Fine mapping of Hyplip1 and the human homolog, a potential locus for FCHL

Familial combined hyperlipidemia (FCHL) is a common genetic dyslipidemia predisposing to premature coronary heart disease (CHD). We previously identified a locus for FCHL on human Chromosome (Chr) 1q21-q23 in 31 Finnish FCHL families. We also mapped a gene for combined hyperlipidemia (Hyplip1) to a potentially orthologous region of mouse Chr 3 in the HcB-19/Dem mouse model of FCHL. The human FCHL locus was, however, originally mapped about 5 Mb telomeric to the synteny border, the centromeric part of which is homologous to mouse Chr 3 and the telomeric part to mouse Chr 1. To further localize the human Hyplip1 homolog and estimate its distance from the peak linkage markers, we fine-mapped the Hyplip1 locus and defined the borders of the region of conserved synteny between human and mouse. This involved establishing a physical map of a bacterial artificial chromosome (BAC) contig across the Hyplip1 locus and hybridizing a set of BACs to both human and mouse chromosomes by fluorescence in situ hybridization (FISH). We narrowed the location of the mouse Hyplip1 gene to a 1.5-cM region that is homologous only with human 1q21 and within approximately 5–10 Mb of the peak marker for linkage to FCHL. FCHL is a complex disorder and this distance may, thus, reflect the well-known problems hampering the mapping of complex disorders. Further studies identifying and sequencing the Hyplip1 gene will show whether the same gene predisposes to hyperlipidemia in human and mouse. Received: 9 September 2000 / Accepted: 30 October 2000     

The linkage map of sheep Chromosome 6 compared with orthologous regions in other species

The genetic linkage map of sheep Chromosome (Chr) 6 has been extended to include 35 loci with the addition of 11 RFLP and 12 microsatellite loci. The sex-averaged linkage map now spans 154 cM from phosphodiesterase cyclic GMP beta polypeptide (PDE6B) to OarCP125, an anonymous sheep microsatellite. The male and female map lengths, at 180 cM and 132 cM respectively, did not differ significantly. The physical assignment of PDE6B to Chr 6q33-qter orientates the linkage map on sheep Chr 6 with PDE6B near the telomere and OarCP125 towards the centromere. The order and genetic distances between loci are similar for the sheep Chr 6 and cattle Chr 6 maps, except for the position of the casein genes. The sheep Chr 6 linkage map is also comparable to portions of human Chr 4, mouse Chrs 5 and 3, and pig Chr 8. The synteny between sheep Chr 6 and human Chr 4 has been extended from PDE6B (4p16.3) to epidermal growth factor (EGF, 4q25-q27). However, a region from platelet-derived growth factor receptor α polypeptide (PDGFRA) to bone morphogenetic protein 3 (BMP3), which spans 19 cM on sheep Chr 6, appears to be inverted with respect to the human and mouse loci. Other differences in the gene order between sheep, pig, and mouse suggest more complex rearrangements. Received: 16 August 1995 / Accepted: 12 December 1995     

Linkage of Agt and Actsk-1 to distal mouse Chromosome 8 loci: a new conserved linkage

Angiotensinogen is an ₂ involved in the maintenance of blood pressure and electrolyte balance. We have refined the position of the mouse angiotensinogen locus (Agt) on Chromosome (Chr) 8 and have also confirmed the assignment of the human angiotensinogen locus (AGT) to Chr 1. The segregation of several restriction fragment length variants (RFLVs) was followed in two interspecific backcross sets and in four recombinant inbred (RI) mouse sets. Analysis of the segregation patterns closely linked Agt to Aprt and Emv-2, which places the angiotensionogen locus on the distal end of mouse Chr 8. Additionally, a literature search has revealed that the strain distribution pattern (SDP) for the mouse skeletal -actin locus 1 (Actsk-1, previously Actal, Acta, or Acts) is nearly identical to the SDP for Agt in two RI sets. On the basis of this information we were able to reassign Actsk-1 to mouse Chr 8. By screening a panel of human-mouse somatic cell hybrids, we confirmed that the human angiotensioogen locus lies on Chr 1. This information describes a new region of conserved linkage homology between mouse Chr 8 and human Chr 1. It also defines the end of a large region of conserved linkage homology between mouse Chr 8 and human Chr 16.     

