Proximal Portion Of Mouse Chromosome Research Articles

A High-Resolution Radiation Hybrid Map of the Proximal Portion of Mouse Chromosome 5

Radiation hybrid (RH) mapping of the mouse genome provides a useful tool in the integration of existing genetic and physical maps, as well as in the ongoing effort to generate a dense map of expressed sequence tags. To facilitate functional analysis of mouse Chromosome 5, we have constructed a high-resolution RH map spanning 75 cM of the chromosome. During the course of these studies, we have developed RHBase, an RH data management program that provides data storage and an interface to several RH mapping programs and databases. We have typed 95 markers on the T31 RH panel and generated an integrated map, pooling data from several sources. The integrated RH map ranges from the most proximal marker, D5Mit331 (Chromosome Committee offset, 3 cM), to D5Mit326, 74.5 cM distal on our genetic map (Chromosome Committee offset, 80 cM), and consists of 138 markers, including 89 simple sequence length polymorphic markers, 11 sequence-tagged sites generated from BAC end sequence, and 38 gene loci, and represents average coverage of approximately one locus per 0.5 cM with some regions more densely mapped. In addition to the RH mapping of markers and genes previously localized on mouse Chromosome 5, this RH map places the α-4 GABAA receptor subunit gene (Gabra4) in the central portion of the chromosome, in the vicinity of the cluster of three other GABAA receptor subunit genes (Gabrg1–Gabra2–Gabrb1). Our mapping effort has also defined a new cluster of four genes in the semaphorin gene family (Sema3a, Sema3c, Sema3d, and Sema3e) and the Wolfram syndrome gene (Wfs1) in this region of the chromosome.

Structure and Localization of Mouse Pmscl1 and Pmscl2 Genes

Sera from some patients with polymyositis–scleoderma overlap syndrome (PM–SCL) recognize two antigenically unrelated proteins, PMSCL1 and PMSCL2. Complete mouse Pmscl1 and Pmscl2 cDNA sequences, chromosomal localizations, exon/intron structure, and promoter region sequences of the mouse Pmscl2 gene are presented. The PMSCL1 gene was found to overlap significantly with cyclin A2 in both human and mouse. As such, it may be deduced that PMSCL1 sequences map to human chromosome 4q27 and the proximal portion of mouse chromosome (Chr) 3 where human and mouse cyclin A2 genes reside. Analysis of human and mouse PMSCL1 cDNA sequences provides evidence that the PMSCL1 protein is 68 amino acids longer than previously thought. A BAC containing mouse Pmscl2 was localized to distal mouse Chr 4 by FISH. This BAC contains the microsatellite D4Mit310. D4Mit310 colocalizes with a number of genes that map to human 1p36. In fact, a STS (G25404) located 54.6 cR from the top of human chromosome 1 was found to contain PMSCL2 sequence upon BLAST search.

Structure and promoter activity of an islet-specific glucose-6-phosphatase catalytic subunit-related gene.

In liver and kidney, the terminal step in the gluconeogenic pathway is catalyzed by glucose-6-phosphatase (G-6-Pase). This enzyme is actually a multicomponent system, the catalytic subunit of which was recently cloned. Numerous reports have also described the presence of G-6-Pase activity in islets, although the role of G-6-Pase in this tissue is unclear. Arden and associates have described the cloning of a novel cDNA that encodes an islet-specific G-6-Pase catalytic subunit-related protein (IGRP) (Arden SD, Zahn T, Steegers S, Webb S, Bergman B, O'Brien RM, Hutton JC: Molecular cloning of a pancreatic islet-specific glucose-6-phosphatase catalytic subunit related protein (IGRP). Diabetes 48:531-542, 1999). We screened a mouse BAC library with this cDNA to isolate the IGRP gene, which spans approximately 8 kbp of genomic DNA. The exon/intron structure of the IGRP gene has been mapped and, as with the gene encoding the liver/kidney G-6-Pase catalytic subunit, it is composed of five exons. The sizes of these exons are 254 (I), 110 (II), 112 (III), 116 (IV), and 1284 (V) bp, similar to those of the G-6-Pase catalytic subunit gene. Two interspecific backcross DNA mapping panels were used to unambiguously localize the IGRP gene (map symbol G6pc-rs) to the proximal portion of mouse chromosome 2. The IGRP gene transcription start site was mapped by primer extension analysis, and the activity of the IGRP gene promoter was analyzed in both the islet-derived HIT cell line and the liver-derived HepG2 cell line. The IGRP and G-6-Pase catalytic subunit gene promoters show a reciprocal pattern of activity, with the IGRP promoter being approximately 150-fold more active than the G-6-Pase promoter in HIT cells.

