Mapping genes in the mouse using single-strand conformation polymorphism analysis of recombinant inbred strains and interspecific crosses

GSK-3 signaling in developing cortical neurons is essential for radial migration and dendritic orientation

GSK-3 is an essential mediator of several signaling pathways that regulate cortical development. We therefore created conditional mouse mutants lacking both GSK-3α and GSK-3β in newly born cortical excitatory neurons. Gsk3-deleted neurons expressing upper layer markers exhibited striking migration failure in all areas of the cortex. Radial migration in hippocampus was similarly affected. In contrast, tangential migration was not grossly impaired after Gsk3 deletion in interneuron precursors. Gsk3-deleted neurons extended axons and developed dendritic arbors. However, the apical dendrite was frequently branched while basal dendrites exhibited abnormal orientation. GSK-3 regulation of migration in neurons was independent of Wnt/β-catenin signaling. Importantly, phosphorylation of the migration mediator, DCX, at ser327, and phosphorylation of the semaphorin signaling mediator, CRMP-2, at Thr514 were markedly decreased. Our data demonstrate that GSK-3 signaling is essential for radial migration and dendritic orientation and suggest that GSK-3 mediates these effects by phosphorylating key microtubule regulatory proteins.

DOI:http://dx.doi.org/10.7554/eLife.02663.001

In the brain, one of the most striking features of the cerebral cortex is that its neurons are organized into different layers that are specifically connected to one another and to other regions of the brain. How newly generated neurons find their appropriate layer during the development of the brain is an important question; and, in humans, when this process goes awry, it can often result in seizures and mental retardation.

An enzyme called GSK-3 regulates several major signaling pathways important to brain development. The GSK-3 enzyme switches other proteins on or off by adding phosphate groups to them.

Morgan-Smith et al. set out to better understand the role of GSK-3 in brain development by deleting the genes for this enzyme specifically in the cerebral cortex of mice. Mice have two genes that encode slightly different forms of the GSK-3 enzyme. Deleting both of these in different groups of neurons during brain development revealed that a major group of neurons need GSK-3 in order to migrate to the correct layer. Specifically, the movement of neurons from where they arise in the central region of the brain to the outermost layer (a process called radial migration) was disrupted when the GSK-3 genes were deleted.

Morgan-Smith et al. further found that cortical neurons without GSK-3 were unable to develop the shape needed to undertake radial migration because they failed to switch from having many branches to having just two main branches. Additional experiments revealed that these abnormalities did not depend on certain signaling pathways, such as the Wnt-signaling pathway or the PI3K signaling pathway that can control GSK-3 activity.

Instead, Morgan-Smith et al. found that two proteins that are normally targeted by the GSK-3 enzyme have fewer phosphate groups than normal in the cortical neurons that did not contain the enzyme: both of these proteins regulate the shape of neurons by interacting with the molecular ‘scaffolding’ within the cell. The GSK-3 enzyme was already known to modify the activities of many other proteins that affect the migration of cells. Thus, the findings of Morgan-Smith et al. suggest that this enzyme may coordinate many of the mechanisms thought to underlie this process during brain development.

DOI:http://dx.doi.org/10.7554/eLife.02663.002

p66Shc deletion confers vascular protection in advanced atherosclerosis in hypercholesterolemic apolipoprotein E knockout mice

Previous studies showed that p66(Shc-/-) mice on a very-high-fat diet (HFD) had reduced oxidative stress, foam cell, and early atherosclerotic lesion formation. Here, the authors have used hypercholesterolemic apolipoprotein E (ApoE(-/-)) mice to investigate the role of p66Shc deletion in advanced atheroma. The authors generated mice deficient of both ApoE and p66Shc genes (ApoE(-/-) /p66(Shc-/-)). They used microsatellite polymerase chain reaction (PCR) analysis to analyze the genetic background and considered only animals with a constant percentages of C57B6L and 129SV background strands (it was obtained the 50.3% +/- 6.4% of C57B6L background). Computer-assisted analysis revealed that advanced atherosclerotic lesions in ApoE(-/-)/p66(Shc+/+) were significantly larger than those observed in ApoE(-/-)/p66(Shc-/-). Accordingly, the lipid-laden macrophage foam cells and oxidation-specific epitopes in ApoE(-/-)/p66(shc+/+) HFD-treated groups were higher than those observed in normal diet (ND)-treated groups. Thus, p66(Shc-/-) plays an important protective role also against advanced atherosclerotic lesion formation. Finally, the authors have used microarray to investigate major changes in gene expression in aortas of mice with ApoE(-/-)/p66(Shc-/-) background treated with a very HFD in comparison to ApoE(-/-)/p66(Shc+/+) (these data have been confirmed by by real-time PCR and immunohistochemistry). DAVID (Database for Annotation, Visualization and Integrated Discovery) analysis revealed that CD36 antigen (CD36), tissue inhibitor of metalloproteinase 2 (TIMP2), apolipoprotein E (ApoE), acetyl-coenzyme A acetyltransferase 1 (ACAT1), and thrombospondin 1 (THBS1) can be involved in p66 deletion-dependent vascular protection through the adipocytokine/lipid signaling pathway.

The development of cortical connections

The cortex receives its major sensory input from the thalamus via thalamocortical axons, and cortical neurons are interconnected in complex networks by corticocortical and callosal axons. Our understanding of the mechanisms generating the circuitry that confers functional properties on cortical neurons and networks, although poor, has been advanced significantly by recent research on the molecular mechanisms of thalamocortical axonal guidance and ordering. Here we review recent advances in knowledge of how thalamocortical axons are guided and how they maintain order during that process. Several studies have shown the importance in this process of guidance molecules including Eph receptors and ephrins, members of the Wnt signalling pathway and members of a novel planar cell polarity pathway. Signalling molecules and transcription factors expressed with graded concentrations across the cortex are important in establishing cortical maps of the topography of sensory surfaces. Neural activity, both spontaneous and evoked, plays a role in refining thalamocortical connections but recent work has indicated that neural activity is less important than was previously thought for the development of some early maps. A strategy used widely in the development of corticocortical and callosal connections is the early overproduction of projections followed by selection after contact with the target structure. Here we discuss recent work in primates indicating that elimination of juvenile projections is not a major mechanism in the development of pathways feeding information forward to higher levels of cortical processing, although its use is common to developing feedback pathways.