Neuropeptide Y Receptor Genes on Human Chromosome 4q31–q32 Map to Conserved Linkage Groups on Mouse Chromosomes 3 and 8

Npy1randNpy2r,the genes encoding mouse type 1 and type 2 neuropeptide Y receptors, have been mapped by interspecific backcross analysis. Previous studies have localized the human genes encoding these receptors to chromosome 4q31–q32. We have now assignedNpy1randNpy2rto conserved linkage groups on mouse Chr 8 and Chr 3, respectively, which correspond to the distal region of human chromosome 4q. Using yeast artificial chromosomes, we have estimated the distance between the human genes to be approximately 6 cM. Although ancient tandem duplication events may account for some closely spaced G-protein-coupled receptor genes, the large genetic distance between the human type 1 and type 2 neuropeptide Y receptor genes raises questions about whether this mechanism accounts for their proximity.     

Comparative mapping of mouse Chromosome 4 and human Chromosome 9: Lv,Orm, and Hxb are closely linked on mouse Chromosome 4

The genes for orosomucoid (ORM-1 and ORM-2), delta-aminolevulinate dehydratase (ALAD), and hexabrachion or tenascin (HXB) all map to the q31-qter region of human Chromosome (Chr) 9. The mouse homolog of each of these genes has been mapped to Chr 4, but hexabrachion has not previously been mapped by linkage analysis. We have now ordered Orm-1, Lv (the mouse homolog of ALAD), and Hxb in an interspecific backcross panel, by use of tyrosinase related protein-1, Tyrp-1, whose human homolog maps to 9p13-pter (Abbott et al., Genomics 1991) as a reference locus. No recombinants were identified in 124 animals between Lv and Orm-1. Hxb was found to be 1.6 cM distal to Lv and Orm-1, and 4.8 cM proximal to Tyrp-1, or b. These data therefore contribute to our knowledge of the conserved synteny between HSA 9q and MMU 4.     

Sequence-ready physical map of the mouse Chromosome 16 region with conserved synteny to the human Velocardiofacial syndrome region on 22q11.2

Proximal mouse Chromosome (Chr) 16 shows conserved synteny with human Chrs 16, 8, 22, and 3. The mouse Chr 16/human Chr 22 conserved synteny region includes the DiGeorge/Velocardiofacial syndrome region of human Chr 22q11.2. A physical map of the entire mouse Chr 16/human Chr 22 region of conserved synteny has been constructed to provide a substrate for gene discovery, genomic sequencing, and animal model development. A YAC contig was constructed that extends ca. 5.4 Mb from a region of conserved synteny with human Chr 8 at Prkdc through the region conserved with human Chr 3 at DVL3. Sixty-one markers including 37 genes are mapped with average marker spacing of 90 kb. Physical distance was determined across the 2.6-Mb region from D16Mit74 to Hira with YAC fragmentation. The central region from D16Jhu28 to Igl-C1 was converted into BAC and PAC clones, further refining the physical map and providing sequence-ready template. The gene content and borders of three blocks of conserved linkage between human Chr 22q11.2 mouse Chr 16 are refined. Received: 4 November 1998 / Accepted: 21 December 1998     

A brain L-type calcium channel alpha 1 subunit gene (CCHL1A2) maps to mouse chromosome 14 and human chromosome 3.

