionary breakpoints identifying 16 segments that are homologous regions in the human genome are defined. These data will facilitate genetic and comparative mapping studies and identification of novel candidate genes for the quantitative trait loci that have been localized to the region.

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.

Allele-specific losses of heterozygosity on chromosomes 1 and 17 revealed by whole genome scan of ethylnitrosourea-induced BDIX x BDIV hybrid rat gliomas

The induction of neural tumors by N-ethyl-N-nitrosourea (EtNU) in inbred strains of rats has evolved as a valuable model system of developmental stage- and cell type-dependent oncogenesis. Tumor yield and latency times are strongly influenced by genetic background. Compared with BDIX rats, BDIV rats are relatively resistant to the induction of brain tumors by EtNU, with a lower tumor incidence and latency periods prolonged by a factor of 3. To characterize genetic abnormalities associated with impaired tumor suppressor gene function in neuro-oncogenesis, losses of heterozygosity (LOHs) and microsatellite instability (MI) were investigated in brain tumors induced by EtNU in (BDIV x BDIX) F(1) and F(2) rats. The polymerase chain reaction was used to amplify 55 polymorphic microsatellite markers spanning the entire rat genome. The tumors displayed different histologies and grades of malignancy, corresponding to part of the spectrum of human gliomas. MI was not observed in any of the tumors. LOH of rat chromosome 1q was predominantly detected in oligodendrogliomas and mixed gliomas, with a 30% incidence in informative cases. 11p15.5, the human genome region syntenic to the consensus region of LOHs observed on rat chromosome 1, has been shown to be involved in the formation of gliomas in humans. Furthermore, rat brain tumors of different histologies often showed allelic imbalances on chromosome 17p. In both cases of LOH, there was a clear bias in favor of the parental BDIV allele, suggesting the involvement of tumor suppressor genes functionally polymorphic between the two rat strains.

Recurrent alterations of the short arm of chromosome 3 define a tumor suppressor region in rat mammary tumor cells

Cytogenetic alterations associated with different stages in carcinogenesis can be distinguished in cultured human or rodent cells transformed by carcinogenic agents. Three tumorigenic rat mammary epithelial cell lines transformed in vitro with 7,12, -dimethylbenz[a]anthracene alone or in combination with 12-O-tetradecanoylphorbol-13-acetate were examined cytogenetically. Non-random alterations consisting of translocations involving the short arm of chromosome 3 and trisomy of chromosomes 14 and X were identified in all three lines. Deletion and inversion of chromosome 1 with the breakpoint at band 1q22 and a duplication 1q 32-43 and trisomy of chromosome 2 were observed in two cell lines. The accumulation of structural alterations and chromosome imbalances during the process of cell immortalization and acquisition of tumorigenicity are required for normal rat mammary cells to become malignant. Unbalanced translocations of chromosome 3 resulting in loss of the short arm had the breakpoint at 3p11. This site is a hotspot of breakage and recombination in various rat tumors and may represent a region of tumor suppressor gene critical to the development of rat mammary tumors, as well as other types of tumors.

Comparative karyotype of rat and mouse using bidirectional chromosome painting

A comparative karyotype of rat (Rattus norvegicus) and mouse (Mus musculus) based on chromosome G-banding morphology, heterologous chromosome painting results and available gene mapping data is proposed. Whole chromosome painting probes from both species were generated by PARM-PCR amplification of flow sorted chromosomes. Bidirectional chromosome painting identifies 36 segments of syntenic homology and allows us to propose a nearly complete comparative karyotype of mouse and rat (except for RNO 13 p and RNO 19 p12-13). Seven segments completely covered the RNO chromosomes 3, 5, 8, 11, 12, 15 and 18. Eight segments completely covered the MMU chromosomes 3, 4, 6, 7, 9, 12, 18 and 19. The RNO chromosomes 5, 8, 18 show complete homology with the MMU chromosomes 4, 9 and 18, respectively. Bidirectional hybridization results clearly assign 16 segments to subchromosomal regions in both species. Interpretation of the results allows subchromosomal assignment of all the remaining segments apart from seven distributed on chromosomes MMU 15, MMU 10 B2-D3 and MMU 17 E3-E5. The proposed comparative karyotype shows overall agreement with available comparative mapping data. The proposed repartition of syntenic homologous segments between the two species provides useful data for gene-mapping studies. In addition, these results will enable the reconstruction of the karyotype of the Cricetidae and Muridae common ancestor and the definition of the precise rearrangements which have occurred in both mouse and rat lineages during evolution.

