Comparative map for mice and humans

An Exploratory Investigation of Genetic Linkage with Body Composition and Fatness Phenotypes: The Québec Family Study

In the present investigation, we have attempted to identify regions of the genome in which "obesity genes" potentially reside using robust sib-pair linkage analysis. Data were collected on 1,628 individuals in 301 nuclear families residing in the environs of Québec City during the period 1978-1981. In addition to traditional blood group antigens and enzyme polymorphisms, several phenotypes in the obesity domain that are associated with increased morbidity were assessed, including measures relating to heaviness (i.e., the body mass index), body composition and nutrient partitioning (i.e., % body fat), and regional fat distribution without and with standardization for total fat mass (i.e., the sum of six skinfold thicknesses, and the ratio of the sums of trunk to extremity skinfold thicknesses). Three consistent patterns of potential linkage relationships with obesity phenotypes were revealed in these data, involving the marker loci adenosine deaminase, the Kell blood group antigen, and esterase D, which identify chromosomal regions 20q13, 7q33, and 13q14, respectively. Other potential linkages also were identified in the short arm of chromosome 1, interesting because of the presence of the db and fa loci on homologous regions of chromosome 1 in mouse and rat models of obesity, respectively. Each of the tentative linkage relationships reported here warrant follow-up using alternative methods and require replication in independent studies.

Human-mouse comparative maps

Homology relationships between human and mouse genomes are very useful for identifying human or mouse homologs of disease traits that have been mapped in the other species. Conservation of genomic organization in human and mouse has long been recognized; however, detailed systematic examination of these relationships on a genome-wide scale has only recently become possible. This appendix presents tables of comparative genetic maps with homology groups for human and mouse chromosomes, sorted by human position. The map locations of 1416 loci (many of which are genes) have been determined, and at least 181 different conserved linkage groups have been defined. Human loci are arranged from the most telomeric marker on the long (q) arm to the most telomeric marker on the short (p) arm of the human chromosome.

Examination of sequence homology between human chromosome 20 and the mouse genome: intense conservation of many genomic elements

The conservation of genomic organization of mammalian species has been of interest for its usefulness in characterizing the genetics of traits and diseases and as one tool for examining evolution. The recent rough draft sequencing of the mouse and human genomes provides the opportunity for more detailed analyses. The current study examines the extent of homology between human chromosome 20 and the mouse genome by comparing putative coding and non-coding sequence to provide insight into organizational and sequence similarities between the species. The relative position of each of 460 putative coding orthologues was the same in both species, except for a single genomic segment rearrangement. The similarity extended to exon/intron structure, the size of introns, as well as strong evidence for the conservation of position of ancient LINE-1, LINE-2 and LTR repetitive sequence and the subtelomeric region of the long arm of human chromosome 20 and that of mouse chromosome 2. There was also evidence for conservation of a limited amount of non-coding single-copy sequence. Together these data provide additional insight into the extent of conservation of mammalian genomic organization and sequence.

Estrogen and progesterone receptors in murine models of systemic lupus erythematosus

Estrogens are believed to play a role in the etiology of both human and murine systemic lupus erythematosus (lupus; SLE), presumably through the agency of their cellular receptor proteins. There is now considerable interest in the molecular mechanism of action of estrogens in immune tissues, particularly with regard to autoimmune disorders, which are generally more prevalent in women. In this laboratory, an attempt is being made to characterize estrogen receptors in murine models of SLE and to try and relate this to estrogen receptor function in vivo. The initial aim was to compare binding properties of estrogen receptors in brain, reproductive and immune tissues of BALB/c and MRL/MP-lpr/lpr mice. The latter strain spontaneously develops an autoimmune disease resembling human systemic lupus erythematosus (lupus; SLE). It is hypothesized that estradiol, through its receptors, mediates the progression of murine SLE, and that in autoimmune disease, the estrogen receptor is functionally and/or structurally changed. Initial studies suggest that there are differences in estrogen receptors between BALB/c mice, which do not get autoimmune disease, and two strains that do, MRL/MP-lpr/lpr and NZB/W mice. In MRL mice, these differences may be reflected in impaired priming of the progesterone receptor.

