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PubMed2001

Genomic structure and chromosomal mapping of the gene coding for ICBP90, a protein involved in the regulation of the topoisomerase IIalpha gene expression.

We have recently identified a novel CCAAT box binding protein (ICBP90) involved in the regulation of topoisomerase IIalpha gene expression. We have observed that it is expressed in non-tumoral proliferating human lung fibroblast cells whereas in HeLa cells, a tumoral cell line, ICBP90 was still present even when cells were at confluence. In the present study, we have determined the ICBP90 gene structure by screening of a human placenta genomic library and PCR analysis. We report that the ICBP90 gene spans about 35.8 kb and contains six coding exons named A to F. In the 5' upstream sequence of the region containing the coding exons, two additional exons (I and II) were found. Additionally, an internal splicing site was found in exon A. A promoter region, including three putative Sp1 binding sites between exons I and A, was identified by transient transfection. Northern blot analysis of several cancer cell lines revealed the existence of two ICBP90 mRNA species of 5.1 and 4.3 kb that are transcribed from the gene. The relative amounts of these mRNAs depended on the cell type. In MOLT-4 cells and Burkitt's lymphoma Raji cells, the 4.3 kb or the 5.1 kb transcripts were mainly observed, respectively. In other cell lines, such as HL-60 cells, chronic myelogenous leukaemia K-562, lung carcinoma A549, HeLa or colorectal SW480, both 4.3 and 5.1 kb forms of ICBP90 mRNA could be detected. Interestingly, western blot analysis showed several ICBP90 protein bands in HeLa but only a single band in MOLT-4 cell extracts. Taken together our results are consistent with the ICBP90 gene exhibiting alternative splicing and promoter usage in a cell-specific manner.

Alternative Splicing↗
PubMed2004

[Chromosome maps of trilliaceae: II. A study of the genome composition in polyploid species of the genus Trillium by fluorescence nucleotide base-specific staining of heterochromatic chromosome regions].

Chromosome banding with nucleotide base-specific fluorochromes chromomycin A3 (CMA) and Hoechst 33258 (H33258) was used to study the karyotypes and to construct cytological maps for diploid Trillium camschatcense (2n = 10), tetraploid T. tschonoskii (2n = 20), hexaploid T. rhombifolium (2n = 30), and a triploid T. camschatcense x T. tschonoskii hybrid (T. x hagae, 2n = 15). With H33258, species- and genome-specific patterns with numerous AT-rich heterochromatin bands were obtained for each of the four forms; CMA revealed a few small, mostly telomeric GC-rich bands. In T. tschonoskii, the two subgenomes were similar to each other and differed from the T. camschatcense genome; on this evidence, the species was considered to be a segmental allotetraploid. In T. x hagae, one T. camschatcense and both T. tschonoskii subgenomes were identified. The subgenomes of T. rhombifolium only partly corresponded to the T. camschatcense and T. tschonoskii genomes, in contrast to the morphologically identical Japanese species T. hagae. This was assumed to indicate that allohexaploids T. rhombifolium and T. hagae originated independently at different times; i.e., their origin is polyphyletic. Based on the chromosome maps, a new nomenclature was proposed for the Trillium genomes examined: K1K1 for T. camschatcense, T1T1T2T2 for T. tschonoskii, T1T1T2T2 for T. x hagae, and K1RK1RT1RT1RT2RT2R for T. rhombifolium.

Chromosome Mapping↗
PubMed1991

Chromosomal mapping of brain-derived neurotrophic factor and neurotrophin-3 genes in man and mouse.

Brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NTF3) are two new members of the nerve growth factor gene family, which play important roles in the development and maintenance of the vertebrate nervous system. Here we describe the assignments of the BDNF and NTF3 gene loci to human and mouse chromosomes and discuss the evolutionary relationship of human chromosomes 11 and 12. BDNF has been mapped to human chromosome 11p15.5-p11.2 and to mouse chromosome 2, and NTF3 to human chromosome 12p and mouse chromosome 6.

Animals↗
PubMed1982

Genetic mapping: chromosomes 6-22.

Using a method that considers physical assignments and the distribution of chiasmata, as well as linkage data, genetic maps are constructed for chromosomes 6, 9, 13, and 16, and unassigned markers are tested for inclusion in these linear maps.

Centromere↗
PubMed1988

Chromosomal mapping of lysosomal enzyme structural genes in the domestic cat.

A panel of 42 rodent x cat somatic cell hybrids has been used to assign seven structural genes for lysosomal enzymes to specific chromosomes in the domestic cat. The assignments include alpha-glucosidase (GANAB) to chromosome D1, alpha-galactosidase (GLA) to the X chromosome, beta-galactosidase 1 (GLB1) to chromosome B3, beta-glucuronidase (GUSB) to chromosome E3, alpha-mannosidase A (MANA) to chromosome B3, alpha-L-fucosidase (FUCA) to chromosome C1, and hexosaminidase A (HEXA) to chromosome B3. In all cases, the feline lysosomal enzyme genes were located in linkage groups which were syntenic with their homologous positions in the human gene map. These assignments expand the genetic map of the cat and reaffirm the extensive syntenic homology between the chromosome maps of man and cat.

