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Rat strains differ strikingly in susceptibility to cancer. The rat strain WKY is highly resistant, while the SPRD- Cu3 strain is susceptible to chemically-induced mammary cancer. We previously showed that two chromosome regions (from chromosomes 5 and 18) contain quantitative trait loci (QTLs) controlling mammary cancer susceptibility. Here we tested the hypothesis that mammary cancer resistance is associated with a prompt and efficient DNA damage response (DDR) leading to a robust anti-cancer barrier. We also hypothesized that an efficient response to carcinogenic ((7,12- dimethyl benz(a)anthracene (DMBA)) treatment could be accompanied by gene activation and changes in mRNA levels. We thus compared the mRNA levels of several genes involved in the DDR in the mammary tissue of DMBA-treated and control WKY, SPRD-CU3 and congenic female rats. Our observations show that DMBA-treatment induces a dramatic increase in the level of several DDR mammary tissue mRNAs in rat strains that are resistant to mammary cancer, but not in the susceptible SPRD-Cu3 strain. Some of the upregulated genes are tumour supressor genes, such as Tp53 and Brca1. Several genes involved in the DDR are thus subject to regulations impacting their mRNA level and our results strongly support the hypothesis that the DDR is a barrier in early tumorigenesis.

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.

The rat Chromosome (Chr) 2 harbors several genes controlling tumor growth or development, blood pressure, and non-insulin-dependent diabetes mellitus. We report that the region (2q1) containing the mammary susceptibility cancer gene Mcs1 also harbors the genes encoding cyclin B1, interleukin 6 signal transducer (gp130), and proprotein convertase 1. We also generated 13 new anonymous microsatellite markers from Chr 2-sorted DNA. These markers, as well as a microsatellite marker in the cyclin B1 gene, were genetically mapped in combination with known markers. A cyclin B1-related gene was also cytogenetically assigned to rat Chr 11q22-q23.

The calcium-sensing receptor (CASR), a member of the G-protein coupled receptor family, is expressed in both parathyroid and kidney, and aids these organs in sensing extracellular calcium levels. Inactivating mutations in the CASR gene have been described in familial hypocalciuric hypercalcemia (FHH) and neonatal severe hyperparathyroidism (NSHPT). Activating mutations in the CASR gene have been described in autosomal dominant hypoparathyroidism and familial hypocalcemia. The human CASR gene was mapped to Chromosome (Chr) 3q13.3-21 by fluorescence in situ hybridization (FISH). By somatic cell hybrid analysis, the gene was localized to human Chr 3 (hybridization to other chromosomes was not observed) and rat Chr 11. By interspecific backcross analysis, the Casr gene segregated with D16Mit4 on mouse Chr 16. These findings extend our knowledge of the synteny conservation of human Chr 3, rat Chr 11, and mouse Chr 16.

Identification and localization of genes that encode regulators of transcription could provide landmarks for functional analysis of the human genome. Toward this goal, we examined a panel of somatic cell hybrids and assigned the gene (TCF12) encoding the helix-loop-helix transcription factors 4 (HTF4) to chromosome 15. Fluorescence in situ hybridization further localized TCF12 to chromosome 15q21. Northern analysis revealed that the relative abundance of HTF4 gene transcripts is not constant but varies depending on the human cell-line or tissue examined.

Using fluorescence in situ hybridization, we determined the regional localization of the 3 rat genes encoding angiotensin II receptors at 17q12 (Agtr1a), 2q24 (Agtr1b) and Xq34 (Agtr2). In parallel, we showed that the type 2 human gene, AGTR2, also maps on the X chromosome, at band Xq22.

Through the use of somatic cell hybrids segregating either human or rat chromosomes, we determined the chromosome localizations of two genes encoding cAMP-specific phosphodiesterases (cAMP-PDEs). PDE4D, the gene encoding the cAMP-PDE isoform 3 (IVd), was assigned to human chromosome 5 and rat chromosome 2, and PDE4B, the gene encoding the cAMP-PDE isoform 4 (IVb), was assigned to human chromosome 1 and rat chromosome 5. These localizations extend the homology between rat chromosome 2 and human chromosome 5, on the one hand, and between rat chromosome 5 and human chromosome 1 on the other hand.

