Chromosome mapping: Radiation hybrid data and stochastic spin models.
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Journal Article↗
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Cytochrome oxidase subunit V gene of Neurospora crassa: DNA sequences, chromosomal mapping, and evidence that the cya-4 locus specifies the structural gene for subunit V.
The sequences of cDNA and genomic DNA clones for Neurospora cytochrome oxidase subunit V show that the protein is synthesized as a 171-amino-acid precursor containing a 27-amino-acid N-terminal extension. The subunit V protein sequence is 34% identical to that of Saccharomyces cerevisiae subunit V; these proteins, as well as the corresponding bovine subunit, subunit IV, contain a single hydrophobic domain which most likely spans the inner mitochondrial membrane. The Neurospora crassa subunit V gene (cox5) contains two introns, 398 and 68 nucleotides long, which share the conserved intron boundaries 5'GTRNGT...CAG3' and the internal consensus sequence ACTRACA. Two short sequences, YGCCAG and YCCGTTY, are repeated four times each in the cox5 gene upstream of the mRNA 5' termini. The cox5 mRNA 5' ends are heterogeneous, with the major mRNA 5' end located 144 to 147 nucleotides upstream from the translational start site. The mRNA contains a 3'-untranslated region of 186 to 187 nucleotides. Using restriction-fragment-length polymorphism, we mapped the cox5 gene to linkage group IIR, close to the arg-5 locus. Since one of the mutations causing cytochrome oxidase deficiency in N. crassa, cya-4-23, also maps there, we transformed the cya-4-23 strain with the wild-type cox5 gene. In contrast to cya-4-23 cells, which grow slowly, cox5 transformants grew quickly, contained cytochrome oxidase, and had 8- to 11-fold-higher levels of subunit V in their mitochondria. These data suggest (i) that the cya-4 locus in N. crassa specifies structural information for cytochrome oxidase subunit V and (ii) that, in N. crassa, as in S. cerevisiae, deficiencies in the production of nuclearly encoded cytochrome oxidase subunits result in deficiency in cytochrome oxidase activity. Finally, we show that the lower levels of subunit V in cya-4-23 cells are most likely due to substantially reduced levels of translatable subunit V mRNA.
Amino Acid Sequence↗
Volume 48, number 2 (1998), in article no. GE975188 "cDNA cloning, mRNA expression, and chromosomal mapping of human and mouse periplakin Genes," by sirpa aho, W. H. Irwin McLean, kehua li, and jouni uitto, pages 242-247:
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Journal Article↗
Detailed deletion mapping at chromosome 9p21 in non-small cell lung cancer by microsatellite analysis and fluorescence in situ hybridization.
We examined 82 cases of primary non-small cell lung cancer (NSCLC) for loss of heterozygosity (LOH) at the chromosome 9p21-24 region using 16 microsatellite markers. A total of 52 tumors (63%) displayed LOH, and 25 of these cases displayed LOH for all markers. Two cases had small hemizygous losses confined to the p16 gene and more distal markers, whereas 3 cases had loss proximal to p16 and extended through marker D9S126. This latter region has recently been described as another minimal region of loss at 9p21 in lung cancer. However, homozygous deletion of the p16 gene was observed in 18 of 85 cases, with only 5 cases having large deletions extended into the D9S126 region. Furthermore, we did not observe homozygous deletion at the 9p21 region that excluded the p16 gene. Fluorescence in situ hybridization (FISH) analysis using genomic probes spanning either the p16 or Hel-N1 (located at D9S126) gene was performed in 14 tumors. The results from FISH correlated with the chromosomal mapping data, suggesting that the p16 region is the major target of deletion at chromosome 9p21 in primary NSCLC.
Carcinoma, Non-Small-Cell Lung↗
Cerebellar degeneration-related antigen: a highly conserved neuroectodermal marker mapped to chromosomes X in human and mouse.