A radiation hybrid map of the rat genome containing 5,255 markers

A whole-genome radiation hybrid (RH) panel was used to construct a high-resolution map of the rat genome based on microsatellite and gene markers. These include 3,019 new microsatellite markers described here for the first time and 1,714 microsatellite markers with known genetic locations, allowing comparison and integration of maps from different sources. A robust RH framework map containing 1,030 positions ordered with odds of at least 1,000:1 has been defined as a tool for mapping these markers, and for future RH mapping in the rat. More than 500 genes which have been mapped in mouse and/or human were localized with respect to the rat RH framework, allowing the construction of detailed rat-mouse and rat-human comparative maps and illustrating the power of the RH approach for comparative mapping.

A genetic linkage map of rat chromosome 9 with a new locus for variant activity of liver aldehyde oxidase

A genetic linkage map of rat chromosome 9 consisting of five loci including a new biochemical marker representing a genetic variation of the activity of the liver aldehyde oxidase, (Aox) was constructed. Linkage analysis of the five loci among 92 backcross progeny of (WKS/Iar x IS/Iar)F1 x WKS/Iar revealed significant linkages between these loci. Minimizing crossover frequency resulted in the best gene order: Aox-D9Mit4-Gls-Cryg-Tp53l1. The homologues of the Cryg, Gls, and Aox genes have been mapped on mouse chromosome 1 and human chromosome 2q. The present findings provide further evidence for the conservation of synteny among these regions of rat, mouse, and human chromosomes.

Identification of a new non-major histocompatibility complex genetic locus on chromosome 2 that controls disease severity in collagen-induced arthritis in rats

OBJECTIVE

To identify novel non-major histocompatibility complex (non-MHC) genetic loci controlling the severity of homologous rat type II collagen-induced arthritis (CIA).

METHODS

We conducted a genome-wide scan to identify CIA regulatory quantitative trait loci (QTL) in an F2 cross between DA (CIA highly susceptible) and ACI (CIA resistant) inbred rats immunized with homologous rat type II collagen (RII). These strains share the MHC/RT1av1 haplotype required for susceptibility to RII-induced CIA.

RESULTS

F2 females had higher median arthritis scores than did males. Relative resistance in the males was determined by inheriting either a DA or an ACI Y chromosome and was independent of the source of the X chromosome. In addition, a major QTL was localized on chromosome 2 (Cia7, logarithm of odds score 4.6). Cia7 is in a region that shows linkage conservation with chromosomal regions that regulate autoimmune diabetes and experimental autoimmune encephalomyelitis in mice and multiple sclerosis in humans.

CONCLUSION

Sex chromosomes and Cia7 play an important role in regulating CIA in response to RII. This rat model should facilitate positional cloning and functional characterization of regulatory genes that may play a role in several forms of autoimmune disease, including rheumatoid arthritis.

Hepatocyte nuclear factor 6: organization and chromosomal assignment of the rat gene and characterization of its promoter

Hepatocyte nuclear factor 6 (HNF-6) is the prototype of a family of tissue-specific transcription factors characterized by a bipartite DNA-binding domain consisting of a single cut domain and a novel type of homeodomain. We have previously cloned rat cDNA species coding for two isoforms, HNF-6alpha (465 residues) and beta (491 residues), which differ only by the length of the spacer between the two DNA-binding domains. We have now localized the rat Hnf6 gene to chromosome 8q24-q31 by Southern blotting of DNA from somatic cell hybrids and by fluorescence in situ hybridization. Cloning and sequencing of the rat gene showed that the two HNF-6 isoforms are generated by alternative splicing of three exons that are more than 10 kb apart from each other. Exon 1 codes for the N-terminal part and the cut domain, exon 2 codes for the 26 HNF-6beta-specific amino acids, and exon 3 codes for the homeodomain and the C-terminal amino acids. The transcription initiation site was mapped by ribonuclease protection and 5' rapid amplification of cDNA ends. Transfection experiments showed that promoter activity was contained within 0.75 kb upstream of the transcription initiation site. This activity was detected by the transfection of liver-derived HepG2 cells, but not of Rat-1 fibroblasts, suggesting that the promoter is sufficient to confer liver-specific expression.