The chromosomal localization of the human and rat genes encoding the kainate-preferring glutamate receptor subunits KA1 and KA2 (GRIK4 and GRIK5, respectively) was determined by Southern analysis of rat x mouse and human x mouse somatic cell hybrid panels and by fluorescence in situ hybridization. The localization of the mouse genes (Grik4 and Grik5) was established by interspecific backcross mapping. GRIK4 and GRIK5 are located on separate chromosomes (Chrs) in all species. GRIK4 mapped to human Chr 11q22.3, mouse Chr 9, and rat Chr 8. GRIK5 mapped to human Chr 19q13.2, mouse Chr 7, and rat Chr 1. The genes encoding the (R,S)-alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)-preferring subunit GluR4, or GluRD (GRIA4), the neural cell adhesion molecule (NCAM), the D2 dopamine receptor (DRD2), and the Thy-1 cell surface antigen (THY1) have all been previously mapped to the human Chr 11q22 region. The mapping of the human GRIK4 and GRIK5 genes confirms and extends the relationship between human Chr 11 and mouse Chr 9 and also human Chr 19 and mouse Chr 7. GRIK4 is the fifth gene shared by human Chr 11 and rat Chr 8, whereas GRIK5 is 1 out of the 12 genes that are located on both human Chr 19 and rat Chr 1. Our data extend the conserved synteny established between certain human, mouse, and rat Chrs.

Objective The chromosomal location of candidate genes for a disease, especially if the disease is multifactorial, is an important datum. The objective of the present study was to determine the chromosomal location of candidate hypertensinogenic genes, both in humans and in the rat, a species widely used for animal models of human hypertension. The type 1 angiotensin II receptor (AT1) genes are obvious hypertension candidate genes, whereas the SA gene has recently been shown to cosegregate with hypertension in the rat. Design The chromosomal location of the relevant genes was determined using somatic cell hybrids segregating either human chromosomes or rat chromosomes. The presence of the human or rat genes was determined by the Southern blot method, using rat probes. Results A single AT1 gene (AT1) was detected in the human genome, and was assigned to chromosome 3, whereas two non-syntenic genes were detected in the rat genome, corresponding to the previously identified A and B subtypes. They were assigned to the rat chromosome 17 (At1a) and 2 (AT1b). The Sa gene was assigned to human chromosome 16 and rat chromosome 1, disclosing a new synteny group retained on rat chromosome 1 and human chromosome 16. Conclusions These chromosomal assignments should be useful for linkage analyses of genes controlling blood pressure. The genes that we studied, and the chromosomes that we identified, deserve special attention in such linkage analyses.

KRAB zinc-finger proteins (KRAB-ZFPs) constitute a large subfamily of ZFPs of the Krüppel C2H2 type. KRAB (Krüppel-associated box) is an evolutionarily conserved protein domain found N-terminally with respect to the finger repeats. We report here the characterization of a particular subgroup of highly related human KRAB-ZFPs. ZNF91 is one representative of this subgroup and contains 35 contiguous finger repeats at its C-terminus. Three mRNA isoforms with sequence identity to ZNF91 were isolated by the polymerase chain reaction. These encode proteins with a KRAB domain present, partially deleted or absent. Five genomic fragments were characterized, each encoding part of a gene: the ZNF91 gene or one of four distinct, related KRAB-ZFP genes. All exhibit a common exon/intron organization with the variant zinc finger repeats organized in a single exon and the KRAB domain encoded by two separate exons. This positioning of introns supports the hypothesis that the mRNA isoforms encoding polypeptides with variability in the KRAB domain could arise by alternative splicing. By in situ chromosomal mapping studies and by analysis of fragments from a human genomic yeast artificial chromosome library containing KRAB-ZFP genes, we show that these genes occur in clusters; in particular, a gene complex containing over 40 genes has been identified in chromosomal region 19p12-p13.1. These ZNF91-related genes probably arose late during evolution since no homologous genes are detected in the mouse and rat genomes. Although the transcription of members of this KRAB-ZFP gene subgroup is detectable in all human tissues, their expression is significantly higher in human T lymphoid cells., Comparative Study, Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., Research Support, U.S. Gov't, P.H.S., SCOPUS: ar.j, FLWIN, info:eu-repo/semantics/published

International audience; By use of rat cDNA probes and a panel of cell hybrids segregating rat chromosomes, the genes encoding three pyridoxal 5'-phosphate (PLP)-dependent decarboxylases-namely, DOPA-decarboxylase (Ddc), glutamic acid decarboxylase 1 and 2 (Gad1 and Gad2)-were assigned to rat Chromosomes (Chrs) 14, 3, and 17, respectively. If one takes into account chromosome localizations in the human and the mouse, the present results (i) show that a synteny group is retained on rat Chr 14, human Chr 7, and mouse Chr 11 (Ddc); (ii) strengthen the homology relation known between rat Chr 3 and human and mouse Chrs 2 (Gad1); (iii) suggest that rat Chr 17 has no extensive homology to any human chromosome; and (iv) suggest the order (Prl, Fdp)-Tpl2-Gad2 on the rat Chr 17.