A rat brain cDNA probe was used to localize a gene encoding the alpha 1 subunit of neuronal dihydropyridine-sensitive L-type calcium channels in the mouse and human genomes. Hybridization of the probe to Southern blots made with DNAs from a Chinese hamster x mouse somatic cell hybrid panel indicated that this gene maps to mouse chromosome 14 (Chr 14). Southern blot analysis of an intersubspecies cross demonstrated that the calcium channel alpha 1 subunit gene, termed Cchl1a2, can be positioned 7.5 cM proximal to Np-1. Similarly, segregation among human X rodent somatic cell hybrids indicated that CCHL1A2 maps to human chromosome 3. These assignments are consistent with a region of linkage homology between human chromosome 3p and a proximal region of mouse Chr 14.     

Comparative mapping of human Chromosome 2 identifies segments of conserved synteny near the bovine mh locus

The ``double-muscling' (mh) locus has been localized to an interval between the centromere and the microsatellite marker TGLA44 on bovine Chromosome (Chr) 2 (BTA2). We identified segments of conserved synteny that correspond to this region of BTA2 by assigning large genomic clones containing bovine homologs of seven genes from the long arm of human Chr 2 (HSA2q). Polymorphic markers developed from these clones integrated the physical and linkage maps of BTA2 from 2q12 to 2q44 and extended genetic coverage towards the centromere. This comparative analysis suggests the mh locus resides on HSA2q near both the protein C and collagen type III alpha-1 genes. Overall, our data reveal a complex rearrangement of gene order between BTA2q12-44 and HSA2q14-37 that underscores the need to establish boundaries of conserved synteny when applying comparative mapping information to identify genes or traits of interest. Received: 3 March 1997 / Accepted: 12 May 1997     

Chromosomal locations of the mouse fatty acid oxidation genes Cpt1a, Cpt1b, Cpt2, Acadvl, and metabolically related Crat gene

Mitochondrial β-oxidation of long-chain fatty acids (LCFA) is essential for mammalian life. Because portions of this metabolic pathway are composed of enzymes that are coordinately regulated and share structural and functional similarities, we evaluated five of these enzyme genes for possible chromosomal linkages. Regulation of LCFA catabolism influences cell signal pathways and apoptosis, as well as energy production from LCFA. Partial cDNA fragments of the mouse mitochondrial proteins carnitine acetyltransferase (Crat), very-long-chain acyl coenzyme A dehydrogenase (Acadvl), the liver and muscle isoforms of carnitine acyltransferase I (Cpt1a and Cpt1b respectively), and a genomic PCR product of mitochondrial protein carnitine acyltransferase II (Cpt2) were used in a previously established mapping panel to determine their chromosomal locations. No pseudogenes were detected for any of the genes in Mus musculus, and all of the genes mapped to different chromosome locations, including the tissue-specific isoforms of carnitine palmitoyltransferase. Crat mapped to Chromosome (Chr) 2, at a position approximately 18 cM from the centromere and 2 cM proximal to the gene Ass1. Acadvl mapped to the middle of Chr 11, 8.3 cM distal to Il4 and 2.8 cM proximal to Mpmv2. Cpt1a mapped to the centromeric region of Chr 19, 8.7 cM proximal to Pomc-ps1. Cpt1b mapped to Chr 15, 4.9 distal to Gpt1 and 3.5 cM proximal to Wnt1. Cpt2 mapped to Chr 4 near the locus Pmv19. Received: 29 January 1998 / Accepted: 25 March 1998     

Gene homologs on human chromosome 15q21-q26 and a chicken microchromosome identify a new conserved segment

The genes for insulin-like growth factor 1 receptor (IGF1R), aggrecan (AGC1), β₂-microglobulin (B2M), and an H6-related gene have been mapped to a single chicken microchromosome by genetic linkage analysis. In addition, a second H6-related gene was mapped to chicken macrochromosome 3. The Igf1r and Agc1 loci are syntenic on mouse Chr 7, together with Hmx3, an H6-like locus. This suggests that the H6-related locus, which maps to the chicken microchromosome in this study, is the homolog of mouse Hmx3. The IGF1R, AGC1, and B2M loci are located on human Chr 15, probably in the same order as found for this chicken microchromosome. This conserved segment, however, is not entirely conserved in the mouse and is split between Chr 7 (Igf1r-Agc) and 2 (B2m). This comparison also predicts that the HMX3 locus may map to the short arm of human Chr 15. The conserved segment defined by the IGF1R–AGC1–HMX3—B2M loci is approximately 21–35 Mb in length and probably covers the entire chicken microchromosome. These results suggest that a segment of human Chr 15 has been conserved as a chicken microchromosome. The significance of this result is discussed with reference to the evolution of the avian and mammalian genomes. Received: 7 December 1996 / Accepted: 7 February 1997     