Correlation between genetic and cytogenetic maps of the rat

To correlate rat genetic linkage maps with cytogenetic maps, we localized 25 new cosmid-derived simple sequence length polymorphism (SSLP) markers and 14 existing genetic markers on cytogenetic bands of chromosomes, using fluorescence in situ hybridization (FISH). Next, a total of 58 anchor loci, consisting of the 39 new and 19 previously reported ones, were integrated into the genetic linkage maps. Since most of the new anchor loci were developed to be localized near the terminals of the genetic or cytogenetic maps for each chromosome, the orientation and coverage of the whole genetic linkage maps were determined or confirmed with respect to the cytogenetic maps. Thus, we provide here a new base for rat genetic maps.

Genomic DNA sequence, promoter expression, and chromosomal mapping of rat muscle carnitine palmitoyltransferase I

Carnitine palmitoyltransferase I (CPT-I) is a key enzyme involved in the regulation of fatty acid oxidation. CPT-IA and CPT-IB are isoforms of carnitine palmitoyltransferase I, of which CPT-IA is expressed in liver, kidney, fibroblasts, and heart and CPT-IB is expressed in skeletal muscle, heart, brown and white adipocytes, and testes. Although the genomic DNA sequence of human CPT-IB is available, the transcription start site and upstream regulatory sequences are not known. For rat CPT-IB, only the cDNA sequence has been published. We have cloned the entire rat CPT-IB gene from a Lambda fix II rat kidney genomic library. The genomic structure contains 19 exons, with the transcription start site for CPT-IB located in a short first exon, which is a 13-bp extension to the previously published cDNA 5' sequence. The coding sequence is identical with the rat muscle cDNA. The rat CPT-IB gene contains 18 introns and 19 exons, the latter 18 exons showing 85% homology to the human CPT-IB cDNA. CPT-IB maps to rat chromosome 7 at band q34. A putative promoter region was identified to within 391 bp of the transcription start site. The muscle specificity of the 5' flanking region was verified by comparison of luciferase expression to that of beta-galactosidase in cardiac myocytes and in HepG2 cells.

Comparative genomic in situ hybridization discloses chromosomal copy number changes in a transplanted brain tumor line of the rat (Rattus norvegicus)

We investigated chromosomal copy number changes in ethylnitrosourea-induced and serially transplanted gliomas of the rat by flow cytometry and Comparative Genomic in situ Hybridization (CGH). CGH analysis of a primary and four transplanted tumors revealed several genomic aberrations, including whole chromosome and subchromosomal gains and losses. Gains involved rat Chromosomes (RNO) 2, 3, 4, 5, 7, 9, 11, 12, 13, and Y, whereas losses affected RNO5, 13, 20, and Y. The primary tumor exhibited gain of RNO2q31qter and gain of RNO4. While gain of RNO2 was seen in nearly all investigated passages, gain of RNO4 was apparent in the primary tumor and in passage 2 and 5 tumors. Chromosomal alterations detected as single events were restricted to the transplanted tumors and included gain of RNO3q11, 3q41qter, 5q36, 7q34qter, 9q37, 11q, and Y, and loss of RNO5, 13, and 20q. Flow cytometry disclosed different aneuploid cell clones in the tumors investigated. The results are discussed in analogy to findings in human glial tumors.

A comparative genetic map of rat, mouse and human genomes

The increasing availability of molecular markers and the development of highly efficient gene mapping strategies for the mouse, rat and human genomes have generated vast quantities of information allowing for the progressive refinement of comparative maps. In this publication we report on an updated version of our rat/mouse/human comparative genetic map, based on the mouse map. Databases for mouse, rat and human gene mapping were used for the collection of homologs mapped in the species. The comparative map was constructed with a total of 1,235 mouse loci having known homologs in the rat and/or human: 16 having homologs only in the rat, 884 having only in the human and 335 both in the rat and human. The combined length of the segments conserved between the rat and mouse spans 758 cM on the mouse map. This indicates that about 47% of the mouse genome is now covered by known rat homologous regions. Five novel regions homologous for the rat and mouse were identified. This comparative genetic map should be useful for researchers working on genetic studies in the rat, mouse and human.