By means of somatic cell hybrids segregating either human or rat chromosomes, we determined the chromosome localization of three genes encoding transcription factors expressed in hepatocytes, namely, C/EBP (CCAAT/enhancer binding protein), DBP (D site of albumin promoter binding protein), and HNF1/LFB-1 (designated transcription factor 1, gene symbol: TCF1), and of the hepatocyte growth factor gene, which is identical to the mitogenic and chemotactic factor designated scatter factor (gene symbol:HGF). The CEBP and DBP genes, encoding two related transcription factors, were found to be syntenic both on human chromosome 19 and on rat chromosome 1. These results provide further evidence for conservation of synteny on these two chromosomes (and on mouse chromosome 7). The TCF1 gene was found to be located on chromosome 12 in both man and rat, thereby defining a new segment of homology between these two species (and a segment of mouse chromosome 5). The HGF gene was mapped to rat chromosome 4, confirming homology between this chromosome and human chromosome 7, which carries the human HGF gene.

By comparing the methylation pattern of Mspl/Hpall sites in the 5' region of the mouse alpha-foetoprotein (AFP) gene of different cells (hepatoma cells, foetal and adult liver, fibroblasts), we found a correlation between gene expression and unmethylation of a site located in the first intron of the gene. Other sites did not show this correlation. In transfection experiments of unmethylated and methylated AFP-CAT chimeric constructions, we then showed that methylation of the intronic site negatively modulates expression of CAT activity. We also found that a DNA segment centered on this site binds nuclear proteins; however methylation did not affect protein binding.

The human genes encoding the α and β forms of the retinoic acid receptor are known to be located on chromosomes 17 (band q21.1: RARA ) and 3 (band p24: RARB ). By in situ hybridization, we have now localized the gene for retinoic acid receptor γ, RARG , on chromosome 12, band q13. We also mapped the three retinoic acid receptor genes in the mouse, by in situ hybridization, on chromosomes 11, band D ( Rar - a ); 14, band A ( Rar - b ); and 15, band F ( Rar - g ), respectively, and in the rat, using a panel of somatic cell hybrids that segregate rat chromosomes, on chromosomes 10 ( RARA ), 15 ( RARB ), and 7 ( RARG ), respectively. These assignments reveal a retention of tight linkage between RAR and HOX gene clusters. They also establish or confirm and extend the following homologies: (i) between human chromosome 17, mouse chromosome 11, and rat chromosome 10 ( RARA ); (ii) between human chromosome 3, mouse chromosome 14, and rat chromosome 15 ( RARB ); and (iii) between human chromosome 12, mouse chromosome 15, and rat chromosome 7 ( RARG ).

We previously defined quantitative trait loci (QTLs) that control susceptibility to 7,12-dimethylbenz(alpha)anthracene-induced mammary carcinoma in SPRD-Cu3 (susceptible) and WKY (resistant) rats. Two of these QTLs, assigned to chromosomes (Chr) 10 and 18, control tumor growth rate and invasiveness. In this study we characterized a congenic strain in which a large segment of WKY Chr 10 was introduced in the SPRD-Cu3 genetic background and demonstrated that this chromosome segment controls this tumor trait. The WKY allele at this QTL (Mcsta1) reduces the growth rate of the fastest growing tumors by 26%. We also previously showed that two SPRD-Cu3-WKY congenic strains containing a WKY chromosome segment derived either from Chr 5 or from Chr 18 exhibit a reduction in tumor multiplicity (QTLs Msctm1 and Mcstm2, respectively) (with no reduction in tumor growth rate in the Chr 18 congenic). In this study we generated a double congenic strain, which contains the two WKY differential segments from Chr 5 and 18, to determine how these two segments interact with one another. Interestingly, two types of epistatic interactions were found: no additive effect was seen with respect to tumor multiplicity, while a reduction in tumor growth rate was observed. It thus appears that WKY alleles located on Chr 5 and Chr 8 interact epistatically in a contrasting manner to modulate tumor multiplicity (in a nonadditive manner) and growth rate (in a synergic manner). Tumor growth rate is thus influenced by two QTLs, on Chr 10 (Mcsta1) and on Chr 18 (Mcsta2), the action of the latter being dependent on the presence of the Chr5 QTL (Mcstm1). The expression level of positional and functional candidate genes was also analyzed. On Chr 5, Pla2g2a is subject to a syntenic control while expression of the Tp53 (Chr 10) and Pmai1/Noxa (Chr 18) genes appears to be controlled by several mammary cancer resistance QTLs.

