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PubMed1997

The human uncoupling protein-3 gene. Genomic structure, chromosomal localization, and genetic basis for short and long form transcripts.

Uncoupling protein-3 (UCP3) is a recently identified candidate mediator of adaptive thermogenesis in humans. Unlike UCP1 and UCP2, UCP3 is expressed preferentially and at high levels in human skeletal muscle and exists as short and long form transcripts, UCP3S and UCP3L. UCP3S is predicted to encode a protein which lacks the last 37 C-terminal residues of UCP3L. In the present study, we have defined the intron-exon structure for the human UCP3 gene and determined that UCP3S is generated when a cleavage and polyadenylation signal (AATAAA) located in the last intron prematurely terminates message elongation. In addition we have mapped UCP3 to the distal segment of human chromosome 11q13 (between framework markers D11S916 and D11S911), adjacent to UCP2. Of note, UCP2 and UCP3 in both mice and humans colocalize in P1 and BAC genomic clones indicating that these two UCPs are located within 75-150 kilobases of each other and most likely resulted from a gene duplication event. Previous studies have noted that mouse UCP2 maps to a region of chromosome 7 which is coincident with three independently mapped quantitative trait loci for obesity. Our study shows that UCP3 is also coincident with these quantitative trait loci raising the possibility that abnormalities in UCP3 are responsible for obesity in these models.

Animals↗
PubMed1982

Clonal structural chromosomal rearrangements in primary fibroblast cultures and in lymphocytes of patients with Werner's Syndrome.

The cytogenetics of six cases of adult progeria (Werner's syndrome) from three Sardinian families were investigated. The overall increased incidence of chromosome breakage found in cultured lymphocytes and fibroblasts seems to be age-dependent. The occurrence of clonal variegated translocation mosaicism, previously found by other authors in fibroblast cell lines derived from Werner patients was demonstrated also in fibroblasts analyzed in situ on the outgrowth halos from primary skin explants; a strong indication that these aberrations are present in the in vivo precursors. The same type of clonal structural aberration was found for the first time also in 72h-cultured lymphocytes. These findings demonstrate that Werner's syndrome is indeed a further example of a chromosome rearrangement syndrome.

Adult↗
PubMed1975

DNA reassociation kinetics and chromosome structure in the crabs Cancer borealis and Libinia emarginata.

DNA reassociation kinetics have been partly elucidated for the higher crabs C. borealis and L. emarginata, using calf thymus DNA as a standard. These crabs contain no detectable repeated DNA in the approximate multiplicity frequency range 2-100 copies, which is unusual for invertebrate DNAs. Each species contains a component renaturing at an intermediate rate, and also a very rapidly renaturing fraction. The very rapidly renaturing fraction is considerably larger than the cesium chloride-resolvable satellites of each species. The fraction reassociating at an intermediate rate includes sequences with a reiteration frequency of up to 9.0 X 10(4) copies. This is unusually high for invertebrate DNAs. The nearly exact correlation between kinetic complexity and independently determined haploid genome size leads to the conclusion that the most slowly renaturing sequences of both crab species are present only once per haploid genome. Therefore the chromatids of these species are uninemic structures, and there has been no detectable occurrence of polyploid speciation in the recent evolutionary history of either species.

Animals↗
PubMed2006

cDNA cloning, genomic structure, chromosomal mapping and expression analysis of ADIPOQ (adiponectin) in chicken.

We report sequence, tissue expression and map position data for the adiponectin gene (ADIPOQ) in chicken. This gene is involved in adipocyte differentiation in mammals and may play similar roles in chicken. The complete coding sequence of chicken ADIPOQ encodes a 244 amino acid protein. The coding region of the chicken ADIPOQ is organized in two exons and spans an approximately 2.1 kb genomic region. Domain/motif structures of the adiponectin protein among chicken and mammalian homologs are highly conserved. Reverse transcription-PCR revealed chicken ADIPOQ mRNA displayed high expression levels in fat tissue, heart, stomach and skin and weak expression in muscle. Analysis of a radiation hybrid panel indicated that ADIPOQ showed the most significant linkage to FOXL2 (LOD = 12.63, 12 cR) and ATSV (LOD = 7.53, 3 cR) both of which are located on chicken chromosome 9. Information provided in this study will be useful in further studies to determine the role the adiponectin gene plays in the regulation of glucose and lipid metabolism and body weight in chicken.