Rump white inversion in the mouse disrupts dipeptidyl aminopeptidase-like protein 6 and causes dysregulation of Kit expression.

The mouse rump white (Rw) mutation causes a pigmentation defect in heterozygotes and embryonic lethality in homozygotes. At embryonic day (E) 7.5, Rw/Rw embryos are retarded in growth, fail to complete neurulation and die around E 9.5. The Rw mutation is associated with a chromosomal inversion spanning 30 cM of the proximal portion of mouse chromosome 5. The Rw embryonic lethality is complemented by the W19H deletion, which spans the distal boundary of the Rw inversion, suggesting that the Rw lethality is not caused by the disruption of a gene at the distal end of the inversion. Here, we report the molecular characterization of sequences disrupted by both inversion breakpoints. These studies indicate that the distal breakpoint of the inversion is associated with ectopic Kit expression and therefore may be responsible for the dominant pigmentation defect in Rw/+ mice; whereas the recessive lethality of Rw is probably due to the disruption of the gene encoding dipeptidyl aminopeptidase-like protein 6, Dpp6 [Wada, K., Yokotani, N., Hunter, C., Doi, K., Wenthold, R. J. & Shimasaki, S. (1992) Proc. Natl. Acad. Sci. USA 89, 197-201] located at the proximal inversion breakpoint.

Linkage mapping of Lims1l, the murine homolog of the human LIM domain gene PINCH, to mouse Chromosome 10

The human LIM domain gene LIMS1 was used to identify a mouse homolog. The resulting mouse sequence was used to identify a polymorphism by SSCP analysis. Linkage studies performed in the EUCIB backcross placed Lims1l on the proximal portion of mouse Chromosome 10. This localisation makes it an interesting candidate for the deafness mutant, waltzer (v).

Calumenin, a Ca2+-binding protein retained in the endoplasmic reticulum with a novel carboxyl-terminal sequence, HDEF.

We have identified and characterized a cDNA encoding a novel Ca2+-binding protein named calumenin from mouse heart by the signal sequence trap method. The deduced amino acid sequence (315 residues) of calumenin contains an amino-terminal signal sequence and six Ca2+-binding (EF-hand) motifs and shows homology with reticulocalbin, Erc-55, and Cab45. These proteins seem to form a new subset of the EF-hand protein family expressed in the lumen of the endoplasmic reticulum (ER) and Golgi apparatus. Purified calumenin had Ca2+-binding ability. The carboxyl-terminal tetrapeptide His-Asp-Glu-Phe was shown to be responsible for retention of calumenin in ER by the retention assay, immunostaining with a confocal laser microscope, and the deglycosylation assay. This is the first report indicating that the Phe residue is included in the ER retention signal. Calumenin is expressed most strongly in heart of adult and 18.5-day embryos. The calumenin gene (Calu) was mapped at the proximal portion of mouse chromosome 7.