Cerebellar degeneration-related antigen (designated CDR34) was previously cloned by antibody screening of a cDNA library and was shown to be one of the target molecules recognized by autoantibodies in patients with paraneoplastic cerebellar degeneration. This molecule is distinctive in that it contains a tandem hexapeptide repetitive structure, presumably the basis for its high immunogenicity. In this study, we cloned the human CDR34 gene and proved that the entire repetitive sequence is encoded by a single exon without introns. We also showed that the nucleotide repeats are preserved only in the protein-coding sequences, suggesting evolutionary constraint in this region of the gene. Corresponding mouse cDNA clones were also isolated, which encoded a larger molecule with very similar hexapeptide repeating units. Comparison of the human and mouse repeats revealed a highly conserved Glu-Asp core in each unit, implicating the functional significance of this motif. Chromosomal mapping by somatic cell hybrid analysis mapped CDR34 to both human and mouse chromosomes X, and in situ hybridization further assigned CDR34 to human Xq24-q27.
Amino Acid Sequence↗
Expression of alternatively terminated unusual human butyrylcholinesterase messenger RNA transcripts, mapping to chromosome 3q26-ter, in nervous system tumors.
To study the molecular origin of the altered regulation of butyrylcholinesterase (BuChE) in nervous system tumors, BuChE complementary DNA (cDNA) sequences from human glioblastoma and neuroblastoma cDNA libraries were compared with BuChE cDNAs from normal fetal and adult tissues. A single 2.6-kilobase BuChE cDNA sequence was found in all normal tissues, whereas an additional alternatively terminated BuChE cDNA clone was found in both tumor libraries. The tumor-specific cDNA contained a 3',0.7-kilobase nontranslatable extension, as well as several nucleotide alterations in the normal polyadenylation site. Single-base mutations in the coding region of this unusual BuChE cDNA infer two amino acid substitutions: Asp70----Gly and Ser425----Pro. The Asp70----Gly change has recently been implicated with "atypical" BuChE, which is deficient in its capacity to hydrolyze succinylcholine. The 3.6-kilobase mRNA was less abundant in RNA blot hybridization than the 2.6-kilobase mRNA, which is in agreement with the low ratios between the 3.6- and 2.6-kilobase BuChE cDNA clones in glioblastoma and neuroblastoma libraries. Furthermore, size fractionation and microinjection of glioblastoma polyadenylated RNA, followed by enzyme activity and selective inhibition measurements, demonstrated two peaks of functional BuChE mRNA, the heavier one probably reflecting the longer transcripts. Chromosomal mapping of the 0.7-kilobase 3' fragment by in situ hybridization localized it to a unique 3q26-ter position, where we recently found an inheritably amplified "silent" defective CHE gene in a family exposed to the cholinesterase inhibitor methyl parathion. Our findings confirm previous genetic linkage mapping of the functional CHE gene to the 3q26-ter position and demonstrate that extended functional mRNA transcripts encoding a BuChE form with two modified amino acids are produced from this gene in glioblastoma and neuroblastoma cells.
Base Sequence↗
The human homologue of the retroviral oncogene qin maps to chromosome 14q13.
Chromosomal mapping of the human QIN gene (renamed FKH2 by the Human Genome Organization Nomenclature Committee) was initially accomplished by correlation of the presence of the QIN locus with specific chromosome regions in a rodent-human hybrid panel. This analysis revealed that the human QIN gene maps to chromosome region 14q11.2-->14q32, between the TCR and IGH loci. Further analysis by fluorescence in situ hybridization techniques with a human QIN genomic clone refined the human QIN gene localization to 14q13.
Chromosome Mapping↗
The mapping of chromosomes in Saccharomyces cerevisiae. I. A cosmid vector designed to establish, by cloning into cdc-mutants, numerous start loci for chromosome walking in the yeast genome.
