Disease genes and chromosomes: disease maps of the human genome. Chromosome 16.
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Chromosome Mapping↗
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Disease genes and chromosomes: disease maps of the human genome. Chromosome 14.
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Chromosome Mapping↗
High-specificity DNA cleavage agent: design and application to kilobase and megabase DNA substrates.
Strategies to cleave double-stranded DNA at specific DNA sites longer than those of restriction endonucleases (longer than 8 base pairs) have applications in chromosome mapping, chromosome cloning, and chromosome sequencing--provided that the strategies yield high DNA-cleavage efficiency and high DNA-cleavage specificity. In this report, the DNA-cleaving moiety copper:o-phenanthroline was attached to the sequence-specific DNA binding protein catabolite activator protein (CAP) at an amino acid that, because of a difference in DNA bending, is close to DNA in the specific CAP-DNA complex but is not close to DNA in the nonspecific CAP-DNA complex. The resulting CAP derivative, OP26CAP, cleaved kilobase and megabase DNA substrates at a 22-base pair consensus DNA site with high efficiency and exhibited no detectable nonspecific DNA-cleavage activity.
Base Sequence↗
Four paralogous protein 4.1 genes map to distinct chromosomes in mouse and human.
Four highly conserved members of the skeletal protein 4.1 gene family encode a diverse array of protein isoforms via tissue-specific transcription and developmentally regulated alternative pre-mRNA splicing. In addition to the prototypical red blood cell 4.1R (human gene symbol EPB41,) these include two homologues that are strongly expressed in the brain (4.1N, EPB41L1; and 4.1B, EPB41L3) and another that is widely expressed in many tissues (4.1G, EPB41L2). As part of a study on the structure and evolution of the 4.1 genes in human and mouse, we have now completed the chromosomal mapping of their respective loci by reporting the localization of mouse 4.1N, 4.1G, and 4.1B, as well as human 4.1B. For the mouse 4.1 genes, Southern blot analysis of RFLPs in The Jackson Laboratory BSS interspecific backcross yielded the following assignments: 4.1N (Epb4.1l1,) chromosome 2; 4.1G (Epb4.1l2,) chromosome 10; and 4.1B (Epb4.1l3,) mouse chromosome 17. Human 4.1B was physically mapped to chromosome 18p11 using fluorescence in situ hybridization. All of the mouse genes mapped within or adjacent to regions of conserved synteny with corresponding human chromosomes. We conclude that a set of four paralogous 4.1 genes has been evolutionarily conserved in rodents and primates.
Animals↗
A single B1 subunit mapped to mouse chromosome 7 may be a common component of Na channel isoforms from brain, skeletal muscle and heart.
A beta 1 subunit associated with one or more isoforms of brain voltage-sensitive Na channels has previously been cloned, sequenced and expressed. Northern and Western blot analyses have suggested that homologues to this protein are expressed in skeletal muscle and heart. Here, reverse transcriptase-polymerase chain reaction (RT-PCR)/cloning reveals that transcripts encoding identical beta 1 subunit ORFs are expressed in adult rat brain, skeletal muscle and heart. Heterologous co-expression of beta 1 with brain (RIIA) and skeletal muscle (mu 1) alpha subunits caused a stabilization of normal, rapidly inactivating (mode 1) gating relative to anomalous, non-inactivating (mode 2) states and a negative shift in steady state inactivation. Chromosome mapping of the beta 1 subunit showed a single locus (Scn1b) in mouse chromosome 7 1.8 cM (+/- 1.2 cM) distal to D19F11S1h and 0.9 cM (+/- 0.9 cM) proximal to Pkca. This locus is in the region of the mouse mutant "quivering," characterized by a variety of neurological disorders and muscle paralysis. A mutation in a single beta 1 subunit forming functional complexes with multiple Na channel isoforms could underlie these deficits.
