Since porcine endogenous retroviruses (PERVs) can infect cultured human cells, they are a potential hazard to xenotransplantation. For this reason, endogenous retroviruses from the Westran (Westmead Hospital transplantation) inbred line of pigs were analyzed by using consensus primers for the type A and type B viruses to amplify 1.8-kb envelope gene fragments. After preliminary analysis with restriction enzymes KpnI and MboI, 31 clones were sequenced. Between types A and B, five recombinant clones were identified. Fifty-five percent of clones (17 of 31) had premature stop codons within the envelope protein-encoding region. Endogenous retroviruses in Westran pigs were physically mapped by fluorescence in situ hybridization (FISH) using PERV-A and PERV-B envelope clones as probes to identify at least 32 integration sites (19 PERV-A sites and 13 PERV-B sites). The chromosomal sites of integration in the Westran strain are quite different from those in the European Large White pig. The recombinant clones suggest that defective PERVs could become infective through recombination and further that PERVs might recombine with human endogenous retroviruses in xenotransplants.

Mammals possess multiple, closely linked beta-globin genes that differ in the timing of their expression during development. These genes have been thought to be derived from a single ancestral gene, by duplication events that occurred after the separation of the mammals and birds. We report the isolation and characterization of an atypical beta-like globin gene (omega-globin) in marsupials that appears to be more closely related to avian beta-globin genes than to other mammalian beta-globin genes, including those previously identified in marsupials. Phylogenetic analyses indicate that omega-globin evolved from an ancient gene duplication event that occurred before the divergence of mammals and birds. Furthermore, we show that omega-globin is unlinked to the previously characterized beta-globin gene cluster of marsupials, making this the first report of an orphaned beta-like globin gene expressed in a vertebrate.

The Drosophila melanogaster small optic lobes gene (sol) is required for normal development of the neuropiles of the medulla and lobula complexes of the adult optic lobes. The predicted protein products of sol and its human homologue SOLH contain zinc-finger-like repeats, a calpain-like protease domain, and a C-terminal domain of unknown function. Long-distance PCR was used to amplify genomic DNA for Solh, the mouse homologue of sol, following the identification of mouse Solh expressed sequence tags. The nucleotide sequence of the Solh coding region (6.0 kb) was determined. The predicted Solh protein of 1095 amino acid residues shows 89% identity (93% similarity) to the human homologue. Solh was localized by in situ hybridization to band A3.3 on mouse Chromosome 17, in a region of maintained homology with human 16p13.3. Antipeptide antibodies were prepared and verified by demonstration of specific reactivity with recombinant human SOLH protein prepared by in vitro transcription/translation and expression in insect cells using the baculovirus system. The antibodies were used to show that the Solh protein localizes to the olfactory bulb in mouse and rat brain, suggesting that it could have an analogous role in development of sensory system neurons in Drosophila and in mammals.

Although largely replaced by the use of fluorescent in situ hybridization (FISH) in animal and human molecular cytogenetics, the technique of radioactive in situ hybridization (RISH) still has some uses. Using practicable exposure times for autoradiographs of 3–4 wk, RISH is approx 50 times more sensitive than FISH using biotin- or digoxygenin-labeled probes, and probably 10 times more sensitive than the recently introduced system of tyramide FISH (NEN Life Sciences Prods., Code NEL 730/730A). In addition, the sensitivity of RISH can be increased with longer exposures, in a roughly linear fashion until the silver bromide grains in the emulsion approach saturation over the target; by contrast, FISH requires instantaneous expression of the signal. Because of its high sensitivity, RISH can be used with short probes (1), down to 200 bp, poorly labeled probes (2), short target sequences, and old slides (Table 1). Bands on the chromosomes can be excellent with RISH (3), requiring no enhancement by image analyzing systems, and observed with simple brightfield microscopy (Fig. 1); although finding a suitable batch of Giemsa stain can be difficult (see Subheading 3.6. and Note 1).