Lupus: why women?

Estrogens are believed to play a role in the etiology of both human and murine systemic lupus erythematosus (lupus, SLE), presumably through the agency of their cellular receptor proteins. There is now considerable interest in the molecular mechanism of action of estrogens in immune tissues, particularly with regard to autoimmune disorders, which are generally more prevalent in women. In this laboratory, an attempt is being made to characterize estrogen receptors in murine models of SLE, namely NZB/W and MRL/MP-lpr/lpr mice, and to try to relate this to estrogen receptor function in vivo. It is hypothesized that estradiol (E(2)), through its receptors, mediates the progression of murine SLE and that in autoimmune disease, the estrogen receptor is functionally or structurally changed, or both. Initial studies suggest there are differences in estrogen receptors between BALB/c mice, which do not get autoimmune disease, and two strains that do, MRL/MP-lpr/lpr and NZB/W mice. There is evidence that in at least one model of SLE, the normal regulation of estrogen action by progesterone may be impaired. In several laboratories, attempts are being made to relate estrogen action to immune function and to autoimmune diseases. The study of estrogen action on the immune system may lead to the development of treatments that attenuate the immunostimulant effects of E(2) in autoimmune diseases such as SLE.

Genomic organization of the human kallikrein gene family on chromosome 19q13.3-q13.4

Kallikreins are a subgroup of serine proteases with diverse physiological functions. Recently, growing evidence indicates that many kallikrein genes are involved in malignancy. In rodents, kallikreins are encoded by a large multigene family, but in humans only three kallikreins were thought to exist. Based on the homology between the human and rodent kallikrein loci, we studied a 300 kb region of genomic sequences around the putative KLK1 gene locus on chromosome 19q13.3-q13.4. By using linear sequence information, restriction analysis, end sequencing, PCR and blotting techniques, as well as bioinformatic approaches, we were able to construct the first detailed map of the human kallikrein gene family. Comparative analysis of genes located in this area, provides strong evidence that the human kallikrein gene family locus on chromosome 19 is considerably larger than previously thought, containing at least fifteen genes. We have established, for the first time, the common structural features that apply to all members of the expanded kallikrein multigene family. Our map specifies the distance between genes to one base pair accuracy, the relative location, and the direction of transcription of all 15 genes. Determination of the true size of the kallikrein family in humans is important for our understanding of the contribution of the kallikreins to human biology and pathophysiology.

Strain differences in binding properties of estrogen receptors in immature and adult BALB/c and MRL/MP-lpr/lpr mice, a model of systemic lupus erythematosus

The aim was to compare binding properties of estrogen receptors in brain, reproductive and immune tissues of immature and adult female BALB/c mice, and in the same tissues of MRL/MP-lpr/lpr mice. The latter strain spontaneously develops an autoimmune disease resembling human systemic lupus erythematosus (lupus; SLE). It is hypothesized that estradiol, through its receptors, mediates the progression of murine SLE. High-speed cytosols were prepared from hypothalamus, spleen, thymus and uterus of both strains, and incubated with the synthetic estrogen (3)H-moxestrol (NEN). Scatchard plots were derived from binding isotherms obtained after in vitro incubation. In addition, cervical lymph nodes from MRL mice could be used, but were too small in BALB/c mice. There was a significant increase in the affinity of the binding reaction i.e. a decrease in the apparent molar dissociation constant (Kd), in immune tissues and uterus with maturation in MRL but not BALB/c mice, whose tissues had, overall, a lower affinity for (3)H-moxestrol. Receptor concentrations were significantly higher in spleen and cervical lymph nodes of adult compared with immature MRL mice, but the opposite pattern was observed in BALB/c mouse spleen on maturation. These properties of estrogen receptors in MRL mice may underlie estrogen-mediated exacerbation of murine SLE.