In the present study, we have examined rat-mouse somatic cell hybrids that segregate rat chromosomes with probes for MHC or MHC-linked genes to determine the chromosomal location of the MHC. We show that the rat MHC and Cbs gene are syntenic and are located on chromosome 20. The entire chromosomal region from Glo-1 to Acry-1 and Cbs is thus syntenic in the rat, as in the mouse

The COP and WKY rat strains are resistant to mammary cancer. It has shown previously that upon chemical carcinogen treatment, COP females exhibit mammary preneoplastic lesions which disappear within a few weeks. We show here that in similar conditions, WKY females do not exhibit any visible preneoplastic lesions. WKY females are characterized by precocious mammary tissue differentiation, including active expression of the beta-casein gene in young virgin females. This trait might be critical in resistance to mammary carcinogenesis of WKY rats. To test this hypothesis, we took advantage of 2 congenic strains that contain a limited chromosome segment of WKY origin, derived either from chromosome 5 or from chromosome 18, introgressed in the susceptible genetic background (SPRD-Cu3). Each of these congenic strains has been shown to be partially resistant to chemically induced mammary carcinogenesis (reduction in tumour multiplicity with respect to the susceptible SPRD-Cu3 rats). We show here that these 2 congenic strains also exhibit precocious mammary differentiation, though to a lower extent than the WKY females. The conclusion of this study is thus 2-fold: (i) eradication of preneoplastic lesions is not a general phenomenon in mammary cancer resistance; (ii) the same segment of rat chromosomes 5 or 18 that controls mammary cancer resistance also contains a quantitative trait locus imposing precocious mammary differentiation. These 2 traits are thus associated, supporting the hypothesis that there might be a cause-effect relationship between precocious mammary differentiation and cancer resistance.

We previously mapped several quantitative trait loci (QTLs) controlling DMBA-induced mammary tumor development in female rats derived from a SPRD-Cu3 (susceptible strain) × WKY (resistant strain) cross. Two of these QTLs were assigned to chromosomes 5 and 18. In the present study, we generated and characterized congenic strains in which a segment of WKY chromosomes 5 or 18 was introduced in the SPRD-Cu3 genetic background, thereby physically demonstrating that each of these two chromosomes controls mammary tumor multiplicity. The chromosome 5 QTL (Mcstm1) accounts for 7 tumors per animal (versus a total of 11 tumors per SPRD-Cu3 rat). The chromosome 18 QTL (Mcstm2) accounts for 3 tumors per animal and is the first chemically-induced mammary cancer susceptibility locus assigned to this chromosome. In addition, the Mcstm1 region was shown to also controls tumor latency. These loci thus play a major role in chemically-induced mammary tumor development. QTLs controlling chemically-induced or estrogen-induced mammary tumor development have independently been identified on chromosomes 5 and 18, using susceptible strains others than SPRD-Cu3. Therefore the haplotype structure of the relevant chromosome regions was analyzed in the different strains. Some chromosome regions were found to be highly mosaic (haplotype blocks < 1 Mb), while one region showed an apparently conserved haplotype block of 7.5 Mb. This analysis points to limited regions that could harbor the causative genes and also indicates that at least Mcstm2 is a novel QTL. © 2007 Wiley-Liss, Inc.

The Rfp (ret finger protein) and Olf89 (olfactory receptor 89) genes were assigned to rat chromosomes 17 and 20, respectively. These two genes are syntenic in human (RFP and OLF89) as they both map to chromosome 6, less than 300 kb apart. The mouse homologs are located on two different chromosomes, namely 13 and 17, respectively. It was shown that these two genes delineate the UA/UB break point, and that this chromosome break occurred in the rodent lineage, before the mouse radiation. Our data indicate that this break occurred before the rat/ mouse split, therefore before the Murinae radiation.

The rat is considered an excellent model for studying human breast cancer. Therefore, understanding the genetic basis of susceptibility to mammary cancer in this species is of great interest. Previous studies based on crosses involving the susceptible strain WF (crossed with the resistant strains COP or WKY) and focusing on tumor multiplicity as the susceptibility phenotype led to the identification of several loci that control chemically induced mammary cancer. The present study was aimed to determine whether other loci can be identified by analyzing crosses derived from another susceptible strain on the one hand, and by including phenotypes other than tumor multiplicity on the other hand. A backcross was generated between the susceptible SPRD-Cu3 strain and the resistant WKY strain. Female progeny were genotyped with microsatellite markers covering all rat autosomes, treated with a single dose of DMBA, and phenotyped with respect to tumor latency, tumor multiplicity, and tumor aggressiveness. Seven loci controlling mammary tumor development were detected. Different loci control tumor multiplicity, latency, and aggressiveness. While some of these loci colocalize with loci identified in crosses involving the susceptible strain WF, new loci have been uncovered, indicating that the use of distinct susceptible and resistant strain pairs will help in establishing a comprehensive inventory of mammary cancer susceptibility loci.