Chromosomal Localization of the Human and Mouse Hyaluronan Synthase Genes

We have recently identified a new vertebrate gene family encoding putative hyaluronan (HA) synthases. Three highly conserved related genes have been identified, designatedHAS1, HAS2,andHAS3in humans andHas1, Has2,andHas3in the mouse. All three genes encode predicted plasma membrane proteins with multiple transmembrane domains and approximately 25% amino acid sequence identity to theStreptococcus pyogenesHA synthase, HasA. Furthermore, expression of any oneHASgene in transfected mammalian cells leads to high levels of HA biosynthesis. We now report the chromosomal localization of the threeHASgenes in human and in mouse. The genes localized to three different positions within both the human and the mouse genomes.HAS1was localized to the human chromosome 19q13.3–q13.4 boundary andHas1to mouse Chr 17.HAS2was localized to human chromosome 8q24.12 andHas2to mouse Chr 15.HAS3was localized to human chromosome 16q22.1 andHas3to mouse Chr 8. The map position forHAS1reinforces the recently reported relationship between a small region of human chromosome 19q and proximal mouse chromosome 17.HAS2mapped outside the predicted critical region delineated for the Langer–Giedion syndrome and can thus be excluded as a candidate gene for this genetic syndrome.     

Localization of the IGHG,PRKACB, and TNP2 genes in pigs by in situ hybridization

The porcine genes encoding the immunoglobulin gamma heavy chain (IGHG), cAMP-dependent protein kinase catalytic beta subunit (PRKACB), and transition protein 2 (TNP2) were mapped to Chromosomes (Chrs) 7 q25–q26, 6q31–q33, and 3p13-cent, respectively, by in situ hybridization. Localization of the IGHG gene confirms the assignment of linkage group III to Chr 7. Our results show that the IGHG locus in pigs, similar to the situation in other mammalian species, viz. humans, mouse, cattle, and river buffaloes, is located on the terminal region of the chromosome. The assignment of the PRKACB gene extends the homology observed between porcine Chr 6q and human Chr 1p. Mapping of the TNP2 gene provides the first marker assigned to the p arm of Chr 3 in pigs. The present study contributes to the development of the physical gene map in pigs and also bears significance in terms of comparative gene mapping.     

Genetic and physical mapping of the natural resistance-associated macrophage protein 1 (NRAMP1) in chicken

The chicken natural resistance-associated macrophage protein 1 (NRAMP1) gene has been mapped by linkage analysis by use of a reference panel to develop the chicken molecular genetic linkage map and by fluorescence in situ hybridization. The chicken homolog of the murine Nramp1 gene was mapped to a linkage group located on Chromosome (Chr) 7q13, which includes three genes (CD28, NDUSF1, and EF1B) that have previously been mapped either to mouse Chr 1 or to human Chr 2q. Physical mapping by pulsed-field gel electrophoresis revealed that NRAMP1 is tightly linked to the villin gene and that the genomic organization (gene order and presence of CpG islands) of the chromosomal region carrying NRAMP1 is well conserved between the chicken and mammalian genomes. The regions on mouse Chr 1, human Chr 2q, and chicken Chr 7q that encompass NRAMP1 represent large conserved chromosomal segments between the mammalian and avian genomes. The chromosome mapping of the chicken NRAMP1 gene is a first step in determining its possible role in differential susceptibility to salmonellosis in this species.     