Preweanling sensorial and motor development in laboratory mice: quantitative trait loci mapping

Chromosomal mapping of genes linked with 19 measures of sensorial, motor, and body weight development were investigated. Chromosomal mapping is the first step towards gene identification. When a genomic region is shown to be linked to a trait, it is possible to select a reduced number of candidate genes that have been previously mapped on this region. The involvement of every gene can be individually tested either by molecular (transgenesis, homologous recombination) or traditional methods (congenicity). Mapping was performed using 389 males and females from two inbred strains of laboratory mice C57BL/6By and NZB/BlNJ, their reciprocal F1s and F2s. Thirty-six Quantitative Trait Loci (QTL) were mapped, 12 reached the 3.13 lod score, being thus considered as confirmed. These QTL were tentatively labeled: Cliff Drop Aversion (Cliff Qtl), Geotaxia (Geot Qtl), Vertical Clinging (VertCling Qtl), Bar Holding with the 4 paws (BH4P Qtl), Age at Eyelid Opening (Aeyo Qtl), Visual Placing (Vispl Qtl), Startle Response (Start Qtl1, Start Qtl2), Body Weight at Day 10 in Males pooled with Females (Bwefmd10 Qtl), and Body Weight at Day 30 in males (Bwemd30 Qtl). For the majority of the developmental measures, the QTL that were mapped contributed little to the phenotypic variance, even when mitochondrial DNA contribution was included: Righting Response (12.7%), Cliff Drop Aversion (10%), Crossed Extensor Response (18.1%), Geotaxia (16.2%), Bar Holding Response for 10 s (12.1%), Bar Holding Response with 4 paws (8.1%), Vertical Clinging (9.3%), Vertical Climbing (5%), Startle Response (21.2%), Eyelid Opening (14.6%), Visual Placing (22%), Body Weight at Day 10 (27%), Body Weight at Day 15 in Females (52.5%), Body Weight at Day 15 in Males (17%), Body Weight at Day 30 in Females (42%), and Body Weight at Day 30 in Males (48%). A factorial analysis of the correlations between the measures of development did not provide evidence of a general factor. A general genetic factor of development was also rejected because few common genetic correlates were discovered for the 19 measures of development (Body Weight at Days 15 and 30 in Females on Chromosome 2, Eyelid Opening and Body Weight at Day 10 on Chromosome 5 and mitochondrial genome for five measures). Co-identification of genes, the function of which were previously known thanks to newly discovered QTL, should help to explain the function of QTL. Present data help to highlight candidate regions including several genes that could be candidates for the QTL function. Large confidence intervals were obtained as usual from the F2 intercrossed population. More stringent methods are suggested for more efficient co-identification.

Quantitative trait loci implicated in corpus callosum midsagittal area in mice

The midsagittal area of the corpus callosum expressed as the percentage of the hemispheric surface is smaller in the NZB/BlNJ than in the C57BL/6By inbred strain of mice. We performed a QTL mapping analysis using 284 F2s. Two loci linked to this measure were found: the CCrSQTL1 and CCrSQTL2 at 87 and 67 centiMorgans from the centromere on chromosomes 1 and 4 respectively. The two loci interacted significantly. The total source of genetic variation contributed to 25% of the observed variance.

Sex-determining genes on mouse autosomes identified by linkage analysis of C57BL/6J-YPOS sex reversal