Animals↗
Chromosomal localization of the human heme oxygenase genes: heme oxygenase-1 (HMOX1) maps to chromosome 22q12 and heme oxygenase-2 (HMOX2) maps to chromosome 16p13.3.
Heme oxygenase catalyzes the oxidation of heme to biliverdin, the precursor of the bile pigment bilirubin, and carbon monoxide, a putative neurotransmitter. We have employed polymerase chain reaction and fluorescence in situ hybridization to determine the chromosome localization of the genes coding for the two known heme oxygenase isozymes. Heme oxygenase-1 (HMOX1), the inducible form, was localized to human chromosome 22q12, while heme oxygenase-2 (HMOX2), the constitutive form, was localized to chromosome 16p13.3.
Animals↗
Physical and genetic mapping of Candida albicans: several genes previously assigned to chromosome 1 map to chromosome R, the rDNA-containing linkage group.
Analysis of the karyotypes of multiple Candida albicans isolates by pulsed-field electrophoresis confirms the observation by Lasker et al. of eight chromosomes. The genes previously assigned to chromosome 1 in fact fall into two groups, one (including ADE1, SOR9, and CDC10) is linked to the ribosomal DNA genes on a chromosome called R, whereas the others are found on chromosome 1. Chromosome R varies in electrophoretic mobility among strains, usually running equal to or faster than chromosome 1 but in rare cases running slower than chromosome 1. In strain 1012A, the decreased mobility of one homolog is associated with the very large majority of the rDNA genes being on that homolog; the second homolog, with only a few copies, migrates with chromosome 2. Linkage analysis by using spheroplast fusion confirms the gene assignments made by hybridization to blots of the electrophoretic karyotype. A newly cloned gene, LYS2, hybridizes to chromosome 1.
Blotting, Southern↗
The tyrosinase-positive oculocutaneous albinism locus maps to chromosome 15q11.2-q12.
Tyrosinase-positive oculocutaneous albinism (ty-pos OCA), an autosomal recessive disorder of the melanin biosynthetic pathway, is the most common type of albinism occurring worldwide. In southern African Bantu-speaking negroids it has an overall prevalence of about 1/3,900. Since the basic biochemical defect is unknown, a linkage study with candidate loci, candidate chromosomal regions, and random loci was undertaken. The ty-pos OCA locus was found to be linked to two arbitrary loci, D15S10 and D15S13, in the Prader-Willi/Angelman chromosomal region on chromosome 15q11.2-q12. The pink-eyed dilute locus, p, on mouse chromosome 7, maps close to a region of homology on human chromosome 15q, and we postulate that the ty-pos OCA and p loci are homologous.
Albinism, Oculocutaneous↗
[The rules for electron microscopic mapping of polytene chromosomes in squashed preparations of Drosophila salivary glands].
The following rules of the polytene chromosome mapping at the submicroscopical level are proposed: 1) using anhydrous mixtures of alcohol with acetic acid for fixation of salivary glands which permits to avoid artifacts in the structure of large bands; 2) using sections 120-150 nm thick which improves the revealing of faint bands; 3) including in the analysis larvae being at different stages, since different bands display puffing at different regions; 4) reproducibility of banding pattern in serial sections of some chromosomes. The use of these rules permits to interpret more strictly the observed pictures of the polytene chromosome banding pattern and to avoid possible mistakes of the mapping.
Animals↗
Integration of the 1993-94 Généthon genetic linkage map for chromosome 18 with the physical map using a somatic cell hybrid mapping panel.
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Chromosome Mapping↗
Computerized EM maps of surface spread polytene chromosomes 1 digitizing and plotting of banding patterns.