Detailed Comparative Map of Human Chromosome 19q and Related Regions of the Mouse Genome

One of the larger contiguous blocks of mouse–human genomic homology includes the proximal portion of mouse chromosome 7 and the long arm of human chromosome 19. Previous studies have demonstrated the close relationship between the two regions, but have also indicated significant rearrangements in the relative orders of homologous mouse and human genes. Here we present the genetic locations of the homologs of 42 human chromosome 19q markers in the mouse, with an emphasis on genes also included in the human chromosome 19 physical map. Our results demonstrate that despite an overall inversion of sequences relative to the centromere, apparent “transpositions” of three gene-rich segments, and a local inversion of markers mapping near the 19q telomere, gene content, order, and spacing are remarkably well conserved throughout the lengths of these related mouse and human regions. Although most human 19q markers have remained genetically linked in mouse, one small human segment forms a separate region of homology between human chromosome 19q and mouse chromosome 17. Three of the four rearrangements of mouse versus human 19q sequences involve segments that are located directly adjacent to each other in 19q13.3–q13.4, suggesting either the coincident occurrence of these events or their common association with unstable DNA sequences. These data permit an unusually in-depth examination of this large region of mouse–human genomic homology and provide an important new tool to aid in the mapping of genes and associated phenotypes in both species.

Absence of Imprinting in U2AFBPL, a Human Homologue of the Imprinted Mouse GeneU2afbp-rs

The mouse gene U2 auxiliary factor binding protein related sequence (U2afbp-rs) has previously been shown to be genomically imprinted with monoallelic expression from the paternal allele. To determine if the human homologue is imprinted and contains conserved structural features which regulate imprinting, we isolated genomic clones from a human P1-derived artificial chromosome (PAC) library that map to human chromosome 5q22-31, a region syntenic to the proximal portion of mouse chromosome 11 whereU2afbp-rsresides. A genomic subclone was isolated which contained an open reading frame with high homology to the mouse gene. This subclone also maintained the intronless character of the mouse gene. AKpnI polymorphism within the open reading frame of the gene was found to occur in 21% (8/38) of the alleles tested from human placental tissue samples. RT-PCR analysis of human placentas using theKpnI polymorphism to determine the parental origin of the alleles indicates biallelic expression of the human chromosome 5 U2AFBPL gene.

Complementary Deoxyribonucleic Acid Cloning and Characterization of mSP-10: The Mouse Homologue of Human Acrosomal Protein Sp-101

Complementary DNA encoding the putative mouse homologue for human acrosomal protein SP-10, a candidate contraceptive vaccinogen, was cloned and sequenced. The entire open reading frame (amino acids 18 to 261) of the mouse SP-10 (mSP-10), with the exception of the signal peptide (amino acids 1 to 17), was placed under the influence of inducible T7 RNA polymerase/promoter system to overproduce recombinant protein (re-mSP-10) in Escherichia coli. A six-histidine tag, which was coexpressed at the carboxyl terminus of re-mSP-10, provided the means for purification of re-mSP-10 by immobilized metal chelation affinity chromatography technique. The level of purity of re-mSP-10 thus obtained was determined by 2-dimensional gel electrophoresis to be 98%. Immunoblotting with monoclonal and polyclonal antibodies previously generated against human or baboon SP-10 showed that mSP-10 shared significant antigenic similarity with its primate counterparts. The position of mSP-10 in the mouse genome was next mapped through segregation analysis of an interspecific backcross panel of 96 animals. Acrv1 (assigned gene symbol for mSP-10) was localized in the proximal portion of mouse chromosome 9 in a region that exhibits synteny with human 11q23, the region to which ACRV1 (gene symbol for human SP-10) was previously mapped. These characterizations by combined immunological and gene mapping techniques established the cloned mSP-10 to be the mouse homologue of SP-10.

Localization of the genes for the 100-kDa complement-activating components of Ra-reactive factor (CRARF and Crarf) to human 3q27–q28 and mouse 16B2–B3

Human and mouse genes for the complement-activating component (P100) of Ra-reactive factor, a novel bactericidal factor (CRARF and Crarf), were mapped to R-banded metaphase chromosomes by fluorescence in situ hybridization with human and mouse P100 cDNA 2.7 and 2.0 kb long, respectively. The localization of fluorescent signals showed that CRARF and Crarf mapped to human 3q27–q28 and mouse 16B2–B3, respectively. This evidence is consistent with the previous assumption that the distal portion of the long arm of human chromosome 3 is homologous to the proximal portion of mouse chromosome 16.