Arginine vasopressin interacts with the vasopressin type 1a receptor (V1aR) to initiate physiological effects such as vasoconstriction of blood vessels and glycogenolysis. AVP is also involved in central nervous effects such as body homeostasis and blood pressure control. The complete genomic organization of the sheep V1aR gene has been determined, including the presence of one major and two minor transcriptional start sites at −321, −206 and −91 bp respectively, relative to the ATG codon. Another more distal minor transcriptional start site was also localized between nucleotides −997 and −892 relative to the ATG codon. One intron exists in the sheep V1aR gene and potential cis- and trans- acting sites were identified in the sheep V1aR promoter. The promoter was also compared to the rat V1aR promoter. The sheep V1aR promoter displays features typical of housekeeping genes, although tissue-specific expression does not support this. V1aR mRNA is absent in the adult sheep liver but not the kidney. One copy of the V1aR gene exists in the sheep genome, which was localized to chromosome 3q23–24, and to the homoeologous position, 5q23–24 in cattle.

Mutations in the Drosophila melanogaster small optic lobes (sol) gene cause a sever reduction in the neuropiles of the medulla and lobula complexes of the adult optic lobes. The predicted protein product of sol contains zinc-finger-like repeats, a calpain-like protease domain, and a C-terminal region of unknown function. We have isolated human brain cDNA for SOLH, a human homologue of sol. The human SOLH gene consists of 14 exons distributed over more than 45 kb of genomic DNA. The encoded SOLH protein of 1086 amino acids has strong similarity to the D. melanogaster protein. The calpain-like domain and C-terminal region are highly conserved (58% identity), and similar Cys2-Cys2 zinc fingers are present in the N-terminal region. A reported Caenorhabditis elegans homologue contains the calpain domain and C-terminal region, but appears to lack the zinc finger region. A single copy of the zinc finger sequence is present in adjacent C. elegans genomic cosmid DNA sequence, and we show that it is part of the C. elegans sol-like transcript. Northern analysis of human tissues revealed a SOLH transcript of approximately 5 kb that was strongest in human brain. We have mapped the SOLH gene to chromosome 16p13.3 by in situ hybridization. SOLH is a candidate gene for CATM (hereditary cataracts with microphthalmia), which maps in this region.

The humanPIN1gene encodes an essential nuclear peptidyl-prolylcis/transisomerase involved in the regulation of mitosis. PIN1 is a member of a new class of peptidyl-prolylcis/transisomerases that includes theEscherichia coliparvulin, yeastESS1,andDrosophila melanogaster dodogene products. Analysis of human ESTs showed that there are two different but closely related human transcripts, one of which corresponds toPIN1.Gene localization, using both FISH and tritium-labeled probes, showed that each of the human transcripts hybridized to 1p31 and 19p13. Primers were designed to discriminate between the two transcripts, and PCR on DNA from hamster/human somatic cell hybrids retaining chromosomes 1 or 19 was used to map the humanPIN1gene to chromosome 19, andPIN1L,a closely related gene, to chromosome 1. The results establish thatPIN1is at 19p13 andPIN1Lat 1p31. PCR was used to clone the coding region forPIN1L.ThePIN1LcDNA is 89% identical at the nucleotide level to thePIN1transcript, but contains a shift in the reading frame. It encodes a 100-amino-acid variant protein consisting of 63 amino acids homologous (90% identical) to PIN1 and containing the entire WW domain, fused to a 37-amino-acid tail. The protein encoded byPIN1Lmay have some functional role or alternativelyPIN1Lmay be a transcribed pseudogene.

The neuropeptide galanin elicits a range of biological effects by interaction with specific G-protein-coupled receptors. Human and rat GALR1 galanin receptor cDNA clones have previously been isolated using expression cloning. We have used the human GALR1 cDNA in hybridization screening to isolate the gene encoding GALR1 in both human (GALNR) and mouse (Galnr). The gene spans approximately 15–20 kb in both species; its structural organization is conserved and is unique among G-protein-coupled receptors. The coding sequence is contained on three exons, with exon 1 encoding the N-terminal end of the receptor and the first five transmembrane domains. Exon 2 encodes the third intracellular loop, while exon 3 encodes the remainder of the receptor, from transmembrane domain 6 to the C-terminus of the receptor protein. The mouse and human GALR1 receptor proteins are 348 and 349 amino acids long, respectively, and display 93% identity at the amino acid level. The mouseGalnrgene has been localized to Chromosome 18E4, homoeologous with the previously reported localization of the humanGALNRgene to 18q23 in the same syntenic group as the genes encoding nuclear factor of activated T-cells, cytoplasmic 1, and myelin basic protein.