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.

There are clear indications that inheritance plays an essential role in certain cases of human endometrial cancer, and there are at least 2 forms of early-onset heritable endometrial adenocarcinomas (EACs). Females of the BDII inbred rat strain are known to be genetically predisposed to endometrial carcinoma, and we have performed a genetic analysis of susceptibility to endometrial cancer in this strain. F(2) populations were generated by crossing BDII females with males from 2 different strains with a low incidence of EAC, and the occurrence of endometrial cancer was studied. Three chromosome regions associated to EAC susceptibility were identified, and the susceptibility genes in these regions were designated Ecs1, Ecs2 and Ecs3. Our results indicate that the genes affecting susceptibility to EAC are different in the 2 crosses, suggesting that the genes behind the susceptibility in BDII animals may interact with different genes in different genetic backgrounds.

The glypicans compose a family of glycosylphosphatidylinositol (GPI)-anchored heparan sulfate proteoglycans that play a role in the control of cell division and growth regulation. So far, six members (GPC1–6) of this family are known in vertebrates. The rat glypican gene 3 (Gpc3) was previously assigned to chromosome Xq36 (Shen et al., 1997). Using standard and radiation cell hybrids, we localized the five other rat glypican genes.

Using the sequence of the SP1 zinc-finger DNA-binding domain as a probe to screen a mouse EST database, we identified two novel members of the SP/XKLF transcription factor family, KLF13 and KLF14. The mouse Klf13 cDNA (1310 bp in length) contains a single open reading frame of 288 amino acids with a DNA-binding domain closely related to that of the human RFLAT-1 protein and a putative transactivator N-terminal domain rich in proline and alanine residues. The mouse Klf13 gene seems to be the homologue of the human RFLAT1 gene. The mouse Klf14 sequence is homologous to a human genomic sequence from chromosome 17 that is believed to code for a protein with three zinc fingers at the end of its C-terminal domain. Using reverse transcription-polymerase chain reaction, we showed ubiquitous expression of Klf13 and Klf14 in adult mice. A third member of this family was also identified in a human EST database; this sequence was found to be identical to KLF11 (TIEG2), recently identified by Cook et al. (1998, J. Biol. Chem. 273: 25929-25936). The corresponding mouse cDNA was isolated and sequenced. The three genes were localized in the human and the rat: chromosomes 15 (human KLF13), 17q21.3-q22 (human KLF14; HGMW-approved symbol SP6), and 2p25 (human KLF11) and chromosomes 1q31-q32 (rat Klf13), 10q31-q32.1 (rat Klf14) (SP6), and 6q16-q21 (rat Klf11).

In order to improve the rat gene map and comparative mapping with the human and the mouse, we determined the chromosome localization of 54 rat genes. Most genes encode transcription factors or other regulatory proteins of cancer relevance. The human homologs of four genes were also assigned to their respective chromosome. These data generated anchor points between the recently established radiation hybrid maps and the genetic and cytogenetic maps. They improve comparative mapping between the rat, the mouse, and the human gene maps, and in particular they disclose four new synteny groups conserved in the rat and the human. These new localizations should also be useful for the identification of genes involved in the control of quantitative traits such as cancer susceptibility or diabetes.

The gene coding for rat parathyroid hormone-like peptide (PTHLH) was previously assigned to rat chromosome 2 (Hendy et al., 1988). We reexamined this assignment. According to our results, the gene is on rat chromosome 4. Taking into account the known localizations of the KRAS2 (Kras-2) oncogene and the PTHLH gene, this assignment strongly suggests that a synteny group is conserved on rat chromosome 4, mouse chromosome 6, and human chromosome 12.