Animals↗
PubMed1999

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.

Animals↗
PubMed1991

The PHO80/TUP7 locus in Saccharomyces cerevisiae is on the left arm of chromosome XV: mapping by chromosome engineering.

The PHO80/TUP7 locus in Saccharomyces cerevisiae is reported to be located on the right arm of chromosome XV close to its centromere. In the present study, the locus has been reassigned to the left arm of the same chromosome by reciprocal recombination between chromosomes V and XV at URA3 (on chromosome V) and PHO80/TUP7 loci by using the site-specific recombination system of the yeast plasmid pSR1.

Chromosome Mapping↗
PubMed1983

A rapid chromosome-mapping method for cloned fragments of yeast DNA.

A rapid and generally applicable method is described for mapping a cloned yeast DNA segment to the chromosome(s) from which it originated. The method is based upon the recent finding that the integration into a yeast chromosome of a segment of the 2 mu plasmid DNA results, in heterozygous diploids, in the specific loss of genetic information from the chromosome into which the 2 mu DNA was integrated (Falco et al. 1982). After verification of the accuracy of the method using several genes whose position was known in advance, the method was used to locate the yeast actin gene, which lies on the left arm of chromosome VI, about 50 cM distal to CDC4.

Actins↗
PubMed2000

Cloning and chromosomal mapping of the mouse and human genes encoding the orphan glucocorticoid-induced receptor (GPR83).

The mouse glucocorticoid-induced receptor (GIR) is an orphan G protein-coupled receptor highly expressed in brain and thymus (Harrigan et al., 1989; 1991). We have cloned the mouse GIR gene (Gpr83), determined its genomic organization and compared it with the human gene. The genomic organization of the gene is similar in both species although differences leading to specific splicing variants in the mouse have been found. Three introns interrupting the coding sequence are common to both mouse and human. A short sequence in the second intron of the mouse gene can be alternatively spliced in, leading to an insertion in the second intracellular loop of the receptor. This insertion constitutes an additional exon which is not present in the human genome. The human GIR polypeptide shares 89.5% and 91.5% identity with its mouse and dog orthologs respectively. Splice variants lacking the first extracellular loop and the third transmembrane domain have been found in human and mouse species. The receptor variants resulting from these minor transcripts are likely to be non functional. Comparative genetic mapping of the Gpr83 gene showed that it maps to regions of conserved synteny on mouse chromosome 9 (A2-3 region) and human chromosome 11 (q21 region).

Amino Acid Sequence↗
PubMed1994

Identification and chromosomal mapping of a receptor tyrosine kinase with a putative phospholipid binding sequence in its ectodomain.

We have cloned a novel receptor tyrosine kinase that has an unusual ectodomain. The extracellular sequence consists of 416 amino acids and has none of the structural motifs that have been found in other receptor tyrosine kinases. The 150 amino acids in the amino terminus of the receptor is homologous to a putative phospholipid-binding sequence that is found also in other cell adhesion molecules such as the neuronal A5 antigen and coagulation factors V and VIII. The kinase domain has a short cytoplasmic tail and contains a short insert between subdomains I and II. The structure of this receptor kinase suggests that it belongs to a new family of receptors involved in cell-cell interactions. The cell adhesion kinase (Cak) is expressed at low levels in most adult tissues and expression is highest in the brain and lung. Using fluorescence in situ hybridization and interspecific backcross mapping, the Cak gene was localized to human chromosome 6 and mouse chromosome 17.

Amino Acid Sequence↗
PubMedDate not supplied

Comparative chromosome mapping of a conserved homoeo box region in mouse and human.

Specific genes are assumed to regulate pattern formation in the mammalian embryo, but as yet none has been identified unequivocally. It is possible that such genes in mammals may be identified by virtue of a conserved coding sequence, because many of the Drosophila melanogaster homoeotic and segmentation genes, which have crucial roles in the regulation of segmental pattern formation during embryonic development, contain a 180-base pair (bp) DNA sequence, the homoeo box, and that sequences homologous to the Drosophila homoeo box are also present in 6-10 copies in higher animals, including mammals. Although the assumption that the homoeo box identifies genes responsible for pattern formation in mammals remains to be validated, it is a particularly attractive hypothesis given the strong conservation of homoeo boxes over vast evolutionary distances. Here we report the localization of a human homoeo box region, previously cloned and shown to contain two homoeo boxes within a sequence of 5-kilobases (kb), to the long arm of chromosome 17. We show that two single-copy homoeo box-flanking probes derived from this region strongly hybridize to single-copy restriction fragments in mouse genomic DNA and that these conserved homoeo box-flanking sequences map to mouse chromosome 11. This may be significant as several genes that map to chromosome 17 in human also map to chromosome 11 in the mouse, implying that a segment of mouse chromosome 11 is homologous to a region of human chromosome 17. Taken together, these data suggest that the homoeo box region detected with our probes is highly conserved in human and mouse.