A standard plotting program for the band-interband pattern of polytene chromosome maps was written in EXTENDED BASIC for a pocket computer coupled to a plotter (Sharp PC-1500 + CE-150). In this program, the individual polytene structure (i.e. one chromosome band and its right-handed interband) was digitized using a set of variables: [A] band diameter, [B] band type (solid, dotted, straight or curved bands), [C] band thickness, [D] interband length, [E] interband as well as puff and Balbiani ring outlines, [R] radius (for curved bands), [W] sectioning (of the pattern in chromosome maps) and [V$] reference numbers. The general use of this technique was tested by digitizing and computerized plotting of data from hand-drawn chromosome maps in Chironomus and Drosophila. Electron micrographs of surface spread polytene (SSP) chromosomes from the salivary glands of Chironomus thummi larvae were used to digitize the pattern of region F1-4 in chromosome I. The computerized EM map of this region was compared with the LM map from chromosome squash preparations.
Animals↗
Mouse Elk oncogene maps to chromosome X and a novel Elk oncogene (Elk3) maps to chromosome 10.
The Elk protein is a member of the Ets family found in both vertebrates and invertebrates. Human ELK1 encoded by ELK1 binds alone or together with serum response factor to DNA and regulates gene expression in a variety of biological processes. Using a panel of interspecific backcross mice, we have mapped the Elk oncogene (Elk) and a novel type Elk oncogene (Elk3), closely related to ELK1. Elk maps to Chr X, and Elk3 maps to the proximal region of Chr 10.
Animals↗
A fine-structure deletion map of human chromosome 11p: analysis of J1 series hybrids.
Deletion analysis offers a powerful alternative to linkage and karyotypic approaches for human chromosome mapping. A panel of deletion hybrids has been derived by mutagenizing J1, a hamster cell line that stably retains chromosome 11 as its only human DNA, and selecting for loss of MIC1, a surface antigen encoded by a gene in band 11p13. A unique, self-consistent map was constructed by analyzing the pattern of marker segregation in 22 derivative cells lines; these carry overlapping deletions of 11p13, but selectively retain a segment near the 11p telomere. The map orders 35 breakpoints and 36 genetic markers, including 3 antigens, 2 isozymes, 12 cloned genes, and 19 anonymous DNA probes. The deletions span the entire short arm, dividing it into more than 20 segments and define a set of reagents that can be used to rapidly locate any newly identified marker on 11p, with greatest resolution in the region surrounding MIC1. The approach we demonstrate can be applied to map any mammalian chromosome. To test the gene order, we examined somatic cell hybrids from five patients, whose reciprocal translocations bisect band 11p13; these include two translocations associated with familial aniridia and two with acute T-cell leukemia. In each patient, the markers segregate in telomeric and centromeric groups as predicted by the deletion map. These data locate the aniridia gene (AN2) and a recurrent T-cell leukemia breakpoint (TCL2) in the marker sequence, on opposite sides of MIC1. To provide additional support, we have characterized the dosage of DNA markers in a patient with Beckwith-Wiedemann syndrome and an 11p15-11pter duplication. Our findings suggest the following gene order: TEL - (HRAS1, MER2, CTSD, TH/INS/IGF2, H19, D11S32) - (RRM1, D11S1, D11S25, D11S26) - D11S12 - (HBBC, D11S30) - D11S20 - (PTH, CALC) - (LDHA, SAA, TRPH, D11S18, D11S21) - D11S31 - D11S17 - HBVS1 - (FSHB, D11S16) - AN2 - MIC1 - TCL2 - delta J - CAT - MIC4 - D11S9 - D11S14 - ACP2 - (D11S33, 14L) - CEN. We have used the deletion map to show the distribution on 11p of two centromeric repetitive elements and the low-order interspersed repeat A36Fc. Finally, we provide evidence for an allelic segregation event in the hamster genome that underlies the stability of chromosome 11 in J1. The deletion map provides a basis to position hereditary disease loci on 11p, to distinguish the pattern of recessive mutations in different forms of cancer and, since many of these genes have been mapped in other mammalian species, to study the evolution of a conserved syntenic group.
Animals↗
Cellular DNA region involved in induction of thymic lymphomas (Mlvi-2) maps to mouse chromosome 15.