Inbred rat strains have distinct susceptibilities to carcinogeninduced mammary cancer. Wistar-Furth (WF) rats are highly susceptible, while Copenhagen (COP) and Wistar-Kyoto (WKY) rats are resistant to this carcinoma and the Fischer-344 (F344) rats have an intermediate susceptibility (Isaacs 1986; Haag et al. 1992). Genetic breeding studies showed that this phenotype is a polygenic trait (Shepel et al. 1998). One of the susceptibility loci, Mcs1, identified at the centromeric end of rat Chr 2 (2q1), has been involved in the modulation of tumor number (Hsu et al. 1994; Shepel et al. 1998). The cyclin B1 gene (Ccnb1) is located in or close to the Mcs1-containing region (Shepel et al. 1998; Szpirer et al. 1999). Since cyclins are key components of the cell cycle progression machinery, a disregulation can potentially lead to uncontrolled cell growth and hence to cancer. Indeed, overexpression of several cyclins has been demonstrated to be associated with cancer (Keyomarsi and Pardee 1993). The rat Ccnb1 gene can thus be considered as an Mcs1 candidate. In order to test this hypothesis, we sequenced the Ccnb1 cDNA in the four strains mentioned (WF, COP, WKy, and F344). Our results do not argue in favor of the candidacy of Ccnb1, and, unexpectedly, disclosed a high level of sequence variation in the expressed region of the gene. Two rat Ccnb1 cDNA isoforms have been described so far. Trembley and colleagues (1994) isolated a 1375-bp cDNA from testes, while Markiewicz and associates (1994) isolated a 2348-bp cDNA from fibroblasts. These cDNAs differ mainly in the two untranslated regions (UTRs). The 58 UTRs have different lengths and also show divergent sequences at their 58 end, while their 38 end (last 65 positions, preceding the translation start) are almost identical, suggesting that the two isoforms are produced by alternative splicing involving distinct exons 1. The two 38 UTRs differ in the use of the polyadenylation site (first site used in the testes form, and second site used in the fibroblast form). Poly(A)-enriched RNA was isolated from mammary glands of WF, COP, WKy, F344 rats (purchased from Harlan), and RTPCR was done with four primer pairs spread along the Ccnb1 cDNA sequence, generating four fragments, which were sequenced in each of the four strains (Fig. 1). Two sequences were obtained, as shown in Fig. 2. Both combine the 58 UTR sequence

The rat gene encoding the microphthalmia-associated transcription factor (Mitf) was assigned to rat Chromosome (Chr) 4q34-q41, as well as the Gata2 and Mem1 genes. Rat Chr 4 is homologous to mouse Chr 6 and human Chr 3, which carry the Mitf (MITF) gene in these species (MMU 6, 40.0 cM, and HSA 3p14.1-p12.3). mib/mib rats, which are characterized by depigmentation, microphtalmy, osteopetrosis, and neurological disorders were shown to bear a deletion covering several kilobases of genomic DNA in the Mitf gene and to lack Mitf mRNA. The Mitf mutation in the mib/mib rats is thus very likely to be a Mitf null mutation, causing a phenotype similar to the one observed in the miVGA-9 mice, but including osteopetrosis as an additional feature.

Two novel KRAB (Kruppel associated box) type zinc finger protein encoding cDNAs, named Kzf1 and Kzf2 (Kzf for KRAB zinc finger), were identified by screening of a rat embryonic brain cDNA library with a human ZNF91 KRAB probe. Kzf1 and Kzf2 encode proteins with an amino-terminal KRAB domain and a carboxy-terminal zinc finger cluster containing 9 and 13 zinc finger units, respectively. While Kzf2 appears to be ubiquitously expressed, Kzf1 is preferentially expressed in the testis. Within the testis, Kzf1 mRNA is restricted to germ cells. The Kzf1 protein exhibits DNA binding activity and its KRAB domain can function as a repressor module in transcription. Using somatic cell hybrid analysis, the Kzf1 gene was mapped to chromosome 6.

By means of somatic cell hybrids segregating rat chromosomes, we determined the chromosome localization of three rat genes of the Jun family: Junb (Chr 19), Jun (=c-Jun) (Chr 5) and Jund (Chr 16). The Jun gene was also localized to the 5q31-33 region by fluorescence in situ hybridization. These rat gene assignments reveal two new homologies with mouse and human chromosomes, and provide a new example of synteny conserved in the human and a rodent species (the mouse), but split between the two rodent species.