Expression of planar cell polarity genes during development of the mouse CNS

Atypical cadherin (Celsr3) and the receptor Frizzled3 (Fzd3) are crucial for the development of axonal tracts in the mouse CNS. Celsr3 and Fzd3 are orthologues of the Drosophila'planar cell polarity' (PCP) genes flamingo/starry night (fmi/stan) and frizzled, respectively. Reasoning that Celsr3 and Fzd3 might interact with PCP orthologues in mammals like they do in flies, we used mRNA in situ hybridization to compare the expression of Celsr3 and Fzd3 with that of dishevelled 1, 2 and 3 (Dvl1-3), van gogh-like 1 and 2 (Vangl1, 2), and prickle-like 1 and 2 (Prickle1, 2), during mouse CNS development, from embryonic day 10.5 to postnatal day 21. With the relative exception of Vangl1, all genes were expressed in the developing CNS. Although Celsr3- and Fzd3-deficient mice have similar phenotypes, Fzd3 expression was more widespread than that of Celsr3. Vangl2 and Dvl2 were preferentially expressed in ventricular zones, in keeping with their role during neural tube closure, where they could be partners of Celsr1. Dvl1 had a broad expression, reminiscent of that of Celsr2, and may be involved in neural maintenance. A large overlap in the expression territories of Dvl genes suggested redundancy. Vangl1 and Prickle1 had expression canvases different from each other and from other candidates, indicating unrelated function. Like Celsr3, Dvl3 and Prickle2 were expressed more strongly in postmitotic neurons than in precursors. Thus, the analogy between the PCP and Celsr3-Fzd3 genetic networks is limited, but may include Dvl3 and/or Prickle2.

Adipogenesis: usefulness of in vitro and in vivo experimental models

The use of experimental models is the foundation of experimental biology, so it is important to know how much the models can tell us about actual animals. Inconsistent or contradictory results from in vitro models are often associated with the perception that a particular model or results are somehow wrong and therefore cannot tell us anything important about how an animal works. In fact, in vitro conditions do not create new biology. Differences between in vitro and in vivo behavior can only result from the actual cellular repertoire, which provides a powerful tool to uncover new information. Adipose tissue research provides a useful context for examining this issue because the regulation of adipose growth and metabolism has important economic implications for livestock production. Examples are discussed in which either excess skepticism or narrow interpretation of results slowed progress toward our current understanding of adipose biology. Similarly, contemporary examples using genomics are used to suggest that large inconsistencies are still apparent with in vitro methods. Careful consideration of these inconsistencies may provide new insights.

Single-strand conformation polymorphism of sequence-tagged site markers based on partial sequences of cDNA clones in Cryptomeria japonica

Sixty-seven sequence-tagged site (STS) markers were identified from partial sequences of cDNA clones obtained from the inner bark of Cryptomeria japonica. Polymorphisms of the STSs were investigated for the parental clones of a mapping population, Haara and Kumotooshi, using both single-strand conformation polymorphism (SSCP) and sequencing analysis. Twenty-two STSs showed nucleotide differences between Haara and Kumotooshi, of which 19 STS differences were detectable under the electrophoresis conditions we used here. We also analyzed SSC-polymorphism in 10 additional clones derived from various Japanese regions to evaluate the usefulness of the STSs developed here among other populations of C. japonica. Twenty-five, about 40%, of the STSs showed polymorphism under selected electrophoresis conditions. The genotype segregation for 19 STSs was investigated among the Haara x Kumotooshi F(1) population, and these STS markers were mapped on a linkage map. SSCP analysis of STSs was efficient in terms of cost and time, and it allows detection of a sufficiently high proportion of polymorphisms to provide a convenient means for mapping of expressed sequences on a linkage map and for studying various aspects of population genetics.

Characterization of the murine Lbx2 promoter, identification of the human homologue, and evaluation as a candidate for Alström syndrome

The murine Lbx2 gene is a member of the ladybird family of homeobox genes, which is expressed in the developing urogenital system, eye, and brain. Using transgenic mice, we demonstrate that 9 kb of the 5' flanking region of mouse Lbx2 is able to direct expression of a reporter gene in a tissue-specific manner recapitulating the endogenous expression pattern. This regulatory region provides a novel reagent allowing for transgenic expression in the developing urogenital ridge. In addition, we describe the identification of the human homologue, LBX2. Comparison of the human LBX2 and mouse Lbx2 sequences upstream of the coding regions reveals sequence conservation suggesting conserved regulatory regions. Both the human LBX2 and the mouse Lbx2 genes have similar genomic structures and are composed of two exons separated by an intron. We mapped the mouse Lbx2 gene to 35 cM on chromosome 6 and the human LBX2 gene to a homologous region of chromosome 2p13. This is a candidate region for several inherited disorders, including Alström syndrome, a disorder that includes ocular, urogenital, and renal abnormalities. Given the expression pattern of Lbx2, the chromosomal location in humans, and the potential function of mammalian ladybird genes, we have begun to analyze patients with ocular disorders and those with Alström syndrome for mutations in LBX2. Although polymorphisms were identified, our results indicate that mutations in the coding region of LBX2 do not account for Alström syndrome in the six kindreds analyzed.

Murine Bv8 gene maps near a synteny breakpoint of mouse chromosome 6 and human 3p21

The genomic structure of the murine Bv8 gene was determined in 129/SvJ mouse, and the chromosomal localization was identified. Bv8 has first been characterized from skin secretion of the yellow-bellied toad, Bombina variegata. When injected into rat brain, this polypetide causes hyperalgesia. The murine Bv8 gene was shown to consist of four exons and was localized on chromosome 6 between the microsatellite markers D6Mit66 and D6Mit36 near the gene mem1, whereas the human counterpart was assigned to the non-syntenic region 3p21.1. Furthermore, the primary Bv8 transcript appeared to be alternatively spliced. The first variant contained all four exons yielding a product with a stretch highly enriched in basic amino acids in its central part. This domain is absent in the peptides from frog as well as in a splice variant expressed in mouse testis. A third variant gives rise to a truncated polypeptide.