A powerful approach for identifying mammalian primary (gonadal) sex determination genes is the molecular genetic analyses of sex reversal conditions (that is, XX individuals with testicular tissue and XY individuals with ovarian tissue). Here we determined the number and chromosomal location of autosomal and X-linked genes that cause sex reversal in C57BL/6J (B6) mice carrying a Y chromosome of Mus domesticus poschiavinus origin (YPOS). B6 XYPOS mice develop either as females with exclusively ovarian tissue or as true hermaphrodites with ovarian and testicular tissue. In contrast, the YPOS chromosome is fully masculinizing on most other inbred strain backgrounds. B6-YPOS sex reversal appears to result from the incompatibility of the Sry (sex determining region, Y chromosome) allele carried on the YPOS chromosome with B6-derived autosomal or X-linked loci. We found strong evidence for the location of one gene, designated tda1 (testis-determining, autosomal 1), at the distal end of Chromosome (Chr) 4 and a second gene, tda2, in the central region of Chr 2. A third gene, tda3, on Chr 5 is implicated, but the evidence here is not as strong. We suggest that B6 alleles at these loci predispose XYPOS fetuses to ovarian tissue development, but no single locus or combination of loci is necessary and sufficient to cause sex reversal. The TDA proteins may regulate Sry expression or form complexes with the SRY protein to regulate other genes, or the tda genes may be activated or repressed by the SRY protein.

Genomic instability in 1p and human malignancies

Both cytogenetic and molecular genetic approaches have unveiled non-random genomic alterations in 1p associated with a number of human malignancies. These have been interpreted to suggest the existence of cancer-related genes in 1p. Earlier studies had employed chromosome analysis or used molecular probes mapped by in situ hybridization. Further, studies of the various tumor types often involved different molecular probes that had been mapped by different technical approaches, like linkage analysis, radioactive or fluorescence in situ hybridization, or by employing a panel of mouse x human radiation reduced somatic cell hybrids. The lack of maps fully integrating all loci has complicated the generation of a comparative and coherent picture of 1p damage in human malignancies even among different studies on the same tumor type. Only recently has the availability of genetically mapped, highly polymorphic loci at (CA)n repeats with sufficient linear density made it possible to scan genomic regions in different types of tumors readily by polymerase chain reaction (PCR) with a standard set of molecular probes. This paper aims at presenting an up-to-date picture of the association of 1p alterations with different human cancers and compiles the corresponding literature. From this it will emerge that the pattern of alterations in individual tumor types can be complex and that a stringent molecular and functional definition of the role that Ip alterations might have in tumorigenesis will require a more detailed analysis of the genomic regions involved.

Mapping of the calcium-sensing receptor gene (CASR) to human chromosome 3q13.3-21 by fluorescence in situ hybridization, and localization to rat chromosome 11 and mouse chromosome 16

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

Homologs of Drosophila Fushi-Tarazu factor 1 map to mouse chromosome 2 and human chromosome 9q33

SF-1, a nuclear receptor that regulates gene expression of the cytochrome P450 steroid hydroxylases, and ELP, an embryonal protein that suppresses expression of the Moloney murine leukemia virus LTR, are isoforms transcribed from the same gene by alternative promoter usage and splicing. This gene is the mammalian homolog of the Drosophila fushi-tarazu factor 1 (FTZ-F1) gene. We have mapped the mouse gene Ftzf1 to the proximal quarter of Chr 2 by a linkage analysis using interspecific backcross mice, and its human homolog FTZ1 to Chr 9q33 by fluorescence in situ hybridization. The mouse and human genes are located in the homologous regions of mouse Chr 2 and human Chr 9, respectively.

Sequence, expression, and chromosomal assignment of a human sperm outer dense fiber gene

Outer dense fibers (ODFs) are located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail and may help to maintain the passive elastic structures and elastic recoil of the sperm tail. We have identified and describe here a human gene that is homologous to the Mst(3)CGP gene family of Drosophila melanogaster and encodes an ODF protein of 241 amino acids. The transcribed region has a size of approximately 1 kb and contains two exons of 416 bp and 406 bp, respectively, not including the 3' untranslated region. The gene is expressed in testis but not in human spleen, kidney, or brain and resembles in this respect the expression of the Drosophila Mst(3)CGP gene family in the male germline. An antiserum raised against a synthetic peptide derived from the N-terminus of the encoded sequence identified a protein of approximately 32 kDa in an extract of human sperm flagella. By Southern-blot analyses and in situ hybridization, the ODF gene was localized to band q22 of chromosome 8. The isolation of a human gene encoding a sperm tail protein may provide the ability to identify and investigate, on the molecular level, possible reasons for human male infertility that are dependent on flagellar disturbances.