Comparative genome mapping: mouse and rat homologies revealed by fluorescence in situ hybridization

Mouse and rat genome studies are vital to the use of rodents as models of biology and human genetic disease. In this study, comparative cytogenetic maps of individual homologous mouse (Mus musculus) and rat (Rattus norvegicus) chromosomal regions are presented as defined by cross-species fluorescence in situ hybridization. Such "Zoo-FISH" methods permit direct visual observation of the location of DNA segments from one species on mitotic chromosomes of evolutionarily diverged species. Mouse whole chromosome paint (WCP) probes generated from microdissection and degenerate oliogonucleotide primed (DOP) PCR were hybridized on slides containing a mixture of both mouse (the reference species) and rat (the diverged/ comparative species) metaphase chromosomes. Using six different mouse WCPs, eight regions on seven rat chromosomes were shown to be evolutionarily conserved between these species. The specific chromosomal sites of homology delineated in this study between mouse (MMU) and rat (RNO) genomes include the following: MMU 1 to RNO 9q21-q36 and to RNO 13 from bands q11 to the telomere, MMU 4 to all of RNO 5, MMU 11 to all of RNO 10 and the distal region of RNO 14 (14q21-q22), MMU 7 and MMU 19 both to RNO 1, from bands 1q21 to 41 (MMU 7) and 1q42 to the telomere (MMU 19), and MMU X to all of RNO X. Additionally, several new mouse and rat map assignments have been predicted based on the observed cross-species hybridization patterns in conjunction with known mapping data for mouse or rat genes.

A non-MHC locus essential for autoimmune type I diabetes in the Komeda Diabetes-Prone rat

The Long-Evans Tokushima Lean (LETL) rat, characterized by rapid onset of insulin-dependent (type I) diabetes mellitus (IDDM), no sex difference in the incidence of IDDM, autoimmune destruction of pancreatic beta cells, and no significant T cell lymphopenia, is a desirable animal model for human IDDM. We have established a diabetes-prone substrain of the LETL rat, named Komeda Diabetes-Prone (KDP) rat, showing a 100% development of moderate to severe insulitis within 220 d of age. The cumulative frequency of IDDM was 70% at 120 d of age, and reached 82% within 220 d of age. Here, we performed the first genome-wide scan for non-MHC IDDM susceptibility genes in this strain. The analysis of three crosses has led to the revelation of a major IDDM susceptibility gene, termed Iddm/kdp1, on rat chromosome (Chr) 11. Homozygosity for the KDP allele at this locus is shown to be essential for the development of moderate to severe insulitis and the onset of IDDM. Comparative mapping suggests that the homologues of Iddm/ kdp1 are located on human Chr 3 and mouse Chr 16 and would therefore be different from previously reported IDDM susceptibility genes.

Chromosomal localization of rat hepatocyte growth factor (Hgf) and HGF receptor (Met) and characterization of HGF receptor cDNA

The Met protooncogene encodes the tyrosine kinase receptor for the hepatocyte growth factor (HGF), a potent mitogen for hepatocytes and other epithelial cells produced by mesenchymal cells. Many of the studies on the physiologic and neoplastic growth of the liver, as well as other organs, have been performed in the rat. Therefore, chromosomal mapping of the rat Hgf gene and the gene of its receptor is of particular value. To achieve this, a probe of the coding part of rat HGF cDNA was used to isolate four genomic probes from a lambda phage rat genomic library. These probes were used to map the Hgf gene to Chromosome (Chr) 4q12 by the FISH technique. To obtain a probe for the mapping of the HGF receptor/Met gene, we cloned the complete coding region of the rat HGF receptor mRNA. Complementary DNA (cDNA) was synthesized with reverse transcriptase from total RNA for use as a template for the PCR. The two PCR primers were designed based on human and mouse sequences and were located in the flanking regions of the open reading frame of the HGF receptor mRNA. Amplification resulted in a band of an estimated size of 4.1 kb, which was cloned and sequenced. The nucleotide sequence showed about 93% and 85% homology compared with mouse and human HGF receptor sequences, respectively. A full-length probe of the coding part of the cDNA was used to map the rat HGF receptor/Met gene to Chr 4q21 by the FISH technique. Therefore, the rat Hgf and HGF receptor/Met genes are located relatively close to each other, in a way similar to humans but not mice.