Zebrafish genes for neuropeptide Y and peptide YY reveal origin by chromosome duplication from an ancestral gene linked to the homeobox cluster

Neuropeptide Y (NPY) and peptide YY (PYY) are related 36-amino acid peptides. NPY is widely distributed in the nervous system and has several physiological roles. PYY serves as an intestinal hormone as well as a neuropeptide. We report here cloning of the npy and pyy genes in zebrafish (Danio rerio). NPY differs at only one to four amino acid positions from NPY in other jawed vertebrates. Zebrafish PYY differs at three positions from PYY from other fishes and at 10 positions from mammals. In situ hybridization showed that neurons containing NPY mRNA have a widespread distribution in the brain, particularly in the telencephalon, optic tectum, and rhombencephalon. PYY mRNA was found mainly in brainstem neurons, as reported previously for vertebrates as divergent as the rat and the lamprey, suggesting an essential role for PYY in these neurons. PYY mRNA was observed also in the telencephalon. These results were confirmed by immunocytochemistry. As in the human, the npy gene is located adjacent to homeobox (hox) gene cluster A (copy a in zebrafish), whereas the pyy gene is located close to hoxBa. This suggests that npy and pyy arose from a common ancestral gene in a chromosomal duplication event that also involved the hox gene clusters. As zebrafish has seven hox clusters, it is possible that additional NPY family genes exist or have existed. Also, the NPY receptor system seems to be more complex in zebrafish than in mammals, with at least two receptor genes without known mammalian orthologues.

Expression of sox11 gene duplicates in zebrafish suggests the reciprocal loss of ancestral gene expression patterns in development

To investigate the role of sox genes in vertebrate development, we have isolated sox11 from zebrafish (Danio rerio). Two distinct classes of sox11-related cDNAs were identified, sox11a and sox11b. The predicted protein sequences shared 75% identity. In a gene phylogeny, both sox11a and sox11b cluster with human, mouse, chick, and Xenopus Sox11, indicating that zebrafish, like Xenopus, has two orthologues of tetrapod Sox11. The work reported here investigates the evolutionary origin of these two gene duplicates and the consequences of their duplication for development. The sox11a and sox11b genes map to linkage groups 17 and 20, respectively, together with other loci whose orthologues are syntenic with human SOX11, suggesting that during the fish lineage, a large chromosome region sharing conserved syntenies with mammals has become duplicated. Studies in mouse and chick have shown that Sox11 is expressed in the central nervous system during development. Expression patterns of zebrafish sox11a and sox11b confirm that they are expressed in the developing nervous system, including the forebrain, midbrain, hindbrain, eyes, and ears from an early stage. Other sites of expression include the fin buds and somites. The two sox genes, sox11a and sox11b, are expressed in both overlapping and distinct sites. Their expression patterns suggest that sox11a and sox11b may share the developmental domains of the single Sox11 gene present in mouse and chick. For example, zebrafish sox11a is expressed in the anterior somites, and zebrafish sox11b is expressed in the posterior somites, but the single Sox11 gene of mouse is expressed in all the somites. Thus, the zebrafish duplicate genes appear to have reciprocally lost expression domains present in the sox11 gene of the last common ancestor of tetrapods and zebrafish. This splitting of the roles of Sox11 between two paralogues suggests that regulatory elements governing the expression of the sox11 gene in the common ancestor of zebrafish and tetrapods may have been reciprocally mutated in the zebrafish gene duplicates. This is consistent with duplicate gene evolution via a duplication-degeneration-complementation process.

Cloning, tissue-specific expression, gene structure and chromosomal localization of human phosphatidylcholine transfer protein

Phosphatidylcholine transfer protein (PC-TP) is a cytosolic protein that catalyzes intermembrane transfer of phosphatidylcholines in vitro. We have cloned a cDNA encoding the human ortholog of PC-TP and have determined its tissue-specific expression as well as genomic organization. Radiation hybrid mapping localized the human gene, PCTP, to chromosome 17q21-22 and PCR-based single strand conformation polymorphism analysis of an interspecific backcross assigned mouse Pctp to the region of syntenic conservation on chromosome 11.

Coding sequence, genomic organization, and conserved chromosomal localization of the mouse gene Scn11a encoding the sodium channel NaN

Previous studies have shown that sodium channel alpha-subunit NaN is preferentially expressed in small-diameter sensory neurons of dorsal root ganglia and trigeminal ganglia. These neurons include high-threshold nociceptors that are involved in transduction of pain associated with tissue and nerve injury. In this study, we show that mouse NaN is a 1765-amino-acid peptide that is predicted to produce a current that is resistant to tetrodotoxin (TTX-R). Mouse and rat NaN are 80 and 89% identical at the nucleotide and amino acid levels, respectively. The Scn11a gene encoding this cDNA is organized into 24 exons. Unlike some alpha-subunits, Scn11a does not have an alternative exon 5 in domain I. Introns of the U2 and U12 spliceosome types are present at conserved positions relative to other members of this family. Scn11a is located on mouse chromosome 9, close to the two other TTX-R sodium channel genes, Scn5a and Scn10a. The human gene, SCN11A, was mapped to the conserved linkage group on chromosome 3p21-p24, close to human SCN5A and SCN10A. The colocalization of the three sodium channel genes supports a common lineage of the TTX-R sodium channels.