Population and molecular genetics of susceptibility to intracellular pathogens

Abstract In the mouse, innate resistance to infection with certain species of Mycobacteria, Salmonella typhimurium and Leishmania donovani is controlled by the expression of a single dominant chromosome 1 gene, designated Bcg. The major effect of the Beg locus is the modulation of the growth rate of these pathogens in cells of the reticuloendothelial tissues during early infection. Using a positional cloning approach, a novel gene designated Nramp has recently been identified as a candidate gene for Bcg. Comparison of linkage and physical maps of mouse, human, bovine and chicken chromosomes indicates that a large cluster of genes in the proximal portion of mouse chromosome 1 is conserved among a variety of species. This has opened up the possibilities of testing the candidacy of Nramp for host resistance and susceptibility to human tuberculosis and leprosy, chicken salmonellosis and cow brucellosis.

Characterization of a Region-Specific Library of Microclones in the Vicinity of the Bcg and splotch Loci on Mouse Chromosome 1

The proximal portion of mouse chromosome 1 harbors a variety of mutant loci that have yet to he characterized at the molecular level. We have constructed a library of genomic DNA fragments from the proximal portion of mouse chromosome 1 by microdissection and microcloning techniques, with the aim of generating genetic markers in close proximity to some of these mutant loci. To facilitate the genetic mapping of 27 microclones from this library, we divided a 56-cM segment of chromosome 1 between the Col3a1 and Ren 1,2 genes into eight intervals defined by anchor loci. Restriction fragment length polymorphisms were determined for each of the microclones and their segregation with the anchor loci was followed in informative animals from a panel of 252 interspecific backcross mice (C57BL/6J × Mus spretus) × C57BL/6J. We were able to assign 26 of 27 (96%) randomly selected microclones to each of the defined chromosome 1 intervals. A total of eight microclones mapped within the large interstitial deletion found in the Spr mouse mutant. Two of these clones were found to be tightly linked to the host resistance locus Bcg and at least one was found to be linked to the neural tube defect mutant splotch. Other clones mapped to intervals containing several other mouse mutants. These novel DNA markers should aid in positional cloning strategies presently employed to identify these mutant loci. These clones should also be useful in the creation of both physical and YAC contiguous maps of the proximal portion of mouse chromosome 1.

Physical Delineation of the Minimal Chromosomal Segment Encompassing the Murine Host Resistance Locus Bcg

The host resistance locus Bcg determines resistance of mice to infection with intracellular pathogens such as certain species of Mycobacteria, Salmonella typhimurium , and Leishmania donovani. Bcg maps on the proximal portion of mouse chromosome 1, very tightly linked to villin (Vil), with the gene order and intergene distances Tp-1 -(1 cM)-D1Mcg105-(0.1 cM)-λMm1C165/Vil/Bcg-(0.2 cM)-λMm1C136-(0.3 cM)-Des-(0.1 cM)-Inha. In an effort to clone genomic sequences overlapping Bcg, we have used pulsed-field gel electrophoresis (PFGE) and fluorescence in situ hybridization to construct a physical map of the 3.9-Mb segment of proximal mouse chromosome 1, near Bcg. In situ hybridization to metaphase mouse chromosomes indicates that the mapped region is within band C5. Physical mapping of the Tp-1-Vil and λMm1C136-Inha intervals was carried out by PFGE analysis, whereas the Vil-Des interval was estimated by in situ hybridization to interphase nuclei. Results of these combined analyses indicate the following locus order and maximal interlocus distances: Tp-1-(1000 kb)-D1Mcg105-(160 kb)-λMm1C165-(180 kb)-Vil-(800 kb)-λMm1C136-(290 kb)-Des-(130 kb)-Inha. Detailed restriction mapping of this region identifies numerous putative CpG islands, suggesting that several transcription units are present in the vicinity of Bcg .

Analysis of the murine All-1 gene reveals conserved domains with human ALL-1 and identifies a motif shared with DNA methyltransferases.