The authors have isolated a collection of human ZFPs encoding cDNAs (HPF1 to -9) by hybridization with a finger motif oligonucleotide probe. Here, they describe the localization of a chromosome 19-linked human ZFP gene (HPF1/ZNF83). They first assigned the ZNF83 gene on chromosome 19 by the screening of a human x rodent hybrid panel by DNA hybridization with a fragment of a previously cloned cDNA (data not shown). To further localize the gene within chromosome 19, the regional assignment of the ZNF83 gene was determined by fluorescence in situ hybridization and digital imaging microscopy as described elsewhere. Human metaphase spreads were hybridized with biotinylated ZNF83 cDNA, and hybridization was detected with fluorescein isothiocyanate-conjugated avidin-DCS. Chromosomes were identified by staining with 4,6-diamino-2-phenylindol dihydrochloride. The fractional length (Flpter) distance of the signal to the p arm terminus relative to the total chromosome length gave a Flpter value between 82.8 and 89.9, which is consistent with an assignment of the ZNF83 gene in ISCN region 19q13.3-q13.4. 14 refs., 1 fig.

DNA polymerase epsilon [DNA pol epsilon (EC 2.7.7.7)] is one of the four nuclear DNA polymerases in eukaryotic cells. The mammalian enzyme is involved in DNA repair and possibly also in replication of chromosomal DNA. The gene encoding pol epsilon (POLE) was assigned to human and rat chromosomes 12 by Southern blot analysis of genomic DNA from mouse-human and mouse-rat somatic cell hybrid panels using human cDNA probe. The human gene was then regionally localized to band 12q24.3 by fluorescence in situ hybridization of metaphase spreads of chromosomes from human lymphocytes using genomic DNA probe. POLE is closely linked to HNF1A, a gene encoding a liver-enriched transcription factor, HNF1 alpha. The two genes thus define a new synteny group retained on human and rat chromosomes 12. Another gene mapping to the same or close-by region as human POLE is a gene for inherited disorder tuberous sclerosis 3, TSC3.

The plasma membrane Na/H exchanger plays an essential role in regulating intracellular pH and Na+ concentration and has been implicated in several pathophysiological conditions, including essential hypertension and congenital secretory diarrhea. Four isoforms of the Na/H exchanger encoded by separate genes have recently been identified by cDNA cloning. To map their locations in the human and rat genomes, rat isoform-specific cDNA probes were hybridized to Southern filters containing panels of somatic cell hybrids that segregate either human or rat chromosomes. The rat Nhe1 gene was assigned to Chromosome (Chr)5, extending the homology with human chromosome 1p that has previously been shown to contain the human NHE1 gene. The genes encoding the NHE-2 and NHE-4 isoforms were syntenic in the two species and assigned to rat Chr 9 and human Chr 2. A single Nhe3 gene was detected in rat and assigned to Chr 1. In contrast, although evidence to date has suggested a single human NHE3 gene on Chr 5, two NHE3 genes, NHE3A and NHE3B, were identified and assigned to Chrs 10 and 5, respectively. Interestingly, rat Chr 1 has recently been found to carry a gene controlling systolic blood pressure upon sodium loading in stroke-prone, spontaneously hypertensive rats. Thus, this and other evidence implicates rat Nhe3 as a possible candidate gene in this disease process.

The homeobox genes are a family of developmental master control genes originally identified in the fruit fly Drosophila. In mammals, the Antennapedia-class homeobox genes are most studied and characterized. These homeobox genes encode sequence-specific DNA-binding proteins and function as transcription regulators to specify positional information in development (for review, see McGinnis and Krumlauf 1992). One striking feature of the Antennapedia-class homeobox genes is that their physical organization in the chromosomes is conserved in evolution. In Drosophila, eight Antennapedia-class homeobox genes are arranged in two clusters, the Antennapedia complex (ANT-C) and the Bithorax complex (BX-C), on Chromosome (Chr) 3. In mice and human, 38 Antennapedia-class homeobox genes have been identified; they are organized in four gene clusters (McGinnis and Krumlauf 1992; Scott 1992). DNA sequence comparisons of the mammalian Antennapedia-class homeobox genes suggest that the four mammalian homeobox gene clusters may have arisen through chromosomal duplications of an ancestral homeobox gene complex (HOM-C) in evolution (Schughart et al. 1989). In both fly and mice, the expression of the Antennapedia-class homeobox genes is in a spatially restricted fashion. Moreover, the physical orders of the homeobox genes in a chromosome are colinear with the spatial domains of expression along the anteroposterior body axis of the embryos (McGinnis and Krumlauf 1992). This conservation of gene order in chromosome and spatial pattern of expression may have important implications in the evolution and function of the homeobox genes. In this report, we describe the chromosomal assignment of seven Antennapedia-class rat homeobox