Neuropeptide Y receptor subtype with unique properties cloned in the zebrafish: the zYa receptor

Neuropeptide Y (NPY) belongs to a family of structurally related neuroendocrine peptides for which five different G-protein-coupled receptor subtypes have been cloned in mammals. To identify additional subtypes we have performed PCR with degenerate primers in different species. We describe here the cloning and pharmacological profile of a unique NPY receptor subtype in the zebrafish that has tentatively been called the zYa receptor. It has 46-50% amino acid identity to the mammalian Y1, Y4 and y6 receptors and the previously cloned zebrafish receptors zYb and zYc, and only about 27% to Y2 and Y5. The zYa receptor binds NPY and PYY from mammals as well as zebrafish with high affinities and has a K(d) of 28 pM for porcine (125)I-PYY. It has a unique binding profile displaying some features in common with each of the mammalian Y1, Y2 and Y5 receptors. In a microphysiometer assay the receptor responds with extracellular acidification. Chromosomal mapping in the zebrafish genome of zYa, zYb and zYc receptor genes indicates a possible orthologous relationship between zYc and mammalian y6, but identifies no obvious mammalian ortholog for zYa (zYb is a recent copy of zYc in the fish lineage). These results imply that previous studies of NPY in fishes, which have striven to interpret the effects within the framework of mammalian Y1, Y2, and Y5 receptors, need to be reevaluated. Thus, the sequence comparisons, pharmacological properties, and chromosomal localization suggest that the zYa receptor is a novel NPY receptor subtype which is likely to be present also in mammals.

Complete exon-intron organization and chromosomal location of the gene for mouse type XIII collagen (col13a1) and comparison with its human homologue

Recent findings indicate that type XIII collagen is a transmembrane protein with a short N-terminal sytocsolic domain, a single transmembrane domain and a large, mainly collagenous ectodomain. The complete exon-intron structure of the gene coding for the mouse alpha1(XIII) collagen chain, col13a1, has now been characterized from genomic clones spanning over 180 kilobases (kb) and shown to be approximately 135 kb in size and to contain 42 exons varying between 8 base pairs (bp), the shortest exon in the genes encoding the various collagens, and 836 bp. Nuclease S1 mapping and 5'RACE resulted in identification of multiple transcription initiation points in the mouse gene, ranging between 470 and 548 bp upstream from the initiation methionine. This is in good agreement with a recently identified human EST clone extending 537 bp upstream from the initiation methionine. The 836-bp first exon of the mouse gene covers both the long 5' untranslated region and also a 36-residue cytosolic portion, a 23-residue transmembrane domain, and 37 residues of the 60-residue non-collagenous ectodomain immediately adjacent to the plasma membrane. One striking feature of the exons encoding solely collagenous sequences is the abundance of 27-bp exons, half the ancestral 54-bp size characteristic of fibrillar collagen genes, while the others vary between 8 and 144 bp, including instances of 36-, 45- and 54-bp exons. Determination of approximately 2.6 kb of sequences upstream of the initiation methionine of both the mouse and human genes and the identification of a clone containing four exons and spanning a gap in the previously characterized human clones allowed detailed comparison of the two genes. The exon-intron structures were found to be completely conserved between the species, and both genes have their 5' untranslated region preceded by a highly homologous apparent promoter region of approximately 350 bp containing a modified TATAA motif and several GC boxes. The chromosomal location of the mouse gene was determined by SSCP and fluorescence in situ hybridization and found to be at chromosome 10, band 4, between markers D1OMit5 -2.3 +/- 1.6 cM -col13a1 - 3.4+/-1.9 cM - D1OMit15. This result indicates that the mouse type XIII collagen gene and its human counterpart are located in chromosomal segments with conserved syntenies (The GenBank accession numbers for the mouse gene are AF063666-AF063693. The new GenBank accession number for the 5' end of the human type XIII collagen gene is AF071009).

Structural organization and chromosomal localization of Hyal2, a gene encoding a lysosomal hyaluronidase

The human HYAL2 gene encodes a lysosomal hyaluronidase that is related to the testicular PH-20 hyaluronidase. Regions conserved in these proteins have been used to design PCR primers suitable for the isolation of a fragment of the murine Hyal2 gene. This fragment was used to isolate the Hyal2 cDNA from a cDNA library. The cloned cDNA has an open reading frame of 473 codons and a 3'-untranslated region of 302 bases plus a poly(A) tail. Using this cDNA, the corresponding genomic DNA was characterized from 129SVJ mice. The murine Hyal2 gene is approximately 3.5 kb, contains the coding sequence for the mRNA on four exons, and is localized on chromosome 9 between the microsatellite markers D9Mit183 and D9Mit17 near the genes for dystroglycan and transferrin. The gene is expressed ubiquitously, the sole exception being adult brain.

Gene mapping in zebrafish using single-strand conformation polymorphism analysis

To exploit fully the power of the zebrafish system as a model for vertebrate development, it will be necessary to develop efficient tools for genomic analysis. In this report we have tested whether single-strand conformation polymorphism analysis (SSCP) can be utilized for gene mapping in zebrafish. Over 100 primer pairs derived from noncoding regions of known genes and partially characterized cDNAs were analyzed, and a polymorphism frequency of approximately 50% was detected in zebrafish strains used for genetic mapping studies. A subset of these polymorphic cDNAs was localized on the zebrafish map. SSCP thus represents an efficient strategy for mapping transcribed sequences with a high resolution in the zebrafish genome, which will facilitate the integration of existing zebrafish framework maps, the generation of a zebrafish EST map, and the application of alternative gene localization strategies such as comparative mapping.

The cloche and spadetail genes differentially affect hematopoiesis and vasculogenesis

In vertebrates, hematopoietic and vascular progenitors develop from ventral mesoderm. The first primitive wave of hematopoiesis yields embryonic red blood cells, whereas progenitor cells of subsequent definitive waves form all hematopoietic cell lineages. In this report we examine the development of hematopoietic and vasculogenic cells in normal zebrafish and characterize defects in cloche and spadetail mutant embryos. The zebrafish homologs of lmo2, c-myb, fli1, flk1, and flt4 have been cloned and characterized in this study. Expression of these genes identifies embryonic regions that contain hematopoietic and vascular progenitor cells. The expression of c-myb also identifies definitive hematopoietic cells in the ventral wall of the dorsal aorta. Analysis of b316 mutant embryos that carry a deletion of the c-myb gene demonstrates that c-myb is not required for primitive erythropoiesis in zebrafish even though it is expressed in these cells. Both cloche and spadetail mutant embryos have defects in primitive hematopoiesis and definitive hematopoiesis. The cloche mutants also have significant decreases in vascular gene expression, whereas spadetail mutants expressed normal levels of these genes. These studies demonstrate that the molecular mechanisms that regulate hematopoiesis and vasculogenesis have been conserved throughout vertebrate evolution and the clo and spt genes are key regulators of these programs.