Chromosomal localization of glutamate receptor genes: relationship to familial amyotrophic lateral sclerosis and other neurological disorders of mice and humans

Receptors for the major excitatory neurotransmitter glutamate may play key roles in neurodegeneration. The mouse Glur-5 gene maps to chromosome 16 between App and Sod-1. The homologous human GLUR5 gene maps to the corresponding region of human chromosome 21, which contains the locus for familial amyotrophic lateral sclerosis. This location, and other features, render GLUR5 a possible candidate gene for familial amyotrophic lateral sclerosis. In addition, dosage imbalance of GLUR5 may have a role in the trisomy 21 (Down syndrome). Further characterization of the murine glutamate receptor family includes mapping of Glur-1 to the same region as neurological mutants spasmodic, shaker-2, tipsy, and vibrator on chromosome 11; Glur-2 near spastic on chromosome 3; Glur-6 near waltzer and Jackson circler on chromosome 10; and Glur-7 near clasper on chromosome 4.

Re-localization of Actsk-1 to mouse chromosome 8, a new region of homology with human chromosome 1

We present here the genetic mapping of the alpha-skeletal actin locus (Actsk-1) on mouse Chromosome (Chr) 8, on the basis of the PCR analysis of a microsatellite in an interspecific backcross. Linkage and genetic distances were established for four loci by analysis of 192 (or 222) meiotic events and indicated the following gene order: (centromere)-Es-1-11.7 cM-Tat-8.3 cM-Actsk-1-0.5 cM-Aprt. Mapping of ACTSK to human Chr 1 and of TAT and APRT to human Chr 16 demonstrates the existence of a new short region of homology between mouse Chr 8 and human Chr 1. Intermingling on this scale between human and mouse chromosomal homologies that occurred during evolution creates disorders in comparative linkage studies.

Localization of the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) in the rat to chromosome 4 and implications for the evolution of mammalian chromosomes

We have isolated a partial cDNA encoding the cystic fibrosis transmembrane conductance regulator (CFTR) in the rat. This cDNA hybridizes to a 6.1-kb RNA transcript from the human T84 epithelial cell line and a similarly sized transcript from the rat parotid gland. The nucleotide sequence of this cDNA shows 80.5% identity to the human CFTR cDNA sequence, and the deduced amino acid sequence of rat CFTR shows 75.5% identity to the amino acid sequence of human CFTR. We have used this cDNA to map the location of the gene encoding CFTR to rat chromosome 4. This result places CFTR within a syntenic group on rat chromosome 4 and on human chromosome 7 that includes the genes encoding interleukin 6 (IL6), erythropoietin (EPO), P-glycoprotein 1 (PGY1), and T cell receptor beta chain (TCRB). This group is divided between chromosomes 5 and 6 in the mouse. Mapping of CFTR to rat chromosome 4 shows that this syntenic group has been divided in the mouse lineage during the past 15 million years and further localizes that breakpoint to a sequence homologous to the human chromosome 7q21.1 and 7q32 region. Similarly, a group of five genes, CFTR, TCRB, HOX1, parathyroid hormone-like hormone (PTHLH), and Kirsten rat sarcoma 2 viral (v-Ki-ras2) oncogene homolog (KRAS2), is syntenic on rat chromosome 4 and mouse chromosome 6, but is divided between human chromosomes 7 and 12. These data suggest that the ancestral mammalian chromosome appeared as the present day rat chromosome 4, with all six genes grouped together, and that chromosomal breakages have occurred in the mouse and human lineages since the mammalian divergence.