A series of vectors for cosmid cloning in yeast has been derived from cosmid pHC79. Vectors pMT4 through pMT6 contain two tandemly arranged cohesive end sites (cos) from the genome of bacteriophage lambda. Their design allows the rapid and simple preparation of cosmid arms by linearizing a vector at the unique PvuII-restriction site located between the two cos-sequences and then cutting the linearized molecule at one of its unique cloning sites for BamHI, ClaI, PvuI, SalI or ScaI. Cosmids generated with arms from the most advanced vector, pMT6, carry the origin of replication (ori) and the ApR gene from pBR322 and the TRP1/ARS1 and URA1 genes from Saccharomyces cerevisiae. A yeast genomic DNA library was established by packaging in vitro, into bacteriophage lambda preheads, of partially restricted yeast DNA fragments ligated to cosmid arms of vector pMT6. About 80% of the clones thus obtained comprise inserts of contiguous genomic DNA over 30 kb in length. Unique DNA probes for the yeast genes CDC10, CDC39, HIS4, LEU2, and PGK1 have successfully been applied when testing for completeness of this library by isolating a series of overlapping cosmid clones that carry the respective genes. The library will thus be useful for the selection of cosmid clones which carry CDC genes from yeast by complementing first, with the vectorial yeast gene URA1, the pyrimidine auxotrophy of most cdc-strains and then, with the respective CDC wild-type genes, of the temperature-sensitive mutant alleles. Most CDC clones thus obtained will provide unique DNA probes which serve as randomly distributed start sequences within the yeast genome for overlap hybridization screening in chromosome mapping studies.
Cell Cycle↗
Seven loci on human chromosome 4 map onto sheep chromosome 6: a proposal to restore the original nomenclature of this sheep chromosome.
Seven new loci, casein alpha-S1 (CSN1S1), casein alpha-S2 (CSN1S2), casein beta (CSN2), the Hardy-Zuckerman 4 feline sarcoma viral (v-kit) oncogene homolog (KIT), albumin (ALB), phosphodiesterase cyclic GMP (rod receptor) beta polypeptide (PDEB), and complement component 1 (IF), were assigned to sheep Chromosome (Chr) 6 by Southern hybridization to a panel of chromosomally characterized sheep x hamster cell hybrids. By isotopic in situ hybridization, CSN2 was regionally localized to sheep Chr (OOV) 6q22-q31, anchoring this syntenic group of markers on to OOV6 and confirming its homology at a molecular and cytological level with cattle Chr 6. The assignment of these loci, from PDEB (located on human Chr 4p16.3) to IF (on HSA4q24-q25), and the observation that interleukin 2 (IL2, on HSA4q26-q27) and tryptophan 2,3-dioxygenase (TDO2, on HSA4q31) are not located on OOV6, is further evidence of the close evolutionary relationship of sheep and cattle and the conserved synteny in these species of this extensive region of human Chr 4. On the basis of this conserved synteny, and the similar G- and Q-banding patterns of this chromosome in cattle and sheep, we propose that this sheep chromosome be numbered as 6, not 4 as recommended by ISCNDA (1990).
Animals↗
Cyclophilin A, the major intracellular receptor for the immunosuppressant cyclosporin A, maps to chromosome 7p11.2-p13: four pseudogenes map to chromosomes 3, 10, 14, and 18.
