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PubMed1995

A second locus for hereditary hemorrhagic telangiectasia maps to chromosome 12.

Hereditary hemorrhagic telangiectasia (HHT) or Osler-Rendu-Weber (ORW) disease is an autosomal dominant vascular dysplasia. Initial linkage studies identified an ORW gene localized to 9q33-q34 but with some families clearly excluding this region. A probable correlation in clinical phenotype between the 9q3-linked families and unlinked families was described with a significantly lower incidence of pulmonary arteriovenous malformations observed in the unlinked families. In this study we examined four unrelated ORW families for which linkage to chromosome 9q33-q34 has been previously excluded. Linkage was established for all four families to markers on chromosome 12, with a combined maximum lod score of 10.77 (theta = 0.04) with D12S339. Mapping of crossovers using haplotype analysis indicated that the candidate region lies in an 11-CM interval between D12S345 and D12S339, in the pericentromeric region of chromosome 12. A map location for a second ORW locus is thus established that exhibits a significantly reduced incidence of pulmonary involvement.

Chromosome Mapping↗
PubMed1988

Refined linkage map of chromosome 7 in the region of the cystic fibrosis gene.

The genetic map in the region of human chromosome 7 that harbors the gene for cystic fibrosis (CF) has been refined by multilocus linkage studies in an expanded database including a large set of normal families. Six loci known to be linked to CF were examined: MET, an oncogene; COL1A2, collagen, TCRB, T-cell-receptor beta polypeptide; and three arbitrary loci--D7S8, D7S13, and D7S16--defined by probes pJ3.11, pB79a, and p7C22, respectively. The gene order with greatest statistical support is COL1A2-D7S13-D7S16-MET-D7S8-TCRB. Linkage analysis in families segregating for CF suggested that the most likely location of the CF gene on this map is between MET and D7S8.

Chromosome Mapping↗
PubMed1997

Cloning of a novel human neural cell adhesion molecule gene (NCAM2) that maps to chromosome region 21q21 and is potentially involved in Down syndrome.

To contribute to the development of the transcription map of human chromosome 21 (HC21), we have used exon trapping to identify portions of HC21 genes. One trapped exon showed strong homology with members of the neural cell adhesion molecule (NCAM) family of genes from different species. We subsequently cloned the complete coding sequence from a human fetal brain cDNA library and determined its nucleotide sequence and predicted amino acid sequence. The predicted polypeptide of this novel NCAM2 gene contains 837 amino acids and shows 62% similarity to the NCAM homologs. It contains five immunoglobulin-like domains, two fibronectin type III domains, a transmembrane domain and a cytoplasmic domain. The gene is expressed most strongly in human adult and fetal brain. Using somatic cell hybrids, we mapped NCAM2 to 21q21, between markers D21S18 and D21S282. Radiation hybrid mapping localized this novel gene between polymorphic markers D21S1914 and D21S265. NCAMs are members of the immunoglobulin superfamily and are essential in the formation and maintenance of tissue structure. To date there are no candidate human disorders on HC21 that could be associated with mutations in NCAM2. In addition, the role of NCAM2 in the pathophysiology of Down syndrome is unknown. However, it is a good candidate for involvement in certain Down syndrome phenotypes because a slight overexpression of NCAMs increases many-fold the homotypic adhesion properties of cells.

Adult↗
PubMed1995

MudSacI, a transposon with strong selectable and counterselectable markers: use for rapid mapping of chromosomal mutations in Salmonella typhimurium.

The transposable bacteriophage Mu and its mini-Mu derivatives are useful tools for the genetic analysis of many bacteria. A variety of antibiotic-resistant Mu derivatives have been constructed, allowing direct selection for cells which contain the transposon. However, in many cases a counterselection against the transposon would greatly facilitate further genetic analysis. In this paper we report the construction of MudSacI, a mini-Mu derived transposon containing the sacB (secretory levansucrase) gene of Bacillus subtilis, which confers sucrose sensitivity upon gram-negative bacteria. We describe the use of this transposon as a tool for rapid genetic mapping of chromosomal genes in Salmonella typhimurium. Simple modifications of this approach should facilitate rapid mapping in many other bacteria as well.