Mapping of the mouse Rxr loci encoding nuclear retinoid X receptors RXRα, RXRβ, and RXRγ

Recently, a novel subgroup of nuclear hormone receptors called RXRs implicated for retinoid-mediated gene regulation have been identified. RXRs appear to interact with many other nuclear hormone receptors and modulate their functions. We have mapped genetic loci Rxra, Rxrb, and Rxrg encoding three RXR subtypes, RXR alpha, RXR beta, and RXR gamma, respectively, using interspecific backcross mice. None of the Rxr loci cosegregated with each other or with the retinoic acid receptor loci (Rar) mapped previously. Rxra mapped to Chr 2 near the centromere, Rxrb mapped to the H-2 region of Chr 17, and Rxrg was tightly linked to the Pbx gene on distal Chr 1. These results underscore that RXR genes are dispersed in the genome.

The gene for the cell adhesion molecule M-cadherin maps to mouse chromosome 8 and human chromosome 16q24.1-qter and is near the E-cadherin (uvomorulin) locus in both species

A mouse myotube-derived cDNA encoding the Ca(2+)-dependent cell adhesion molecule M-cadherin was used to study the segregation of the corresponding gene Cdh3 in a mouse interspecific backcross. Cdh3 was found to be unlinked to the N-cadherin gene but linked to the E-cadherin (uvomorulin) locus on chromosome 8 in a region of conserved synteny with human chromosome 16q. The gene order cen-Junb-Um-Tat-(Cdh3/Aprt) was determined. The human homologue CDH3 was mapped to chromosome 16q24.1-qter by analyzing human/mouse somatic cell hybrids.

Linkage of epidermolytic hyperkeratosis to the type II keratin gene cluster on chromosome 12q

We investigated the molecular genetics of epidermolytic hyperkeratosis (EHK), a dominant disorder characterized by epidermal blistering, hyperkeratosis, vacuolar degeneration and clumping of keratin filaments. Based on this pathology, we have excluded by linkage analysis several candidate genes for the disease; in contrast, complete linkage was obtained with the type II keratin, K1, on 12q11-q13. Linkage in this region of chromosome 12 was confirmed using several other markers, and multi-locus linkage analyses further supported this location. Keratins are excellent EHK gene candidates since their expression is specific to the suprabasal epidermal layers. In the pedigree studied here, a type II keratin gene, very probably K1, is implicated as the site of the molecular defect causing EHK.

A single cyclin A gene and multiple cyclin B1-related sequences are dispersed in the mouse genome

Cyclin activation of protein serine/threonine kinases plays a pivotal role in regulating the cell cycle. Multiple cyclins that fall into at least five classes, A, B, C, D, and E, have been identified. In some organisms, more than one member of a single cyclin class has been observed. To gain insight into the function of cyclin multiplicity, we determined the number of cyclin A- and B1-related sequences present in the mouse genome, the relationship between these cyclin-related sequences and previously described mutations in the mouse, and cyclin A and B1 mRNA expression in mouse embryos. By genetic mapping using human cyclin A and B1 probes, we identified 1 cyclin A gene located on chromosome 3 and 10 cyclin B1-related sequences located on chromosomes 4, 5, 7, 8, 13, 14, 15, and 17. Cyclin B1-related sequences map in the vicinity of the metaphase-arrest mutation oligosyndactyly (Os) and embryonic lethal mutations associated with the albino (c) locus and the t-complex. In Northern analysis, two cyclin A-related transcripts of 2.1 and 3.4 kb and three cyclin B1-related transcripts of 1.7, 2.1, and 2.7 kb were detected in embryonic stem cells and postimplantation embryos from Day 9.5 to 15.5 of development. Identification of multiple cyclin B1-related sequences in the mouse genome and multiple cyclin B1 mRNAs raises the possibility that seemingly redundant cyclin B genes might have developmental- and/or cell-type-specific functions.