Cyclophilin A (CyP-A), the major intracellular receptor for the immunosuppressant cyclosporin A (CsA), is a member of the immunophilin class of proteins, which all possess peptidyl-prolyl cis-trans isomerase activity and, therefore, are believed to be involved in protein folding and/or intracellular protein transport. The CyP-A protein is encoded by a single gene; in addition, 15 pseudogenes have been identified. Recently, specific binding of CyP-A to the human immunodeficiency virus type 1 (HIV-1) gag protein has been reported. Interestingly, this interaction can be inhibited by the immunosuppressant CsA and also by nonimmunosuppressive, CyP-A-binding CsA derivatives, which were also shown to exhibit potent anti-HIV-1 activity. Results thus indicate that CyP-A may have an essential function in HIV-1 replication. Using a panel of somatic rodent-human cell hybrids and PCR technology, we localized the coding cyclophilin A gene (PPIA) on chromosome 7 and four pseudogenes (PPIP2, PPIP3, PPIP4, and PPIP6) on chromosomes 14, 10, 18, and 3, respectively. Using chromosome 7 and chromosome 10 deletion hybrid panels, we were able to localize further the coding gene to the region 7p11.2-p13, as confirmed by fluorescence in situ hybridization analysis, and one pseudogene (PPIP3) to the region 10q11.2-q23. This is the first report on the regional mapping of members of the CyP-A gene family.
Amino Acid Isomerases↗
Homologs of genes and anonymous loci on human chromosome 13 map to mouse chromosomes 8 and 14.
To enhance the comparative map for human Chromosome (Chr) 13, we identified clones for human genes and anonymous loci that cross-hybridized with their mouse homologs and then used linkage crosses for mapping. Of the clones for four genes and twelve anonymous loci tested, cross-hybridization was found for six, COL4A1, COL4A2, D13S26, D13S35, F10, and PCCA. Strong evidence for homology was found for COL4A1, COL4A2, D13S26, D13S35, and F10, but only circumstantial homology evidence was obtained for PCCA. To genetically map these mouse homologs (Cf10, Col4a1, Col4a2, D14H13S26, D8H13S35, and Pcca-rs), we used interspecific and intersubspecific mapping panels. D14H13S26 and Pcca-rs were located on the distal portion of mouse Chr 14 extending by approximately 30 cM the conserved linkage between human Chr 13 and mouse Chr 14, assuming that Pcca-rs is the mouse homolog of PCCA. By contrast, Cf10, Col4a1, Col4a2, and D8H13S35 mapped near the centromere of mouse Chr 8, defining a new conserved linkage. Finally, we identified either a closely linked sequence related to Col4a2, or a recombination hot-spot between Col4a1 and Col4a2 that has been conserved in humans and mice.
Animals↗
Large genome rearrangements discovered by the detailed analysis of 21 Pseudomonas aeruginosa clone C isolates found in environment and disease habitats.
In order to determine primary genetic events which occur during the diversification of a Pseudomonas aeruginosa clone in natural habitats, comparative genome analysis of 21 isolates of a predominant clone, called clone C, derived mainly from patients with cystic fibrosis (CF) and the aquatic environment, was carried out. Physical chromosome maps were constructed for the restriction enzymes SpeI, PacI, SwaI and I-CeuI by one and two-dimensional pulsed-field gel electrophoresis and by comparison with the existing strain C map. The positioning of 26 genes generated the genetic maps. Chromosome size varied between 6345 and 6606 kilobase-pairs (kb). A plasmid of 95 kb was detected in the strains of non-CF origin and, in addition, was found to be integrated into the chromosome of all strains but one CF isolate. Four subgroups of clone C strains were discriminated by the acquisition and loss of large blocks of DNA that could cover more than 10% of the chromosome size. The exchange of DNA blocks which ranged in size from 1 kb to 214 kb occurred preferentially around the terminus of replication region which is poor in biosynthetic genes. Genetic material which was additionally introduced into strain C in comparison with strain PAO seems to be a target of mutational processes in clone C strains. Within and among subgroups CF isolates frequently exhibited large inversions affecting the whole chromosomal structure. We concluded that the exchange of DNA blocks by mechanisms of horizontal transfer and large chromosomal inversions are major factors leading to the divergence of a clone in the species P. aeruginosa.
Chromosome Mapping↗
Multi-directional chromosome painting maps homologies between species belonging to three genera of New World monkeys and humans.