Bacteriophage mu↗
PubMed1989

Human ret proto-oncogene mapped to chromosome 10q11.2.

Using cosmid clones derived from human ret protooncogene as probes, we determined its chromosome localization by fluorescence in situ hybridization. Two overlapping clones, cret-1 and -2, which were cloned using the most 5' part of human ret proto-oncogene cDNA, hybridized to chromosome 10q11.2. Sixty-three and 52% of the grains obtained by cret-1 and -2, respectively, were localized to the same site. No other specific hybridization site was observed. From these data, we assigned the site of ret proto-oncogene to chromosome 10q11.2, where the possible locus responsible for multiple endocrine neoplasia type 2A (MEN2A) was mapped by linkage analysis using interstitial retinol binding protein cDNA and D10S5. These findings suggest that ret proto-oncogene might be a suitable probe for approaching the MEN2A locus.

Chromosome Mapping↗
PubMed1990

A detailed multipoint gene map of chromosome 1q.

Utilizing genotyping data for 23 markers, we have constructed a 21-locus multipoint genetic map of the long arm of chromosome 1. Five new RFLPs are reported. The map integrates anonymous loci from previous primary linkage maps and incorporates markers for 10 coding sequences. These markers form a continuous linkage group of 85 cM in males and 141 cM in females. The map was constructed employing the LINKAGE and CRIMAP computational methodologies via a stepwise algorithm.

Algorithms↗
PubMed1997

Cloning and characterization of freac-9 (FKHL17), a novel kidney-expressed human forkhead gene that maps to chromosome 1p32-p34.

We describe the cloning of a near full-length cDNA of 4258 nucleotides encoding freac-9 (HGMW-approved symbol FKHL17), a novel human forkhead gene. The 5' untranslated region is unusual since it is very long, 2127 nucleotides, and contains 15 upstream AUG codons. Hybridization to a panel consisting of RNA derived from 50 different tissues showed that freac-9 is transcribed exclusively in the kidney. The kidney-derived cell lines COS-7 and 293 are shown to express freac-9. A combination of fluorescence in situ hybridization and somatic cell hybrids localizes freac-9 to the chromosomal region of 1p32-p34. The conceptual translation product predicts a protein of 372 amino acids with an N-terminal domain rich in acidic amino acids and with a high likelihood of forming an amphipatic helix, a DNA binding forkhead domain, and a C-terminal region that has a high probability of forming an amphipatic beta-sheet. The amino acid sequence of the DNA binding forkhead motif of FREAC-9 is identical to that of another forkhead protein, FREAC-4, whereas 12 substitutions are present at the nucleotide level. There are no similarities in regions outside of the DNA binding domains of FREAC-9 and FREAC-4 and since freac-4 maps to a different chromosome (5q12-q13) it is likely that an evolutionary selection has acted to maintain identical DNA binding domains between these two kidney expressed transcription factors.

Amino Acid Sequence↗
PubMed2006

High-resolution radiation hybrid map of wheat chromosome 1D.

Physical mapping methods that do not rely on meiotic recombination are necessary for complex polyploid genomes such as wheat (Triticum aestivum L.). This need is due to the uneven distribution of recombination and significant variation in genetic to physical distance ratios. One method that has proven valuable in a number of nonplant and plant systems is radiation hybrid (RH) mapping. This work presents, for the first time, a high-resolution radiation hybrid map of wheat chromosome 1D (D genome) in a tetraploid durum wheat (T. turgidum L., AB genomes) background. An RH panel of 87 lines was used to map 378 molecular markers, which detected 2312 chromosome breaks. The total map distance ranged from approximately 3,341 cR(35,000) for five major linkage groups to 11,773 cR(35,000) for a comprehensive map. The mapping resolution was estimated to be approximately 199 kb/break and provided the starting point for BAC contig alignment. To date, this is the highest resolution that has been obtained by plant RH mapping and serves as a first step for the development of RH resources in wheat.