Adiponectin↗
PubMed1987

Chromosome structure in four wild-type polytene tissues of Drosophila melanogaster. The 87A and 87C heat shock loci are induced unequally in the midgut in a manner dependent on growth temperature.

A systematic screen of wild-type Drosophila melanogaster larval organs has revealed three tissues besides the salivary gland with suitable polyteny for detailed cytogenetic analysis: the prothoracic gland, hindgut, and middle midgut. Chromosome banding patterns are very similar between tissues, but puffing patterns show considerable differences. In intact nuclei, oblique substructural elements can sometimes be detected in bands from some of the tissues. As a way of exploiting these newly characterized chromosomes, the heat shock puff response in midgut cells has been studied in detail. The puffing pattern is very similar to that in salivary glands, but an unexpected difference is found in the relative activity of the 87A7 and 87C1 loci, which contain the hsp70 genes. When larvae are raised at 16 degrees C, heat shocks ranging from 10 to 60 min induce only a weak midgut puff at 87A7 that is much smaller than that at 87C1, in contrast to other tissues where both are strongly induced. In pulse-labeled nuclei, an approximately five fold difference in transcriptional activity at the two loci is observed. However, when larvae are raised at 25 degrees C, the converse is found: the 87A7 puff is large, and little or no puffing is detectable at 87C1. Thus, in the midgut, heat shock induced puffing at these two loci is inversely modulated by a mechanism dependent on growth temperature.

Animals↗
PubMed1983

Properties of DNA rosettes and their relevance to chromosome structure.

We have studied the spreading conditions that lead to the formation of rosettes in DNA and chromatin preparations from the amphibians Bufo marinus and Bolitoglossa subpalmata and the bacterium Shigella. Both nuclear preparations and extensively deproteinized DNA produced rosettes. The longest fibers and the most symmetric rosettes were observed in amphibian nuclear spreadings. In this procedure purified nuclei were submitted immediately to Kleinschmidt spreading over various types of hypophase. Distilled-water hypophases were most conducive for rosette production or stability. Rosettes were observed with cytochrome C as the basic protein, but not with ribonuclease A and bovine serum albumin. We cannot prove that all rosettes are artifacts of the spreading procedure, but we believe that at least some result from the expansion of compact DNA doughnuts and other structures that are apparently formed in the presence of basic proteins in salt concentrations over 40 mM (Olins and Olins 1971; Manning 1979). The dilute hypophase requirements is explainable by the assumption that dilution and spreading effects unfold a compact precursor. Occasionally we have detected structures that appear to be intermediates in the process of doughnut unfolding and that illustrate a procedure that may give rise to rosettes.

Animals↗
PubMed2001

The mouse lp(A3)/Edg7 lysophosphatidic acid receptor gene: genomic structure, chromosomal localization, and expression pattern.

The extracellular signaling molecule, lysophosphatidic acid (LPA), mediates proliferative and morphological effects on cells and has been proposed to be involved in several biological processes including neuronal development, wound healing, and cancer progression. Three mammalian G protein-coupled receptors, encoded by genes designated lp (lysophospholipid) receptor or edg (endothelial differentiation gene), mediate the effects of LPA, activating similar (e.g. Ca(2+) release) as well as distinct (neurite retraction) responses. To understand the evolution and function of LPA receptor genes, we characterized lp(A3)/Edg7 in mouse and human and compared the expression pattern with the other two known LPA receptor genes (lp(A1)/Edg2 and lp(A2)/Edg4non-mutant). We found mouse and human lp(A3) to have nearly identical three-exon genomic structures, with introns upstream of the coding region for transmembrane domain (TMD) I and within the coding region for TMD VI. This structure is similar to lp(A1) and lp(A2), indicating a common ancestral gene with two introns. We localized mouse lp(A3) to distal Chromosome 3 near the varitint waddler (Va) gene, in a region syntenic with the human lp(A3) chromosomal location (1p22.3-31.1). We found highest expression levels of each of the three LPA receptor genes in adult mouse testes, relatively high expression levels of lp(A2) and lp(A3) in kidney, and moderate expression of lp(A2) and lp(A3) in lung. All lp(A) transcripts were expressed during brain development, with lp(A1) and lp(A2) transcripts expressed during the embryonic neurogenic period, and lp(A3) transcript during the early postnatal period. Our results indicate both overlapping as well as distinct functions of lp(A1), lp(A2), and lp(A3).