We mapped chromosomal homologies in two species of Chiropotes (Pitheciini, Saki Monkeys) and one species of Aotus (Aotinae, Owl Monkey) by multi-directional chromosome painting. Human chromosome probes were hybridized to Chiropotes utahicki, C. israelita and Aotus nancymae metaphases. Wooly Monkey chromosome paints were also hybridized to Owl Monkey metaphases. We established Owl Monkey chromosome paint probes by flow sorting and reciprocally hybridized them to human chromosomes. The karyotypes of the Bearded Saki Monkeys studied here are close to the hypothesized ancestral platyrrhine karytoype, while that of the Owl Monkey appears to be highly derived. The A. nancymae karyotype is highly shuffled and only three human syntenic groups were found conserved coexisting with 17 derived human homologous associations. A minimum of 14 fissions and 13 fusions would be required to derive the A. nancymae karyotype from that of the ancestral New World primate karyotype. An inversion between homologs to segments of human 10 and 16 suggests a link between Callicebus and Chiropotes, while the syntenic association of 10/11 found in Aotus and Callicebus suggests a link between these two genera. Future molecular cytogenetic work will be needed to determine whether these rearrangements represent synapomorphic chromosomal traits.
Animals↗
The mouse glutathione peroxidase Gpx2 gene maps to chromosome 12; its pseudogene Gpx2-ps maps to chromosome 7.
The GPX2 gene codes for GSHPx-GI, a glutathione peroxidase whose mRNA is readily detectable in the gastrointestinal tract. Although GPX2 is a single gene in humans, there are two genes in the mouse genome with homology to GPX2. By analyzing a panel of mouse interspecies DNA from the Jackson Laboratory's backcross resource, we have chromosomally mapped these two genes. One was mapped to the central region of mouse chromosome 12 between D12Mit4 and D12Mit5, near fos and Tgfb3. This region is homologous to human 14q24.1, where human GPX2 has been mapped, and most likely represents the functional mouse Gpx2 gene. The other Gpx2-like gene was mapped to mouse chromosome 7 between Pcsk3 and Hbb. We have isolated the latter gene from a P1 phage library. Its pseudogene nature is revealed by the sequence analysis: (a) it is intronless; (b) it has a single nucleotide deletion in the coding region; and (c) it has a poly(A) tail at its 3'-untranslated region.
Amino Acid Sequence↗
Familial hypomagnesemia maps to chromosome 9q, not to the X chromosome: genetic linkage mapping and analysis of a balanced translocation breakpoint.
Familial hypomagnesemia with secondary hypocalcemia (HSH) (MIM 307600) was studied in three inbred Bedouin kindreds from Israel. The three kindreds, one extended and two nuclear families, contained 13 affected individuals, 11 males and two females. Assuming that the individuals affected with hypomagnesemia shared a chromosomal region inherited from a common ancestor, we used a DNA pooling strategy in a genome-wide search for loci which show homozygosity for shared alleles in affected individuals. DNA samples from affected individuals within a single kindred were pooled and used as the template for PCR amplification of short tandem repeat polymorphic markers (STRPs). Pooled DNA from unaffected siblings and parents were used as controls. A shift towards homozygosity was observed in the affected DNA pool compared with the control pools with D9S301 (GATA7D12). Genotyping of individual DNA samples with D9S301 and several flanking markers confirmed linkage to chromosome 9 with maximum LOD scores of 3.4 (theta = 0.05), 3.7 (theta = 0) and 2.3 (theta = 0) for the three families. We have identified a 14 cM interval on chromosome 9 (9q12-9q22.2), flanked by proximal marker D9S1874 and distal marker D9S1807, within which all affected individuals from the three kindreds are homozygous for a shared haplotype. The disease segregates with a common affected haplotype in the three families, suggesting that hypomagnesemia is caused by a common ancestral mutation in these families. Although HSH has been previously reported to be X linked, these linkage data demonstrate that the disorder is an autosomal recessive disease in these kindreds. Mapping of a chromosomal breakpoint in a somatic cell line established from a patient with HSH and a balanced X;9 translocation placed the chromosomal breakpoint in a 500 kb region flanked by D9S1844 and D9S273. Identification of the gene responsible for hypomagnesemia will provide insight into the regulation of this essential cation.