The mouse chondroadherin gene: characterization and chromosomal localization

The mouse chondroadherin gene was isolated from a cosmid genomic library by the use of a rat chondroadherin cDNA probe. Southern blot analysis of mouse genomic DNA revealed a simple pattern of hybridization indicating a single copy gene for chondroadherin. The mouse chondroadherin gene encompasses 4.1 kb and consists of four exons separated by one large intron of 1929 bp followed by two smaller introns of 247 and 225 bp, respectively. Most of the translated region, including the start codon and the main part of a leucine-rich region, is contained within the first exon. Two small exons of 164 and 146 bp encode the rest of the protein. Interestingly, 4 bases from the stop codon, in the 3'-UTR, a third intron is located. A putative promoter region of 669 bp was sequenced and shown to contain a potential TATAA-box signal 29 bp upstream of the transcription start site and several recognition sites for transcription factors. The exon/intron organization of the chondroadherin gene differs from those of the other known genes of the leucine-rich repeat (LRR) family in the extracellular matrix. Taken together with comparison of protein sequences of other members of the LRR family in the extracellular matrix, the data suggest that chondroadherin has evolved along a different pathway. The chondroadherin gene was mapped to mouse chromosome 11, near D11Mit14, by single-strand conformation polymorphism linkage analysis.

Expansion of the pig comparative map by expressed sequence tags (EST) mapping

We have used a PCR-based approach for the genetical and physical mapping of 34 transcripts isolated from a porcine small intestine cDNA library. All but one gene were regionally localized by using a somatic pig-rodent cell hybrid panel, and 12 genes were mapped by linkage analysis of single-stranded conformational polymorphisms developed in 3' untranslated regions of transcripts. For 20 of the transcripts, the human homolog has already been mapped. This study thus represents a significant contribution to the pig comparative map. Some important findings were that we could clarify the extent of a previously identified inversion event in a region of conserved synteny between SSC6q and HSA1p, that SSC14q does contain a region homologous to HSA1, a situation not clear from earlier ZOO-FISH studies, and that the homology between SSC17 and HSA20 includes the p-arm of HSA20.

Genetic mapping of 262 loci derived from expressed sequences in a murine interspecific cross using single-strand conformational polymorphism analysis

We have demonstrated previously that noncoding sequences of genes are a robust source of polymorphisms between mouse species when tested using single-strand conformation polymorphism (SSCP) analysis, and that these polymorphisms are useful for genetic mapping. In this report we demonstrate that presumptive 3'-untranslated region sequence obtained from expressed sequence tags (ESTs) can be analyzed in a similar fashion, and we have used this approach to map 262 loci using an interspecific backcross. These results demonstrate SSCP analysis of genes or ESTs is a simple and efficient means for the genetic localization of transcribed sequences, and is furthermore an approach that is applicable to any system for which there is sufficient sequence polymorphism.

cDNA cloning of a human dishevelled DVL-3 gene, mapping to 3q27, and expression in human breast and colon carcinomas

dishevelled (Dsh) is a member of the segment polarity gene family in Drosophila which plays an important role in the early developmental patterning processes. A human homologue of Dsh (DVL-1) has recently been described. Here, we report the cloning of a second human homologue of Dsh (called DVL-3) by cDNA library screening. The human DVL-3 gene encodes a predicted 716 amino acid protein which exhibits 98% amino acid identity with mouse Dvl-3 and 49% with Drosophila Dsh. DVL-3 was mapped to 3q27. The expression of DVL-3 mRNA was detected in 30 human cell lines and 2 primary cell cultures. DVL-3 mRNA was detected in normal human breast tissues (n = 4) and tumours (n = 25). Statistically, there was no difference in DVL-3 mRNA level between normal breast tissues and tumours. In human colorectal samples, DVL-3 was expressed equally in matched normal tissues, polyps and tumours. The data indicates that DVL-3 is widely expressed in human cells and supports the notion of a new developmental gene family for dishevelled which may have a widespread role in signal transduction.

Social interaction and sensorimotor gating abnormalities in mice lacking Dvl1

Mice completely deficient for Dvl1, one of three mouse homologs of the Drosophila segment polarity gene Dishevelled, were created by gene targeting. Dvl1-deficient mice are viable, fertile, and structurally normal. Surprisingly, these mice exhibited reduced social interaction, including differences in whisker trimming, deficits in nest-building, less huddling contact during home cage sleeping, and subordinate responses in a social dominance test. Sensorimotor gating was abnormal, as measured by deficits in prepulse inhibition of acoustic and tactile startle. Thus, Dvl1 mutants may provide a model for aspects of several human psychiatric disorders. These results are consistent with an interpretation that common genetic mechanisms underlie abnormal social behavior and sensorimotor gating deficits and implicate Dvl1 in processes underlying complex behaviors.

Sequence and chromosomal localization of the mouse brevican gene

Brevican is a brain-specific proteoglycan belonging to the aggrecan family. Phage clones containing the complete mouse brevican open reading frame of 2649 bp and the complete 3'-untranslated region of 341 bp were isolated from a mouse brain cDNA library, and cosmid clones containing the mouse brevican gene were isolated from a genomic library using a PCR-generated DNA fragment as probe. The obtained genomic sequence of 13,700 nucleotides revealed that the murine gene has a size of approximately 13 kb and contains the sequence of the mRNA for the secreted brevican isoform on 14 exons. The exon-intron structure reflected the structural organization of the multidomain protein brevican. No consensus TATA sequence was found upstream of the first exon, and RNase protection experiments revealed multiple transcriptional start sites for the brevican gene. The first part of the sequence of intron 8 corresponded to an alternative brevican cDNA, coding for a GPI-linked isoform. Single strand conformation polymorphism analysis mapped the brevican gene (Bcan) to chromosome 3 between the microsatellite markers D3Mit22 and D3Mit11.