A series of translocation break points found in a subset of human acute leukemias have one of the breaks on human chromosome 11q23. This region has recently been cloned and a large gene, ALL-1, with homology to the Drosophila trithorax gene has been identified. This paper describes the cloning, sequencing, and mapping of the mouse homolog of ALL-1. We have found a motif present in All-1 that shows homology to the zinc-binding domain of DNA (cytosine-5) methyltransferases (EC 2.1.1.63). Sequence analysis of the murine All-1 gene has identified distinct regions of homology with the human ALL-1 gene; these highly conserved domains may define regions of functional significance in mammals. In addition, we have identified alternatively spliced forms of All-1 within one of the zinc-finger domains, suggesting that there may be different targets and/or functions for All-1 proteins. Finally, we report that All-1 resides in the proximal portion of mouse chromosome 9 and is a candidate for a mutation that results in skeletal transformations during embryonic development.

Cloning, Analysis, and Chromosomal Localization of Notch-1, a Mouse Homolog of Drosophila Notch

The Notch gene of Drosophila encodes a large transmembrane protein involved in cell-cell interactions and cell fate decisions in the Drosophila embryo. We report here the isolation of cDNA clones encompassing the full-length coding sequence of Notch-1, a mouse homolog of Drosophila Notch. The predicted amino acid sequence of the Notch-1 protein retains all of the conserved amino acid motifs of Notch and the other vertebrate Notch homologs. The cDNA sequence predicts a 2531-amino-acid protein containing a signal peptide, 36 epidermal growth factor-like repeats, 3 Notch/lin-12 repeats, a transmembrane domain, and 6 cdc10/ankyrin repeats. The Notch-1 gene was localized to the proximal portion of mouse chromosome 2 by mapping with an interspecific backcross panel.

Molecular characterization of a deletion encompassing the splotch mutation on mouse chromosome 1

We have used a set of markers newly assigned to the proximal portion of mouse chromosome 1 to characterize the chromosomal segment deleted in the splotch-retarded ( Sp r) mouse mutant. Among nine markers tested in the heterozygote Sp r/+ mouse, we have identified four genes, Vil, Des, Inha, and Akp-3, which map within the Sp r deletion. The closest distal marker to the deletion is the Acrg gene, with the distal deletion breakpoint mapping within the 0.8-cM segment separating Akp-3 and Acrg. The most proximal gene to the Sp r deletion is Tp1. The proximal deletion breakpoint maps within the 0.8-cM segment separating Tp1 and Vil. The minimum size of the Sp r deletion would therefore be limited to 14 cM, the genetic distance between Vil and Akp-3. The maximum size of the Sp r deletion is estimated to be 16 cM, the genetic distance between Tp1 and Acrg.

Mapping of Col3a1 and Col6a3 to proximal murine chromosome 1 identifies conserved linkage of structural protein genes between murine chromosome 1 and human chromosome 2q

We have investigated the degree of synteny between the long arm (q) of human chromosome 2 and the proximal portion of mouse chromosome 1. To define the limits of synteny, we have determined whether mouse homologs of seven human genes mapping to chromosome 2q cosegregated with anchor loci on mouse chromosome 1. The loci investigated were NEB Neb , ELN Eln , COL3A1 Col3a1 , CRYG len-2 , FN1 Fn-1 , VIL Vil , and COL6A3 Col6a3 . Ren-1,2 and Acrg were included as two proximal mouse chromosome 1 anchor loci. The segregation of restriction fragment length polymorphisms at these loci was analyzed in the progeny of Mus spretus × C57BL 6J hybrids backcrossed to the C57BL 6J inbred strain. We found that five of the structural protein loci and the two anchor loci form a linkage group on proximal murine chromosome 1. The proposed gene order of this group of linked markers is centromere -Col3a1 - Len-2-Fn-1-Vil-Acrg-Col6a3-Ren1,2-Neb and Eln are linked neither to each other nor to any other marker on proximal mouse chromosome 1. Therefore, the mouse loci Col3a1 and Col6a3 are identified as flanking markers of the linkage group of structural protein loci. The estimated genetic map distances are Col3a1-13.3 cM- Len-2-3.4 cM- Fn-1-3.8 cM- Vil-9.6 cM- Acrg-2.1 cM- Col6a3-18.3 cM- Ren1,2. The available map information for human chromosome 2q markers and mouse chromosome 1 markers presented here tentatively identifies Col3a1 and Col6a3 as the border markers that define the limits of the syntenic chromosome segment. The order of mouse genes on chromosome 1 and their human homologs on chromosome 2q also appears to be conserved, suggesting that mapping of murine genes on the conserved segment may be useful to predict gene order in man.