Isolation and characterization of human cDNA clones encoding a high mobility group box protein that recognizes structural distortions to DNA caused by binding of the anticancer agent cisplatin

Human cDNA clones encoding a structure-specific recognition protein, SSRP1, that binds specifically to DNA modified with cisplatin have been isolated and characterized. The SSRP1 gene maps to human chromosome 11q12. The cDNA clones, obtained by using partial-length cDNAs described previously, predict an 81-kDa protein containing several highly charged domains and a stretch of 75 amino acids 47% identical to a portion of the high mobility group (HMG) protein HMG1. This HMG box most likely constitutes the structure recognition element for cisplatin-modified DNA, with the probable recognition motif being the local duplex unwinding and bending toward the major groove that occurs upon formation of intrastrand cis-[Pt(NH3)2]2+ d(GpG) and d(ApG) cross-links. Although the DNA recognition properties of members of the HMG-box family of proteins have been characterized with respect to their sequence specificity, the present work demonstrates that proteins with this domain can recognize particular DNA structures as well. The Pt-DNA SSRP described here is the human homolog of a recently identified mouse protein that binds to recombination signal sequences [Shirakata, M., Hüppi, K., Usuda, S., Okazaki, K., Yoshida, K. & Sakano, H. (1991) Mol. Cell. Biol. 11, 4528-4536]. These sequences have been postulated to form stem-loop structures, further implicating local bends and unwinding in DNA as a recognition target for HMG-box proteins. Expression analysis in a variety of tissues and cisplatin-resistant cell lines and the inability of cisplatin to induce the message in HeLa cells argue against a direct link between SSRP1 mRNA levels and the response of cells to the drug.

Structure of the murine tissue factor gene. Chromosome location and conservation of regulatory elements in the promoter

Tissue factor (TF) is a transmembrane glycoprotein that mediates cellular initiation of the coagulation serine protease cascades. Moreover, expression of TF in human atherosclerotic plaques is likely to play a significant role in the thrombotic complications associated with plaque rupture. In this study the complete murine TF gene, Cf-3, was isolated from mouse NIH 3T3 cells and was found to consist of six exons spanning about 11 kilobase pairs (kbp) of DNA. A major transcriptional start site was located 24 bp downstream of a TATA box. Cf-3 was mapped to chromosome 3 by analysis of an intersubspecies test cross. Conserved transcription factor-binding sites were identified by comparison of 5' flanking regions of the murine and human TF genes. A region of the TF promoter required for constitutive expression exhibited 85% identity in DNA sequence and included two conserved binding sites for Sp1. Furthermore, two AP-1 sites and an NF-kappa B site were conserved in a 56-bp region necessary for transcriptional activation in response to bacterial lipopolysaccharide. These highly conserved regions of the TF promoter, which contain several binding sites for well-characterized transcription factors, are likely to be functionally important in the complex pattern of TF gene expression observed in a variety of cell types.

Chromosome mapping of the rod photoreceptor cGMP phosphodiesterase beta-subunit gene in mouse and human: tight linkage to the Huntington disease region (4p16.3)

The retinal degeneration mouse (gene symbol, rd) is an animal model for certain forms of human hereditary retinopathies. Recent findings of a nonsense mutation in the rd mouse PDE beta-subunit gene (Pdeb) prompted us to investigate the chromosome locations of the mouse and human genes. We have utilized backcross analysis in mice to verify and define more precisely the location of the Pdeb locus 6.1 +/- 2.3 cM distal of Mgsa on mouse chromosome 5. We have determined that the human gene (PDEB) maps to 4p16.3, very close to the Huntington disease (HD) region. Analysis of the comparative map for mice and humans shows that the mouse homologue of the HD gene will reside on chromosome 5. Linkage of the mouse Pdeb locus with other homologues in the human 4p16.3 region is maintained but gene order is not, suggesting at least three possible sites for the corresponding mouse HD gene.