The TI1/UPK1b gene codes for a protein of the “tetraspan” family and is expressed as a differentiation product of the mammalian urothelium. A partial genomic clone of the human homologue of the TI1/UPK1b gene was isolated and used as probe to localize the human gene to chromosome 3q13.3–q21 byin situhybridization. Using the same probe, aTaqI restriction fragment length polymorphism, with 29% heterozygosity, was identified by Southern analysis.

The Gbx2 homeodomain is widely conserved in metazoans. We investigated the mouseGbx2locus by isolation and characterization of genomic clones and by physical localization to the genome. TheGbx2gene contained a single intron that separated the proposed functional protein domains. This organization was conserved with humanGBX2.Physical localization ofGbx2to Chromosome 1C5–E1 indicated that the genomic relationship between the linkedGbx2andEn1genes differs between mouse and human, making it unlikely to be of functional significance. We also extended the known expression pattern ofGbx2beyond the gastrulation stage embryo and the developing CNS to pluripotent cellsin vitroandin vivo. Gbx2expression was demonstrated in undifferentiated embryonic stem cells but was downregulated in differentiated cell populations. In the embryo,Gbx2expression was detected before primitive streak formation, in the inner cell mass of the preimplantation embryo.Gbx2is therefore a candidate control gene for cell pluripotency and differentiation in the embryo.

In a search for new protein tyrosine kinases (PTKs) in early hemopoietic cells, we have identified a sequence closely related to the Fibroblast Growth Factor Receptor (FGFR) family. A cDNA isolated from a mouse embryo library was 89% identical to FGFR-3 in both its coding and 3′ untranslated regions. However, the region homologous to exons 5 to 9 of FGFR-3 was missing. In addition, the ORF was interrupted by several stop codons and frame shifts, indicating that this sequence is not functional. These transcripts were therefore copied from a novel FGFR-3 pseudogene, that we called ψFGFR-3. Partial analysis of this gene showed the absence of introns, which is a characteristic feature of a processed pseudogene. ψFGFR-3 gene was localized on Chromosome 1H4-6. Its transcription was shown to be antisense and its expression was restricted to fetal tissues. These results indicate that ψFGFR-3 has been inserted in Chromosome 1 in antisense orientation close to a heterologous promoter.

In this study, we have isolated and characterized a gene and cDNA encoding a mouse Theta class GST. The gene,mGSTT2,spans approximately 3.1 kb and is composed of five exons interrupted by four introns. The gene was localized to Chromosome 10B5–C1 byin situhybridization. Southern blot analysis of mouse genomic DNA suggests that there is only one copy ofmGSTT2in the mouse genome. The cDNA derived frommGSTT2was isolated from a mouse liver cDNA library and has an open reading frame of 732 bp encoding a peptide of 244 amino acids with a calculated molecular weight of 26,676 Da. The encoded protein shares amino acid sequence identities of 92, 77, 51, and 55% with rat subunit Yrs, human subunit GSTT2, rat subunit 5, and human subunit GSTT1, respectively.

cDNA clones corresponding to the sequence for human early pregnancy factor were isolated from a human melanoma library and hybridized to DNA digested with four restriction enzymes obtained from twelve different subjects. Up to 20 cross hybridizing bands were observed. When hybridized to metaphase spreads from four different humans, significant signals were present in nine locations, on eight different chromosome arms. These results suggest that the early pregnancy factor gene is a member of a large gene family. The coding sequence for early pregnancy factor has a high degree of homology with the sequence for human chaperonin 10, and the gene family described here should contain the genes for both of these proteins.