Pax8, a murine paired box gene expressed in the developing excretory system and thyroid gland

Several mouse genes designated 'Pax genes' contain a highly conserved DNA sequence homologous to the paired box of Drosophila. Here we describe the isolation of Pax8, a novel paired box containing clone from an 8.5 day p.c. mouse embryo cDNA library. An open reading frame of 457 amino acids (aa) contains the 128 aa paired domain near the amino terminus. Another conserved region present in some other paired box genes, the octapeptide Tyr-Ser-Ile-Asn-Gly-Leu-Leu-Gly, is located 43 aa C-terminal to the paired domain. Using an interspecies backcross system, we have mapped the Pax8 gene within the proximal portion of mouse chromosome 2 in a close linkage to the surf locus. Several developmental mutations are located in this region. In situ hybridization was used to determine the pattern of Pax8 expression during mouse embryogenesis. Pax8 is expressed transiently between 11.5 and 12.5 days of gestation along the rostrocaudal axis extending from the myelencephalon throughout the length of the neural tube, predominantly in two parallel regions on either side of the basal plate. We also detected Pax8 expression in the developing thyroid gland beginning at 10.5 days of gestation, during the thyroid evagination. In the mesonephros and metanephros the expression of Pax8 was localized to the mesenchymal condensations, which are induced by the nephric duct and ureter, respectively. These condensations develop to functional units, the nephrons, of the kidney. These data are consistent with a role for Pax8 in the induction of kidney epithelium. The embryonic expression pattern of Pax8 is compared with that of Pax2, another recently described paired box gene expressed in the developing excretory system.

The α-A-crystallin and cystathionine β-synthase genes are physically very closely linked in proximal mouse chromosome 17

Murine genes homologous to those contributing to the Down syndrome (DS) phenotype in man are currently of interest because of their potential for providing animal models for the study of specific DS symptoms. Most of the genes mapping to human chromosome 21q22, where the DS genes are concentrated, are related to sequences located on mouse chromosome 16. Others, however, are known to map to mouse chromosome 10, and two genes, cystathionine β-synthase ( Cbs) and α-A-crystallin ( Crya-1), have been localized to the proximal portion of mouse chromosome 17. In this paper, we show that the two genes mapping to human chromosome 21q22 and mouse chromosome 17 are very tightly linked in mouse, being separated by at least 70 kb, but not more than 130 kb. The very close physical linkage of mouse Cbs and Crya-1, combined with data that localize homologs of the closely flanking markers H2k and Pim-1 to human chromosome 6, suggests that the human 21q22/mouse chromosome 17 conserved segment is of a very limited total physical size and is likely to contain a relatively small number of genes.

The HOX-5 and surfeit gene clusters are linked in the proximal portion of mouse chromosome 2

Using an interspecies backcross, we have mapped the HOX-5 and surfeit ( surf) gene clusters within the proximal portion of mouse chromosome 2. While the HOX-5 cluster of homeobox-containing genes has been localized to chromosome 2, bands C3-E1, by in situ hybridization, its more precise position relative to the genes and cloned markers of chromosome 2 was not known. Surfeit, a tight cluster of at least six highly conserved “housekeeping” genes, has not been previously mapped in mouse, but has been localized to human chromosome 9q, a region of the human genome with strong homology to proximal mouse chromosome 2. The data presented here place HOX-5 in the vicinity of the closely linked set of developmental mutations rachiterata, lethargic, and fidget and place surf close to the proto-oncogene Abl, near the centromere of chromosome 2.