Two cellular DNA regions representing common domains for proviral DNA integration ( Mlvi -1 and Mlvi -2) have been identified in Moloney murine leukemia virus-induced rat thymic lymphomas. Cellular sequences which were free of repeated DNA derived from a clone that defines the Mlvi -2 integration domain (lambda Cl228 ) were found to be highly conserved in a variety of vertebrate species that we examined, including mice, hamsters, cats, and humans. In this study, we identified the chromosomal map location of the Mlvi -2 homologous sequences in mice by using hamster-mouse somatic cell hybrids. The results show that Mlvi -2 is present on mouse chromosome 15 but is unrelated to the c-myc and c-sis proto-oncogenes, which map on the same chromosome. Since aberrations on chromosome 15 have been observed reproducibly in mouse thymomas, our data suggest that Mlvi -2 may define a novel sequence involved in the induction or progression of murine thymic lymphomas.
Animals↗
Compositional mapping of chicken chromosomes and identification of the gene-richest regions.
'Compositional chromosomal mapping', namely the assessment of the GC level of chromosomal bands, led to the identification, in the human chromosomes, of the GC-richest H3+ bands and of the GC-poorest L1+ bands, which were so called on the basis of the isochore family predominantly present in the bands. The isochore organization of the avian genome is very similar to those of most mammals, the only difference being the presence of an additional, GC-richest, H4 isochore family. In contrast, the avian karyotypes are very different from those of mammals, being characterized, in most species, by few macrochromosomes and by a large number of microchromosomes. The 'compositional mapping' of chicken mitotic and meiotic chromosomes by in-situ hybridization of isochore families showed that the chicken GC-richest isochores are localized not only on a large number of microchromosomes but also on almost all telomeric bands of macrochromosomes. On the other hand, the GC-poorest isochores are generally localized on the internal regions of macrochromosomes and are almost absent in microchromosomes. Thus, the distinct localization of the GC-richest and the GC-poorest bands observed on human chromosomes appears to be a general feature of chromosomes from warm-blooded vertebrates.
Animals↗
A yeast artificial chromosome-based map of the region of chromosome 20 containing the diabetes-susceptibility gene, MODY1, and a myeloid leukemia related gene.
We have generated a physical map of human chromosome bands 20q11.2-20q13.1, a region containing a gene involved in the development of one form of early-onset, non-insulin-dependent diabetes mellitus, MODY1, as well as a putative myeloid tumor suppressor gene. The yeast artificial chromosome contig consists of 71 clones onto which 71 markers, including 20 genes, 5 expressed sequence tags, 32 simple tandem repeat DNA polymorphisms, and 14 sequence-tagged sites have been ordered. This region spans about 18 Mb, which represents about 40% of the physical length of 20q. Using this physical map, we have refined the location of MODY1 to a 13-centimorgan interval (approximately equal to 7 Mb) between D20S169 and D20S176. The myeloid tumor suppressor gene was localized to an 18-centimorgan interval (approximately equal to 13 Mb) between RPN2 and D20S17. This physical map will facilitate the isolation of MODY1 and the myeloid tumor suppressor gene.
Base Sequence↗
The mouse homolog of the human Miller-Dieker chromosomal region (MDCR) maps to mouse chromosome 11 in close proximity to Mov9 and D11Nds1.
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1-Alkyl-2-acetylglycerophosphocholine Esterase↗
Practicable approaches to targeted comparative mapping of rat chromosome regions: linkage mapping of five genes on rat chromosome 13.
We demonstrate feasible approaches to comparative mapping between the region near the renin locus on rat chromosome 13 and human chromosome 1q by assigning five additional genes as anchor loci. Base-substitution polymorphisms were sought in the 3'- and/or 5'-untranslated regions for subsequent development of PCR-amplified markers, which, in turn, could be used for either restriction fragment analysis or allele-specific PCR.
Animals↗