The inhibitory glycine receptor (GlyR) is a pentameric receptor comprised of alpha and beta subunits, of which the beta subunit has not been characterised in humans. A 2106 bp cDNA, isolated from a human hippocampal cDNA library, contained an open reading frame of 497 amino acids which encodes the beta subunit of the human GlyR. The mature human GlyR beta polypeptide displays 99% amino acid identity with the rat GlyR beta subunit and 48% identity with the human GlyR alpha 1 subunit. Neither [3H]strychnine binding nor glycine-gated currents were detected when the human GlyR beta subunit cDNA was expressed in the human embryonic kidney 293 cell line. However, co-expression of the beta subunit cDNA with the alpha 1 subunit cDNA resulted in expression of functional GlyRs which showed a 4-fold reduction in the EC50 values when compared to alpha 1 homomeric GlyRs. Glycine-gated currents of alpha 1/beta GlyRs were 17-fold less sensitive than homomeric alpha 1 GlyRs to the antagonists picrotoxin, picrotoxinin and picrotin, providing clear evidence that heteromeric alpha 1/beta GlyRs were expressed. The beta subunit appears to play a structural rather than ligand binding role in GlyR function. Fluorescence in situ hybridisation was used to localise the gene encoding the human GlyR beta subunit (GLRB) to chromosome 4q32, a position syntenic with mouse chromosome 3. In situ hybridisation using the human GlyR beta subunit cDNA showed that the murine GlyR beta subunit gene (Glrb) maps to the spastic (spa) locus on mouse chromosome 3 at bands E3-F1. This is consistent with the recent finding that a mutation in the murine GlyR beta subunit causes the spa phenotype. It also raises the possibility that mutations in the human beta subunit gene may cause inherited disorders of the startle response.

We have cloned and characterized the mouse gene encodingKiz1/Limk1,a new member of the zinc-finger LIM family that also has a kinase domain. The gene encompasses 25 kb of the mouse genome, and the organization of its 16 exons does not correlate with its functional domains. The promoter region ofKiz1/Limk1was identified by cloning a 1.06-kb genomic fragment upstream from the first ATG in a promotorless CAT vector. This construct was demonstrated to drive CAT expression in Jurkat cells. The promoter sequence lacks conventional TATA and CAAT motifs but contains consensus binding sequences for several transcriptional regulators implicated in control of transcription in many different cell types, including Sp1, Ets, and E2A. Analysis of the chromosomal localization ofKIZ1/LIMK1indicates that it lies on human chromosome 17 in the region 17q25 and on mouse Chromosome 5, band G2.

Two forms of glutathione synthetase deficiency have been described. While one form is mild, causing hemolytic anemia, the other more severe form causes 5-oxo-prolinuria with secondary neurological involvement. Despite the existence of two deficiency phenotypes, Southern blots hybridized with a glutathione synthetase cDNA suggest that there is a single glutathione synthetase gene in the human genome. Analysis of somatic cell hybrids showed the human glutathione synthetase gene (GSS) to be located on chromosome 20, and this assignment has been refined to subband 20q11.2 using in situ hybridization.

Until recently the Theta-class glutathione S-transferases (GSTs) were largely overlooked due to their low activity with the model substrate 1-chloro-2,4-dinitrobenzene (CDNB) and their failure to bind to immobilized glutathione affinity matrices. Little is known about the number of genes in this class. Recently, Pemble et al. (Biochem J. 300: 271–276, 1994) reported the cDNA cloning of a human Theta-class GST, termed GSTT1. In this study, we describe the molecular cloning of a cDNA encoding a second human Theta-class GST (GSTT2) from a λgt11 human liver 5′-stretch cDNA library. The encoded protein contains 244 amino acids and has 78.3% sequence identity with the rat subunit 12 and only 55.0% identity with human GSTT1. GSTT2 has been mapped to chromosome 22 by somatic cell hybrid analysis. The precise position of the gene was localized to subband 22q11.2 by in situ hybridization. The absence of other regions of hybridization suggests that there are no closely related sequences (e.g., reverse transcribed pseudogenes) scattered throughout the genome and that if there are closely related genes, they must be clustered near GSTT2. Southern blot analysis of human DNA digested with BamHI shows that the size of the GSTT2 gene is relatively small, as the coding sequence falls within a 3.6-kb BamHI fragment.