Chromosome Breakage↗
PubMed1996

The active gene that encodes human high mobility group 1 protein (HMG1) contains introns and maps to chromosome 13.

The human genome contains a large number of sequences related to the cDNA for High Mobility Group 1 protein (HMG1), which so far has hampered the cloning and mapping of the active HMG1 gene. We show that the human HMG1 gene contains introns, while the HMG1-related sequences do not and most likely are retrotransposed pseudogenes. We identified eight YACs from the ICI and CEPH libraries that contain the human HMG1 gene. The HMG1 gene is similar in structure to the previously characterized murine homologue and maps to human chromosome 13 band q12, as determined by in situ hybridization. The mouse Hmg1 gene maps to the telomeric region of murine Chromosome 5, which is syntenic to the human 13q12 band.

Amino Acid Sequence↗
PubMed1983

Mapping of chromosomal IS5 elements that mediate type II F-prime plasmid excision in Escherichia coli K-12.

Three IS5 elements were mapped in overlapping chromosomal segments on a series of F-prime plasmids by restriction analysis and hybridization. IS5A was located clockwise of proA near 6 min, IS5B was located clockwise of purE near 12 min, and IS5C was tentatively located near 14 min on the Escherichia coli K-12 map. The physical structures of nine type II F-prime plasmids that contain chromosomal DNA from this region indicated that these plasmids were excised from the chromosome by recombination between pairs of IS5 elements.

Base Sequence↗
PubMed1998

Human ARHGDIG, a GDP-dissociation inhibitor for Rho proteins: genomic structure, sequence, expression analysis, and mapping to chromosome 16p13.3.

GDP-dissociation inhibitors (GDIs) play a primary role in modulating the activity of GTPases. We recently reported the identification of a new GDI for the Rho-related GTPases named RhoGDIgamma. This gene is now designated ARHGDIG by HUGO. Here, in a detailed analysis of tissue expression of ARHGDIG, we observe high levels in the entire brain, with regional variations. The mRNA is also present at high levels in kidney and pancreas and at moderate levels in spinal cord, stomach, and pituitary gland. In other tissues examined, the mRNA levels are very low (lung, trachea, small intestine, colon, placenta) or undetectable. RT-PCR analysis of total RNA isolated from exocrine pancreas and islets shows that the gene is expressed in both tissues. We also report the genomic structure of ARHGDIG. The gene spans over 4 kb and is organized into six exons and five introns. The upstream region lacks a canonical TATA box and contains several putative binding sites for ubiquitous and tissue-specific factors active in central nervous system development. Using FISH, we have mapped the gene to chromosome band 16p13.3. This band is rich in deletion mutants of genes involved in several human diseases, notably polycystic kidney disease, alpha-thalassemia, tuberous sclerosis, mental retardation, and cancer. The promoter structure and the chromosomal location of RhoGDIgamma suggest its importance and underscore the need for further investigation into its biology.

Base Sequence↗
PubMed1995

CEPH consortium map of chromosome 14.

Families from the linkage panel of Centre d'Etude du Polymorphisme Humain have been used to generate a linkage map containing 68 loci; 13 genes, 33 di- and 4 tetranucleotide repeats, one oligonucleotide ligation assay (OLA), and 17 RFLPs. This map integrates markers from several previous maps, and has undergone further error checking. 43 loci have been placed with odds of 1000:1 or greater, five with odds of 100:1, with an average interval of 3.5 cM. An additional 20 loci have been placed within defined intervals.

Chromosome Mapping↗
PubMed1992

The human gene for oxytocin-neurophysin I (OXT) is physically mapped to chromosome 20p13 by in situ hybridization.

Two posterior pituitary hormones oxytocin and arginine-vasopressin control the important activities of water excretion, parturition and lactation. Both these hormones are synthesized as inactive precursors in the hypothalamus along with their carrier proteins neurophysin I and neurophysin II respectively and are activated upon transport to posterior pituitary. Human genes for both oxytocin-neurophysin I (OXT) and arginine-vasopressin-neurophysin II (ARVP) are cloned and found to be linked on chromosome 20 separated by approximately 12 kb of intergenic sequences. Though OXT is not yet associated with any disease, ARVP is linked to the autosomal dominant disease neurohypophyseal diabetes insipidus (AD-NDI). We have mapped regionally the OXT locus to chromosome 20p13 by both radioactive (ISH) and fluorescence in situ hybridization (FISH).