Molecular cloning and characterization of the mouse UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I gene

The biosynthesis of protein-bound complex N-glycans in mammals requires a series of covalent modifications governed by a large number of specific glycosyltransferases and glycosidases. The addition of oligosaccharide to an asparagine residue on a nascent polypeptide chain begins in the endoplasmic reticulum. Oligosaccharide processing continues in the Golgi apparatus to produce a diversity of glycan structures. UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (EC 2.4.1.101; GlcNAc-TI) is a key enzyme in the process because it is essential for the conversion of high-mannose N-glycans to complex and hybrid N-glycans. We have isolated the mouse gene encoding GlcNAc-TI (Mgat-1) from a genomic DNA library. The mouse sequence is highly conserved with respect to the human and rabbit homologs and exists as a single protein-encoding exon. Mgat-1 was mapped to mouse Chromosome 11, closely linked to the gene encoding interleukin-3 by the analysis of multilocus interspecies backcrosses. RNA analyses of Mgat-1 expression levels revealed significant variation among normal tissues and cells.

Close linkage of retinoic acid receptor genes with homeobox- and keratin-encoding genes on paralogous segments of mouse chromosomes 11 and 15

Retinoic acid is essential for normal development and growth of structures such as head and limbs, and it can act as morphogen or teratogen. Retinoic acid induces expression of genes such as the homeobox genes and keratin type I and type II genes. Retinoic acid receptors are nuclear transcription factors that play a key role in retinoid physiology. As part of the characterization of retinoic acid receptor gene family, linkage of genes encoding the three receptors was determined by using interspecific backcross and recombinant inbred strain analysis of restriction fragment variants. Retinoic acid receptor alpha is located on mouse Chromosome (Chr) 11 near the homeobox-2 complex and the keratin type I gene complex, whereas retinoic acid receptor gamma is on mouse Chr 15 near the homeobox-3 complex and the keratin type II complex. Close genetic proximity of these functionally related genes may be significant. We confirmed assignment of retinoic acid receptor beta to the centromeric portion of Chr 14. These linkage assignments provide further evidence for duplicated segments in the mouse genome.

Linkage, but not gene order, of homologous loci, including alpha-L-iduronidase (Idua), is conserved in the Huntington disease region of the mouse and human genomes

alpha-L-iduronidase (IDUA), which when deficient causes mucopolysaccharidosis type I, is located near the Huntington disease locus (HD) on human Chromosome (Chr) 4p16.3, approximately 10(6) base pairs (bp) from the telomere. As part of our continuing efforts to define a detailed comparative map for this chromosomal segment in mice and humans, we have used an interspecific backcross between C57BL/6J and an inbred strain derived from Mus spretus to map Idua, the mouse homolog of IDUA. We also mapped the mouse homolog of D4S115, an anonymous locus approximately 250 kb proximal to IDUA. As expected, both Idua and D4S115h are located on the proximal portion of mouse Chr 5 near homologs for other loci on human Chr 4p. Comparison of gene order in mice and humans demonstrates, however, that a chromosomal rearrangement within this conserved synteny has occurred since divergence of lineages leading to mice and humans.

The murine leukemia inhibition factor gene (Lif) is located on proximal chromosome 11, not chromosome 13

Lif, the murine gene encoding leukemia inhibition factor (LIF), has been previously localized to proximal Chromosome (Chr) 11. Hilda, the murine gene encoding "human interleukin in DA cells" (HILDA) has been localized to Chr 13. Since these two growth factors are identical, the proposal for two different structural loci is intriguing. To address this issue, blot hybridization methods have been used to establish the position of the structural gene sequence unambiguously. DNAs from somatic cell hybrids, recombinant inbred mice, and backcross mice have been probed with a sequence that encodes LIF/HILDA. The results support the assignment of this sequence to proximal Chr 11. These studies also establish a synteny group, including Lif and Tcn-2, the structural gene for transcobalamin 2, that is conserved between man and mouse.

Assignment of three rat integrin genes to chromosome 19 (ITGB1), chromosome 3 (ITGA4), and chromosome 7 (ITGA5)

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