Mapping of 22 expressed sequence tags isolated from a porcine small intestine cDNA library

Complementary DNA sequences were selected from a resource of tentatively identified clones from a porcine small intestine cDNA library. Forty PCR primer pairs were designed to amplify 101-309 base pairs of the 3' untranslated region of the genes. The PCR conditions were optimized by altering both formamide and magnesium concentrations on samples of pig, mouse, and hamster DNA. Twenty primer pairs that, under stringent conditions, were pig-specific and amplified the expected fragments were chosen for regional assignment in a pig/rodent hybrid cell panel. Furthermore, 22 primer pairs were chosen to amplify DNA from the parental animals of the PiGMaP shared reference families in order to detect possible polymorphisms. Primer pairs that generated polymorphisms were used for genetic mapping. A total of 22 porcine expressed sequence tags (ESTs) were cytogenetically or genetically mapped by this approach. Twelve of the mapped ESTs could be added to the human-porcine comparative map.

Molecular cloning and characterization of NKT, a gene product related to the organic cation transporter family that is almost exclusively expressed in the kidney

We have identified a gene product (NKT) encoding an apparently novel transcript that appears to be related to the organic ion transporter family and is expressed almost exclusively in the kidney. Analysis of the deduced 546-amino acid protein sequence indicates that NKT is a unique gene product which shares a similar transmembrane domain hydropathy profile as well as transporter-specific amino acid motifs with a variety of bacterial and mammalian nutrient transporters. Nevertheless, the overall homology of NKT to two recently cloned organic ion transport proteins (NLT and OCT-1) is significantly greater; together these three gene products may represent a new subgroup of transporters. The NKT was characterized further with respect to its tissue distribution and its expression during kidney development. A 2.5-kilobase transcript was found in kidney and at much lower levels in brain, but not in a number of other tissues. Studies on the embryonic kidney indicate that the NKT transcript is developmentally regulated with significant expression beginning at mouse gestational day 18 and rising just before birth, consistent with a role in differentiated kidney function. Moreover, in situ hybridization detected specific signals in mouse renal proximal tubules. NKT was mapped by linkage disequilibrium to mouse chromosome 19, the same site to which several mouse mutations localize, including that for osteochondrodystrophy (ocd). Although initial experiments in a Xenopus oocyte expression system failed to demonstrate transport of known substrates for OCT-1, the homology to OCT-1 and other transporters, along with the proximal tubule localization, raise the possibility that this gene may play a role in organic solute transport or drug elimination by the kidney.

Murine monocyte chemoattractant protein (MCP)-5: a novel CC chemokine that is a structural and functional homologue of human MCP-1

The chemokines are a large family of cytokines that control the recruitment of leukocytes in immune and inflammatory responses. We describe the isolation of a novel murine CC chemokine that, based on its biological and structural features, we have named monocyte chemoattractant protein (MCP)-5. MCP-5 mapped to the CC chemokine cluster on mouse chromosome 11 and was most closely related to human MCP-1 in structure (66% amino acid identity). Purified recombinant MCP-5 protein was a potent chemoattractant for peripheral blood monocytes, was only weakly active on eosinophils at high doses, and was inactive on neutrophils. MCP-5 induced a calcium flux in peripheral blood mononuclear cells, but not in purified murine eosinophils or neutrophils. Consistent with these results, MCP-5 induced a calcium flux in human embryonic kidney (HEK)-293 cells transfected with human and murine CCR2, a CC chemokine receptor expressed on monocytes. MCP-5 did not induce a calcium flux in HEK-293 cells transfected with CCR1, CCR3, or CCR5. Constitutive expression of MCP-5 mRNA was detected predominantly in lymph nodes, and its expression was markedly induced in macrophages activated in vitro and in vivo. Moreover, MCP-5 expression was up-regulated in the lungs of mice following aerosolized antigen challenge of sensitized mice, and during the host response to infection with Nippostrongylus brasiliensis. These data indicate that MCP-5 is a novel and potent monocyte active chemokine that is involved in allergic inflammation and the host response to pathogens.

Isolation and characterization of mouse dishevelled-3

The Drosophila dishevelled (dsh) segment polarity gene is required to establish cell fates specified by wingless/Wnt signal transduction during development. We have previously reported the cloning and characterization of a mouse homolog of dishevelled, Dvl1. Utilizing RT-PCR with degenerate primers, we isolated another member of the mouse Dishevelled (Dvl) gene family, Dvl3. The Dvl3 gene maps to mouse chromosome 16. The predicted amino acid sequence shares 64 and 62% identity to Dvl1 and Dvl2, respectively. The region of highest conservation between all three Dvl coding regions, at 97% identity, is noted at the PDZ domain (also termed the DHR domain or GLGF motif), a motif of 60 amino acids present in all dishevelled encoded proteins and first described in the Drosophila discs large (dlg) tumor suppressor gene. In adult mice, Dvl3 expression is widespread with highest levels exhibited in brain, ovary, and heart. In embryos, Dvl3 is expressed in every tissue between 7.5 and 9.5 days postcoitum, and by 10.5 days postcoitum highest expression was seen in the dorsal root ganglia, somites, limb buds, branchial arches, heart, gut and throughout the developing central nervous system.

Human homologue sequences to the Drosophila dishevelled segment-polarity gene are deleted in the DiGeorge syndrome

DiGeorge syndrome (DGS) is a developmental defect of some of the neural crest derivatives. Most DGS patients show haploinsufficiency due to interstitial deletions of the proximal long arm of chromosome 22. Deletions of 22q11 have also been reported with patients with the velocardio-facial syndrome and familial conotruncal heart defects. It has been suggested that the wide phenotype spectrum associated with 22q11 monosomy is a consequence of contiguous-gene deletions. We report the isolation of human cDNAs homologous to the Drosophila dishevelled (dsh) segment-polarity gene. Sequences homologous to the 3' UTR of these transcripts (DVL-22) were positioned within the DGS critical region and were found to be deleted in DGS patients. Human DVL mRNAs are expressed in several fetal and adult tissues, including the thymus and, at high levels, the heart. Two transcripts, 3.2 and 5kb, were detected, in northern blot analysis, with different expression patterns in the surveyed tissues when different cDNAs were used. The isolated cDNAs exhibit high amino acid homology with the mouse and Xenopus Dvl-1 gene, the only other vertebrate dsh homologues so far isolated. The pivotal role of dsh in fly development suggests an analogous key function in vertebrate embryogenesis of its homologue genes. Since DGS may be due to perturbation of differentiation mechanisms at decisive embryological stages, a Dsh-like gene in the small-region overlap (SRO) might be a candidate for the pathogenesis of this disorder.