Arginine Vasopressin↗
PubMed1997

The human gene encoding FKBP-rapamycin associated protein (FRAP) maps to chromosomal band 1p36.2.

FKBP-rapamycin associated protein (FRAP) is a phosphatidylinositol kinase (PIK)-related kinase implicated in the inhibition of progression through G1 of the cell cycle. The PIK-related kinases are a growing family of proteins involved in cell-cycle checkpoints, DNA repair and recombination. We have mapped the human FRAP gene to chromosome 1p36.2, a region consistently deleted in neuroblastomas.

Base Sequence↗
PubMed1998

The human poly(ADP-ribose) glycohydrolase maps to chromosome 10q11.23-21.1 by fluorescence in situ hybridization.

Poly(ADP-ribose) glycohydrolase (PARG) digests poly(ADP-ribose), which is synthesized by poly(ADP-ribose) polymerase (PARP) after DNA damage. We mapped the human poly(ADP-ribose) glycohydrolase gene to chromosome 10q11.23-21.1 by fluorescence in situ hybridization analysis. Since chromosomal rearrangements in thyroid papillary carcinoma and loss of heterozygosity in glioblastoma are frequently observed in this region, genetic alteration of PARG could be implicated in these diseases.

Base Sequence↗
PubMed1994

A yeast artificial chromosome clone map of the Drosophila genome.

We describe the mapping of 979 randomly selected large yeast artificial chromosome (YAC) clones of Drosophila DNA by in situ hybridization to polytene chromosomes. Eight hundred and fifty-five of the clones are euchromatic and have primary hybridization sites in the banded portions of the polytene chromosomes, whereas 124 are heterochromatic and label the chromocenter. The average euchromatic clone contains about 211 kb and, at its primary site, labels eight or nine contiguous polytene bands. Thus, the extent as well as chromosomal position of each clone has been determined. By direct band counts, we estimate our clones provide about 76% coverage of the euchromatin of the major autosomes, and 63% coverage of the X. When previously reported YAC mapping data are combined with ours, euchromatic coverage is extended to about 90% for the autosomes and 82% for the X. The distribution of gap sizes in our map and the coverage achieved are in good agreement with expectations based on the assumption of random coverage, indicating that euchromatic clones are essentially randomly distributed. However, certain gaps in coverage, including the entire fourth chromosome euchromatin, may be significant. Heterochromatic sequences are underrepresented among the YAC clones by two to three fold. This may result, at least in part, from underrepresentation of heterochromatic sequences in adult DNA (the source of most of the clones analyzed), or from clone instability.

Animals↗
PubMed1999

Cloning and expression of a murine histone deacetylase 3 (mHdac3) cDNA and mapping to a region of conserved synteny between murine chromosome 18 and human chromosome 5.

Histone deacetylases (HDACs) are enzymes that play a pivotal role in transcription, differentiation, and cell cycle progression. We previously cloned human HDAC3 cDNA and showed that its transfection into THP-1 cells results in G2/M cell cycle accumulation. Using bioinformatic screening and PCR, we have now cloned the murine Hdac3 cDNA, which encodes a 428-amino-acid protein with near complete identity to its human ortholog. To establish a link to a potential disease locus, we performed PCR-based chromosomal mapping for the mHdac3 gene and chromosomal fluorescence in situ hybridization (FISH) for the human gene. mHdac3 localizes to chromosome 18 and human HDAC3 gene localizes to a syntenic region in chromosome 5 at band q31.3-q32 telomeric to the cytokine gene cluster. Transfection of mHdac3 into HeLa cells led to accumulation in G2/M. Our results suggest a cell cycle function for murine Hdac3, reflecting the complex regulatory roles of this gene family.

Amino Acid Sequence↗