Animals↗
PubMed1983

Plasmids, recombination and chromosome mapping in Streptomyces lividans 66.

Streptomyces lividans 66 was shown to harbour two self-transmissible plasmids: SLP2, which acts as a sex factor, and SLP3. Derivatives of this strain which had lost both plasmids were used as host strains to study a range of Streptomyces plasmids for their ability to promote their own transfer and to mobilize chromosomal markers. A linkage map of the S. lividans chromosome containing ten markers was derived from the results of matings using several different sex plasmids, and protoplast fusions. SLP2 was transferred interspecifically to S. parvulus ATCC 12434 and to S. coelicolor A3(2); in the latter it acted as a fertility factor. Interspecific crosses also led to the discovery of a further plasmid, SLP4, from S. coelicolor, SLP2, SLP3 and SLP4 could not be visualized on agarose gels using standard plasmid isolation procedures, but their presence was detected by transformation into S. lividans.

Chromosome Mapping↗
PubMed1982

Isolation of a human repetitive sequence and its application to regional chromosome mapping.

Recombinant lambda phage Charon 4A with repetitive human DNA inserts have been constructed by using cellular DNA from a human-Chinese hamster ovary cell hybrid retaining the complete hamster genome and a single human chromosome 12. One recombinant phage, 12-11, contains several repetitive sequences, each with a different repetition pattern in the human genome. A 2.2-kilobase (kb) EcoRI fragment of this phage was subcloned in pBR325. This sequence has fewer than 5,000 copies in the human genome and does not cross-hybridize with Chinese hamster DNA. When the labeled 2.2-kb probe was hybridized to human chromosome 12 DNA digested with EcoRI, there was an intense band at the 2.2-kb position and a series of other discrete bands. The band pattern at positions other than 2.2 kb appears to be distinct for each human chromosome. The 2.2-kb fragment is composed of at least three subregions. The ends of the fragment are repeated more frequently in the genome than is the middle portion. Hybridization of chromosome 12 DNA with probes made to these subregions yielded simpler band patterns. By using a series of cell hybrids containing various deletions of human chromosome 12, five sequences related to the 2.2-kb fragment have been assigned regionally to a specific portion of the short arm of chromosome 12. These results demonstrate that certain repetitive sequences in the human genome can be used as genetic markers and may permit detailed regional mapping of human chromosomes.

Animals↗
PubMed2002

Chromosomal map of the model legume Lotus japonicus.

Lotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F(1) hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

Centromere↗
PubMed1994

Physical mapping of 5S rDNA reveals a new locus on 3R and unexpected complexity in a rye translocation used in chromosome mapping.

Using fluorescence in situ hybridization (FISH) with probe pScT7, three different 5S rDNA loci were detected in the satellite of rye chromosome 1R (5SDna-R1) and in the short arms of chromosomes 3R (5SDna-R3) and 5R (5SDna-R2) respectively. All three loci showed polymorphism for the hybridization signal intensity. In order to determine the localization of these rye 5S rDNA multigene loci with higher precision within the corresponding chromosome arms, the probe pScT7 was physically mapped by FISH in relation to the following five translocations (Wageningen Tester Set): T850W (1RS/4RL), T248W (1RS/6RS), T273W (1RS/5RL), T305W (2RS/5RS) and T240W (3RS/5RL). Accurate physical maps of the translocation breakpoints had previously been made using electron microscope analysis of spread pachytene synaptonemal complexes of heterozygotes for the different translocations. The results indicate that locus 5SDna-R3 is located between the breakpoint of translocation T240W and the telomere, whereas locus 5SDna-R2 is located between the breakpoint of translocation T305W and the centromere, the hybridization of probe pScT7 on T305W translocated chromosomes demonstrating the complex nature of this translocation. On the other hand, the simultaneous detection of probes pScT7 and pTA71 (18S-5.8S-26S rDNA) with two different fluorochromes, indicated that the breakpoints of translocations T850W and T248W are located between loci Nor-R1 and 5SDna-R1.

Chromosome Mapping↗
PubMed1987

[Creation of a clone panel of fox x Chinese hamster somatic cell hybrids and chromosome mapping of genes for LDHA, LDHB, GPI, ESD, G6PD, HPRT, alpha-GALA in the silver fox].

A clone panel of fox-hamster somatic cell hybrids which can be used for fox gene mapping was set up. Analysis of patterns of chromosome-enzyme segregation made it possible to assign gene GPI to chromosome 1, LDHA to chromosome 11, LDHB to chromosome 8, ESD to chromosome 6 and G6PD, HPRT, alpha-GALA to chromosome X.

Animals↗