Arabs↗
Integration of physical, breakpoint and genetic maps of chromosome 22. Localization of 587 yeast artificial chromosomes with 238 mapped markers.
Detailed physical maps of the human genome are important resources for the identification and isolation of disease genes and for studying the structure and function of the genome. We used data from STS content mapping of YACs and natural and induced chromosomal breakpoints to anchor contigs of overlapping yeast artificial chromosome (YAC) clones spanning extensive regions of human chromosome 22. The STSs were assigned to specific regions (bins) on the chromosome using cell lines from a somatic hybrid mapping panel defining a maximum of 25 intervals. YAC libraries were screened by PCR amplification of hierarchical pools of yeast DNA with 238 markers, and a total of 587 YAC clones were identified. These YACs were assembled into contigs based upon their shared STS content using a simulated annealing algorithm. Fifteen contigs, containing between 2 and 74 STSs were assembled, and ordered along the chromosome based upon the cytogenetic breakpoint, meiotic and PFG maps. Additional singleton YACs were assigned to unique chromosomal bins. These ordered YAC contigs will be useful for identifying disease genes and chromosomal breakpoints by positional cloning and will provide the foundation for higher resolution physical maps for large scale sequencing of the chromosome.
Chromosome Mapping↗
Characterization of four yeast artificial chromosome clones mapped to human chromosome 21q22.1 with eight markers.
Yeast artificial chromosome (YAC) clones have been successfully utilized to generate a YAC contig map of the long arm of human chromosome 21 (Hu21q). The chromosome subband of 21q22.1 where five genetic loci (IFNAR1, IFNAR2, CRFB4, AF-1, and GART) are mapped is a gene-rich region and needs to be characterized in further detail. YAC D142H8 and YAC F136C5, which were characterized previously by a functional YAC expression procedure, and two new YAC clones, YAC 872B5 and YAC 876D4 located at 21q22.1 whose YAC sizes are 800 kb and 1,500 kb, respectively, were used in this study. To obtain more markers useful for making a detailed physical map of the region, a purified yeast artificial chromosome (YAC D142H8) was used to screen the 3 x 1 S cDNA library. As a result three anonymous cDNA clones (Kmy1, Kmy2, and Qorf4) were obtained, and the nucleotide sequences of Kmy1 and Kmy2 were determined. In an attempt to make a detailed physical map of the region, the locations of five known genes as well as the three new markers were determined on the four YACs by Southern blot analysis. YAC 872B5 contained all markers except GART while YAC F136C5, YAC D142H8, and YAC 876D4 contained three markers (CRFB4, IFNAR1, and IFNAR2), four markers (Kmy1, Kmy2, Qorf4 and AF-1), and four markers (Kmy1, Kmy2, Qorf4 and GART), respectively. YAC 872B5 may represent 1,500 kb of the 21q22.1 subband and half of the 3 x 1 S region, so it should be very useful for studying the relevent region of the human chromosome functionally and physically.
Base Sequence↗
A human SHC-related sequence maps to chromosome 17, the SHC gene maps to chromosome 1.
The SHC gene encodes a protein that is thought to act as an adapter in many signal transduction pathways; the SHC protein probably facilitates the activation of RAS proteins in response to a variety of factors. We have mapped the human SHC gene and have identified a new SHC-related sequence. We have sequenced the region corresponding to the SHC 3' UTR from both loci and have mapped cosmids by fluorescence in situ hybridization. The human SHC gene maps to the proximal long arm of chromosome 1 and the SHC-related sequence maps to the proximal long arm of chromosome 17. A number of cancers have been positioned in the proximal long arm of chromosome 1; this is of interest given the oncogenic potential of the SHC protein.
Base Sequence↗