S-Adenosylmethionine decarboxylase (AdoMetDC) is a ubiquitous enzyme in eukaryotic cells and responds to a wide variety of stimuli affecting growth. To provide a framework for understanding the molecular basis of the mechanisms responsible for regulating the expression of this enzyme activity, we recently cloned and sequenced the rat gene for AdoMetDC. Now we have isolated another, slightly different AdoMetDC gene from a rat genomic library. Comparison of the two genes shows a high degree of conservation of sequence and structural organization. The two genes share the following characteristics: (1) both are approximately 16 kb in size, have identical exon/intron boundaries, and exhibit similar intron/exon structural organization; and (2) the nucleotide sequences are highly conserved in the coding regions and in many introns. Analysis of mouse-rat somatic cell hybrids has localized both rat genes to chromosome 20. The most interesting feature of these genes is that their 5' flanking regions are totally different. The promoter activities of the 5' regulatory regions were assessed by transient gene expression assays in Rat-2 cells after fusion to the chloramphenicol acetyltransferase gene. Transient transfections with the chimeric DNAs demonstrated that these fragments were able to function as efficient promoters, indicating that the diverging 5' regions of two AdoMetDC genes contain functional, but different, regulatory transcription elements.

By means of somatic cell hybrids segregating rat chromosomes, we determined the chromosome localization of three rat beta 1 family integrin genes. ITGB1 was assigned to Chromosome (Chr) 19, ITGA4 to Chr 3, and ITGA5 to Chr 7. These chromosome assignments reveal or confirm homology between two pairs of rat and human chromosomes (rat Chr 3-human Chr 2; rat Chr 7-human Chr 12).

By means of somatic cell hybrids segregating either human or rat chromosomes, the genes encoding the transcription factor Sp1 (SP1) and the 1,25-dihydroxyvitamin D3 receptor (VDR) were both assigned to human chromosome arm 12q and to rat chromosome 7. This result implies that the locus for the clinical disorder vitamin D dependency rickets type II maps on 12q. The phenylalanine hydroxylase (PAH) and the retinoic acid receptor-gamma (RARG) genes also map on human chromosome arm 12q and rat chromosome 7, indicating that a synteny group is conserved on these chromosomes.

Using two panels of somatic cell hybrids segregating either human or rat chromosomes, the gene encoding the interleukin-6-dependent DNA-binding protein, also called liver activator protein (designated transcription factor 5: TCF5), was assigned to human chromosome 20 and to rat chromosome 3. The TCF5 gene might be identical with the NF-IL6 gene. The locus encoding the IL6 receptor gene (IL6R) was localized to human chromosome 1 and rat chromosome 2. An IL6R-like (IL6RL) locus was also assigned to human chromosome 9. In addition, the rat interleukin-6 (IL6) gene was assigned to rat chromosome 4. These mapping data allow one to extend comparison between the rat, mouse, and human gene maps.

Using Southern blot analysis of DNAs from human×rodent cell hybrids, we have mapped the CD23 leukocyte antigen gene (FCE2) to human chromosome 19.

Twelve loci have been assigned to rat chromosome 5: aldolase B (ALDOB), atrial natriuretic factor (ANF = pronatriodilatin, PND), D4RP1, DSI1, galactosyltransferase (GGTB2), glucose transporter (GLUT1), interferon alpha 1 and related interferon alpha (INFA), interferon beta (INFB), lymphocyte-specific protein-tyrosine kinase (LCK), oncogene MOS, alpha 2U-globulin (major urinary protein, MUP), and orosomucoid (ORM, also called alpha 1-acid glycoprotein, AGP). Among these, the interferon alpha and beta genes map in the q22-23 region, which also contains a transformation suppressor gene (SAI1). The other loci reside outside this region. This study also indicated that the rat genome contains 2 LCK genes, unlike the human and murine genomes. These new assignments on rat chromosome 5 demonstrate that this chromosome is highly homologous to mouse chromosome 4 and carries synteny groups conserved on human chromosome 9 (interferon alpha and beta, galactosyltransferase, orosomucoid, and aldolase B genes) and on the short arm of human chromosome 1 (MYCL, glucose transporter, protein kinase LCK, and atrial natriuretic factor genes).

A cluster of Krüppel type zinc finger genes of the KRAB subclass has recently been localized on human chromosome 19p12-p13.1. We now report that ZNF117 (HPF9), a closely related zinc finger gene of this KRAB subfamily, has been assigned to a distinct locus in the human genome: chromosome band 7q11.2.

From the analysis of mouse × rat cell hybrids which segregate rat chromosomes, the rat genes coding for the enzymes medium-chain acyl-CoA dehydrogenase, isovaleryl-CoA dehydrogenase, and the β-subunit of propionyl-CoA carboxylase have been assigned to chromosomes 2, 3, and 8, respectively.