The transmembrane tyrosine phosphatase DLAR controls motor axon guidance in Drosophila

DLAR is a receptor-like, transmembrane protein-tyrosine phosphatase in Drosophila that is expressed almost exclusively by developing neurons. Analysis of Dlar loss-of-function mutations shows that DLAR plays a key role during motoneuron growth cone guidance. Segmental nerve b (SNb) motor axons normally exit the common motor pathway, enter the ventral target region, and then synapse on specific ventral muscles. In Dlar mutant embryos, SNb axons bypass their normal target region and instead continue to extend along the common pathway. SNd motor axons also make pathfinding errors, while SNa and SNc axons appear normal. Thus, DLAR controls the ability of certain motor axons to navigate specific choices points in the developing Drosophila nervous system.

Organization and promoter analysis of the mouse dishevelled-1 gene

We have characterized the genomic organization of a mouse homolog (Dvl-1) of Drosophila dishevelled, a segment polarity gene required for wingless signal transduction. The Dvl-1 gene is organized into 15 exons ranging in size from 68 to 1315 bp spanning a region of 12,409 bp, with the largest and smallest intron being 5545 and 71 bp, respectively. Sequence analysis of the 5'-flanking region of the gene revealed a high GC content, six CCGCCC Sp-1-binding motifs, CREB, LBP-1 (leader-binding protein 1), and TGGCA-binding consensus sites. However, neither TATA or CAAT boxes are present, a characteristic shared by other GC-rich promoters. The 5'-flanking region has strong promoter activity when placed upstream of the luciferase gene. Promoter-luciferase constructs have demonstrated that the promoter is functional in transfection assays and that its activity is orientation dependent. Promoter deletions were used to define the 5' and 3' boundaries for promoter activity and revealed the presence of both positive and negative regulatory elements. Multiple transcription initiation sites were mapped by primer extension analysis and confirmed by reporter gene assay.

A high-resolution map of the brown (b, Tyrp1) deletion complex of mouse chromosome 4

For over 40 years germ-cell mutagenesis experiments have generated many new mutations at the brown (b or Tyrp1) locus on mouse Chromosome (Chr) 4. These mutations, many of which are deletions, were recovered by the specific-locus mutagenesis technique. Previous analysis of a panel of brown deletions, generated at Oak Ridge, has enabled both a preliminary molecular and a functional map around the locus to be generated. We have used a panel of hybrid DNA from 25 Oak Ridge deletions, where the deleted chromosome was heterozygous with a Mus spretus chromosome, to map polymorphic markers including microclones, microsatellites, and cloned DNA markers. We have generated a fine structure map, based on 25 new markers, of an 8.5-cM region surrounding the brown locus. This map will prove useful in future mapping studies of this region and in the isolation of the genes that lie within it.

Haplotype analysis of intra-specific backcross curly-tail mice confirms the localization of ct to chromosome 4

We have determined the order of a number of SSR and SSC polymorphic markers that map to distal mouse Chromosome (Chr) 4 and have used analysis of these markers in backcrosses designed to test the localization of the curly-tail (ct) mutation. We have confirmed that ct maps to this region, close to the locus D4Mit69. Our results also support the hypothesis that ct is a semidominant, rather than a recessive, mutation, since we have identified abnormal-tailed mice that are likely to be heterozygous at the ct locus. Finally, we examined Pax7 as a candidate gene for the ct mutation and found no evidence of protein sequence differences in ct compared with wild-type mice.

A high-resolution map of the chromosomal region surrounding the nude gene

The nude mutation produces the apparently disparate phenotypes of hairlessness and congenital thymic aplasia. These pleiotropic defects are the result of a single, autosomal recessive mutation that was previously mapped to a 9-cM region of murine chromosome 11 bounded by loci encoding the acetylcholine receptor beta subunit and myeloperoxidase. In this study, exclusion mapping of a panel of congenic nude strains was used to place the nude locus between the microsatellite loci D11Nds1 and D11Mit8. The relative distance from nude to each of these loci was determined by analyzing a large segregating cross. Thus, nude lies 1.4 cM distal to D11Nds1 and is 0.5 cM proximal to D11Mit8. Mice that carried recombinational breakpoints between D11Nds1 and D11Mit8 were further analyzed at the loci Evi-2 and D11Mit34, which placed nu 0.2 cM proximal to these markers. D11Nds1 and Evi-2/D11Mit34 thus define the new proximal and distal boundaries, respectively, for the nu interval. We also report the typing of the above microsatellite markers in the AKXD, AKXL, BXD, CXB, and BXH recombinant inbred strains, which confirmed the relative order and separation of loci in this region.

Genetic map of the region surrounding the retrovirus restriction locus, Fv1, on mouse chromosome 4

The Friend virus susceptibility-1 (Fv1) gene maps to mouse Chromosome (Chr) 4 close to a cluster of four endogenous murine leukemia viruses (MLVs). To investigate the feasibility of cloning Fv1 by a positional approach, we have performed an extensive genetic analysis of this region of Chr 4. We have typed 368 backcross mice for the four proviruses, Nppa, Lck, and D4Smh6b. Recombinant animals were screened in a hierarchical fashion with a variety of other markers, including Fv1 and the isozyme marker Gpd1. A detailed genetic map of the region surrounding Fv1 was derived. Three markers, Xmv9, Nppa, and Iap3rc11, were identified that showed no recombination with Fv1. By combining backcross and recombinant inbred strain data, we estimated that Xmv9 and Nppa must lie within 0.6 cM of one another and Fv1.