Chromosomal localization of murine interleukin-1 alpha and beta genes

DNA analyses of mouse X Chinese hamster somatic cell hybrids and of recombinant inbred mouse strains have previously shown that the interleukin-1 alpha and beta genes are tightly linked on murine chromosome 2, approximately 4.7 cM distal to beta-2-microglobulin. In this study, using in situ chromosome hybridization, we show that the two interleukin-1 genes are located in the F region of murine chromosome 2 and discuss this physical map position in relation to conserved genetic linkage groups.     

Chromosome assignment of four plexin A genes (Plxna1, Plxna2, Plxna3, Plxna4) in mouse, rat, Syrian hamster and Chinese hamster

We determined chromosome locations of four plexin A subfamily genes, Plxna1, Plxna2, Plxna3 and Plxna4, in four rodent species, mouse, rat, Syrian hamster and Chinese hamster, by fluorescence in situ hybridization. Plxna1, Plxna2, Plxna3 and Plxna4 were localized to Chr 6E2, 1H6, XB-C1 and 6B1 in mouse, Chr 4q34.1, 13q26-->q27, Xq37.1-->q37.2 and 4q21.3-->q22 in rat, Chr 8qb1.1-->qb1.3, 11qb8, Xpb8 and 5qb3.3 in Syrian hamster, and Chr 8q1.2, 5q3.7, Xp2.7 and 1q2.2-->q2.3 in Chinese hamster, respectively. All the mouse and rat plexin A genes were localized to chromosome regions where conserved homology has been identified among human, mouse and rat.     

Genomic structure and chromosomal localization of the mouse gene Punc

The mouse gene Punc encodes a member of the immunoglobulin superfamily of cell surface proteins. It is highly expressed in the developing embryo in nervous system and limb buds. At mid-gestation, however, expression levels of Punc decrease sharply. To allow investigation of such a regulatory mechanism, the genomic locus encompassing the Punc gene was cloned, characterized, and mapped. Fluorescent in situ hybridization was used to determine the chromosomal location of the Punc gene of mouse and human. Mouse Punc maps to Chromosome (Chr) 9 in the region D-E1, whereas the human PUNC gene is localized to Chr 15 at 15q22.3-23, a region known to be syntenic to mouse 9D-E1. The human PUNC gene therefore maps close to a genetic locus that is linked to Bardet-Biedl Syndrome, an autosomal recessive human disorder. Confirmation for the location of human PUNC was obtained through sequence relationships between mouse Punc cDNA, human PUNC cDNA, genomic sequence upstream of the murine Punc gene, and human STS markers that had been previously mapped on Chr 15. The STS sequence WI-14920 is in fact derived from the 3′-untranslated region of the human PUNC gene. WI-14920 had been placed at 228cR from the top of the Chr 15 linkage group, which provided positional information for the human PUNC gene at high resolution. Thus, this study identifies PUNC as the gene corresponding to a previously anonymous marker and serves as a basis to investigate its role in genetic disorders. Received: 8 July 1998 / Accepted: 14 October 1998     

Chromosomal localization of opioid peptide and receptor genes in the mouse

Opiate receptors are the primary targets for the drugs of abuse morphine and heroin. In this study, we completed the localization on mouse chromosomes of the genes encoding mu (Oprm) and kappa (Oprk) receptors, as well as the genes for the opioid propeptides proenkephalin (Penk) and prodynorphin (Pdyn). The genetic mapping was performed using a panel of DNA samples from an interspecific cross [C3H/HeJ-gld and (C3H/HeJ-gld x Mus spretus)Fi] that has been characterized for more than 800 markers throughout the genome. The genes are localized on mouse Chr 1 (Oprk, 10 cM from the centromere), Chr 2 (Pdyn, 75 cM from the centromere), Chr 4 (Penk, 1 cM from the centromere) and Chr 10 (Oprm, 10 cM from the centromere). Interestingly, the gene for the mu receptor is located in the same region as a Quantitative Trait Locus for high morphine consumption, thus raising the possibility of its direct role in drug abuse mechanisms.