Analysis of DES-induced micronuclei in binucleated rat fibroblasts: comparison between FISH with a rat satellite I probe and immunocytochemical staining with CREST serum

The usefulness of fluorescence in situ hybridization (FISH) with rat satellite I DNA was compared with immunocytochemical staining with CREST serum for the analysis of the content of micronuclei from primary rat fibroblasts. We analyzed micronuclei induced in vitro by the aneugenic compound diethylstilbestrol (DES) or the clastogenic compound mitomycin C (MMC). Since a centromeric probe was not available for the rat, we isolated rat satellite I DNA by PCR with primers designed on the basis of the known rat satellite I DNA sequence. The PCR products obtained as well as the cloned PCR products showed hybridization to the centromeric regions of a large number of chromosomes, but not of chromosome 1, 19, 20, X and Y. Clone 18-5 was further analyzed and was shown to contain at least 4 repeats of the rat satellite I family. This probe, which hybridizes in the centromeric region of 34 of the 42 chromosomes, was used throughout the study as a probe for the FISH analysis of the micronuclei. For the immunocytochemical staining, the commonly used commercial anti-centromeric antibodies could not be used because of the weakness of the fluorescent signals given. Consequently, CREST serum of a single patient was used, which showed bright and distinct signals on the kinetochores of each chromosome. After treatment of the cells with the aneugen DES an increase in centromere (FISH) and kinetochore (CREST) positive micronuclei was found, whereas after treatment with the clastogen MMC, the percentage of centromere-positive micronuclei was similar to that observed in controls. Analysis of a large number of DES-induced micronuclei showed that the immunocytochemical method is equally as or slightly less sensitive for the detection of chromosomes in micronuclei and we therefore recommend FISH with probe 18-5 for the detection of chromosome loss in rat cells.

Localization of a putative liver tumor suppressor locus to a 950-kb region of human 11p11.2-p12 using rat liver tumor microcell hybrid cell lines

We previously demonstrated that a locus (or loci) linked to the D11S436 marker, which is within the approximately 6-Mb cen-p12 region of human chromosome 11, suppresses the tumorigenic potential of some rat liver epithelial tumor microcell hybrid (MCH) cell lines. To more precisely map this putative liver tumor suppressor locus, we examined 25 loci from human chromosome 11 in suppressed MCH cell lines. Detailed analysis of these markers revealed a minimal area of overlap among the suppressed MCH cell lines corresponding to the chromosomal region bounded by (but not including) microsatellite markers D11S1319 and D11S1958E and containing microsatellite markers D11S436, D11S554, and D11S1344. Direct examination of the kang ai 1 (KA/1) prostatic adenocarcinoma metastasis suppressor gene (which is closely linked to D11S1344) produced evidence suggesting that this locus was not responsible for tumor suppression in this model system. In addition, our data strongly suggested that the putative liver tumor suppressor locus was distinct from other known 11p tumor suppressor loci, including the multiple exotoses 2 locus (at 11p11.2-p12), Wilms' tumor 1 locus (at 11p13), and Wilms' tumor 2 locus (at 11p15.5). The results of this study significantly narrowed the chromosomal location of the putative liver tumor suppressor locus to a region of human 11p11.2-p12 that is approximately 950 kb. This advance forms the basis for positional cloning of candidate genes from this region and, in addition, identified a number of chromosomal markers that will be useful for determining the involvement of this locus in the pathogenesis of human liver cancer.

Mapping genes controlling hematocrit in the spontaneously hypertensive rat

The genes that determine the baseline hematocrit level in humans and experimental animals are unknown. The spontaneously hypertensive rat (SHR), the most widely used animal model of human essential hypertension, exhibits an increased hematocrit when compared with the normotensive Brown Norway (BN-Lx) strain (0.54 +/- 0.02 vs. 0.44 +/- 0.02, p < 0.01). Distribution of hematocrit values among recombinant inbred (RI) strains derived from SHR and BN-Lx progenitors was continuous, which suggests a polygenic mode of inheritance. The narrow heritability of the hematocrit was estimated to be 0.32. The Eno2 marker on Chromosome (Chr) 4 showed the strongest association (p < 0.0001) with the observed variability of hematocrit among RI strains. The erythropoietin (Epo) gene, originally reported to be syntenic with Eno2, has been mapped to Chr 12, thus excluding it as a potential candidate gene for the increased hematocrit in the SHR. The current linkage data extend homologies between rat, mouse, and human chromosomes.

A linkage map of the rat genome derived from three F2 crosses

We report the construction of a dense linkage map of the rat genome integrating 767 simple sequence length polymorphism markers, combined over three crosses with high rates of polymorphism. F2 populations from WKY x S (n = 159), BN x S (n = 91), and BN x GK (n = 139) were selected and genotyped for combinations of microsatellite markers. The loci define 21 linkage groups corresponding to the 20 rat autosomal chromosomes and the X chromosome. The map spans a genetic length of 1998 cM. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of rat models characterized for complex phenotypes.