A genetic linkage map of the mouse using restriction landmark genomic scanning (RLGS)

We have developed a multiplex method of genome analysis, restriction landmark genomic scanning (RLGS) that has been used to construct genetic maps in mice. Restriction landmarks are end-labeled restriction fragments of genomic DNA that are separated by using high resolution, two-dimensional gel electrophoresis identifying as many as two thousand landmark loci in a single gel. Variation for several hundred of these loci has been identified between laboratory strains and between these strains and Mus spretus. The segregation of more than 1100 RLGS loci has been analyzed in recombinant inbred (RI) strains and in two separate interspecific genetic crosses. Genetic maps have been derived that link 1045 RLGS loci to reference loci on all of the autosomes and the X chromosome of the mouse genome. The RLGS method can be applied to genome analysis in many different organisms to identify genomic loci because it uses end-labeling of restriction landmarks rather than probe hybridization. Different combinations of restriction enzymes yield different sets of RLGS loci providing expanded power for genetic mapping.

Mapping of PCR-based markers for mouse chromosome 4 on a backcross penetrant for the misty (m) mutation

A genetic linkage map for mouse Chromosome (Chr) 4 (MMU 4) has been constructed with an intersubspecific backcross between the C57BL/KsJ strain homozygous for the misty (m) coat color locus and the inbred Mus musculus musculus Czech II strain. Several recently developed PCR-based simple sequence length polymorphism (SSLP) markers have been intercalated among gene-based markers including six anchor loci on mouse Chr 4 to assemble this map. Marker order and genetic distances are similar to the composite genetic linkage map compiled from crosses between a variety of other inbred and feral mouse strains. Transmission ratio distortion in favor of feral alleles is apparent for a region of distal MMU 4. In addition, the misty phenotype is more fully penetrant in the present backcross than in other reported interspecific and intersubspecific crosses. Backcrosses employing inbred Mus musculus musculus strains may allow reliable phenotyping and mapping of mouse mutations displaying complex phenotypes with incomplete and/or ambiguous penetrance on other feral genetic backgrounds.

Molecular genetics of the brown (b)-locus region of mouse chromosome 4. I. Origin and molecular mapping of radiation- and chemical-induced lethal brown deletions

Over a period of many years, germ-cell mutagenesis experiments using the mouse specific-locus test have generated numerous radiation- and chemical-induced alleles of the brown (b; Tyrp 1) locus in mouse chromosome 4. We describe here the origin, maintenance and initial molecular characterization of 28 b mutations that are prenatally lethal when homozygous. Each of these mutations is deleted for Tyrp 1 sequences, and each of 25 mutations tested further is deleted for at least one other locus defined by molecular clones previously found to be closely linked to b by interspecific backcross analysis. A panel of DNAs from mice carrying a lethal b mutation and a Mus spretus chromosome 4 was used in the fine structure mapping of these molecularly defined loci. The deletional nature of each of these prenatally lethal mutations is consistent with the hypothesis that the null phenotype at b has an effect only on the quality (color) of eumelanin produced in melanocytes. The resulting deletion map provides a framework on which to build future molecular-genetic and biological analyses of this region of mouse chromosome 4.

Arbitrarily primed PCR fingerprints resolved on SSCP gels

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Multifactorial inheritance of neural tube defects: localization of the major gene and recognition of modifiers in ct mutant mice

Neural tube defects (NTD) in humans have been considered to have a multifactorial aetiology, however the participating genes have not been identified. The curly-tail (ct) mutant mouse develops NTD that resemble the human malformations in location, pathology and associated abnormalities. Moreover, there appears to be multifactorial influence on the incidence of NTD in offspring of curly-tail mice. We now describe a linkage analysis that localizes the ct gene to distal chromosome 4 in mice. Further analysis using recombinant inbred strains demonstrates the presence of at least three modifier loci that influence the incidence of NTD. This study provides definitive evidence for multifactorial inheritance in a mouse model of human NTD.

CD19 maps to a region of conservation between human chromosome 16 and mouse chromosome 7

CD19 is a B lymphocyte cell surface protein expressed from the earliest stages of B lymphocyte development until their terminal differentiation into plasma cells. In this report the human CD19 gene (hCD19) was localized to band p11.2 on the proximal short arm of chromosome 16 by in situ hybridization to metaphase chromosomes, using hCD19 cDNA as probe. hCD19 gene localization was confirmed by polymerase chain reaction based analysis with hCD19-specific primers, using a panel of human/hamster somatic cell hybrid DNA as templates. The mouse CD19 gene (mCd19) was mapped to bands F3-F4 of chromosome 7 by in situ hybridization to metaphase chromosomes, using a mCD19 cDNA probe. Segregation analysis of nucleotide sequence polymorphisms in interspecific backcross progeny revealed linkage of mCd19 with hemoglobin beta (Hbb), Int-2, and H19, other loci previously mapped to the same region of mouse chromosome 7, confirming the localization of mCd19 to this region. The order of these loci was determined to be centromere--Hbb--mCd19--H19--Int-2--telomere. The genetic distances between the loci examined, calculated from the recombination frequencies, suggested that mCd19 was located centrally between Hbb and H19. This region of mouse chromosome 7 is homologous to the region of human chromosome 16 to which the hCD19 gene maps. Multiple genes with a lymphocyte-related function also map to this conserved region including genes encoding the IL-4 receptor, CD11a, CD11b, CD11c, CD43 (leukosialin), and protein kinase C beta polypeptide.

TAP1 alleles in insulin-dependent diabetes mellitus: a newly defined centromeric boundary of disease susceptibility

It has been previously demonstrated that individuals with certain DR alleles have an increased relative risk of developing insulin-dependent diabetes mellitus (IDDM). The disease association is even stronger with certain DQ alleles but there is little association with DP providing a boundary of disease association to the 430 kb between DQ and DP. The recently described TAP (transporter associated with antigen processing) genes have been mapped approximately midway between DP and DQ. Therefore, it was of interest to determine if any TAP alleles were associated with IDDM. In addition to the alleles of TAP1 that have been described, others were identified during this study. Diabetics and normal controls were screened for TAP1 using single-stranded conformational polymorphism and relative risk was determined. In the same population group we have studied extensively in the past, we found a higher association of a TAP1 allele with IDDM than with any single HLA-DP allele but the risk was lower than with HLA-DQB1*0302. These data provide new limits for IDDM susceptibility to the 190-kb interval between TAP1 and HLA-DQB1.