Alternative Splicing↗
PubMed1995

Gene structure, chromosomal localization, and expression of the murine homologue of human proteinase inhibitor 6 (PI-6) suggests divergence of PI-6 from the ovalbumin serpins.

Human proteinase inhibitor 6 (PI-6) is a recently described protein belonging to the serine proteinase inhibitor (serpin) superfamily. Sequence similarity suggests that PI-6 most resembles the ovalbumin (ov) serpins which include plasminogen activator inhibitor-2, the squamous cell carcinoma antigen, monocyte/neutrophil elastase inhibitor, and maspin. Although these proteins are associated with carcinomas and inflammation, they appear to have diverse functions and little is known of their physiological roles. In this study we have characterized cDNA and genomic clones encoding mouse PI-6 in order to analyze the localization, structure, and expression of the gene. The reactive center residues (Arg-Cys) are conserved in the mouse molecule, and recombinant mouse PI-6 was shown to bind thrombin, indicating that it has similar inhibitory properties to its human counterpart. Using reverse transcriptase-polymerase chain reaction assays on RNA isolated from 15-day-old embryos and adult mice, we have shown that mouse PI-6 expression is developmentally regulated, and that, unlike human PI-6, it is absent from the placenta. The mouse homologue of the human PI-6 gene has been designated Spi3 and was mapped to chromosome 13 between the Pl1 and ctla2 alpha genes. It spans 20 kilobases, consists of 7 exons and 6 introns, and contains a TATA motif 24 nucleotides upstream of the transcriptional start site. A 680-base pair DNA fragment containing this motif and 31 nucleotides of the 5'-untranslated region of the structural gene directed transcription of a bacterial cat gene, demonstrating the presence of a functional promoter. The PI-6 gene lacks an intron present in the ovalbumin and PAI-2 genes; otherwise it is identical in terms of the numbers, position, and phasing of the intron/exon boundaries. These results suggest that PI-6 and the ov-serpin genes have diverged and do not belong to the same subgroup.

Amino Acid Sequence↗
PubMed2000

Molecular cloning, genomic structure, chromosomal localization, and alternative splice forms of the platelet collagen receptor glycoprotein VI.

Glycoprotein VI (GPVI) is the major collagen receptor underlying platelet activation. We cloned the full-length cDNA for GPVI (GPVI-1) and its two isoforms (GPVI-2 and -3) from phorbol-ester-stimulated CMK cells. The GPVI-1 cDNA was identical in the coding region with the cDNA that has recently been reported to belong to the immunoglobulin superfamily. The GPVI gene consisted of 8 exons spanning over 23 kbp and was mapped on the chromosome 19q13. 4. The promoter of GPVI gene lacked TATA and CAAT boxes and had multiple transcription start sites like other megakaryocytic genes. When COS-7 cells were cotransfected with the GPVI isoforms and Fc receptor gamma chain, Fc receptor gamma chain was associated with GPVI-1 and -2 but did not affect the GPVI expression levels. GPVI-1 and -2 could bind the collagen-related peptide, which exhibits triple-helical and polymeric structure of collagen to activate platelets via GPVI.

Alternative Splicing↗
PubMed1990

Structure, chromosome mapping and expression of the murine Fgf-6 gene.

The sixth member of the fibroblast growth factor gene family was cloned and analysed in the mouse. It is composed of three coding exons and encodes a putative growth protein of 198 amino acids, possessing a potential signal peptide, and presenting 79% and 93.5% sequence similarity with the mouse Hst/K-fgf and human FGF-6 genes products, respectively. The murine Fgf-6 gene is located in a region distinct from the Int-41 locus and belongs to a linkage group conserved between chromosome 12 in man and chromosome 6 in mouse. It presents an intrinsic oncogenic capacity since it is able to transform cultured fibroblasts. Fgf-6 mRNA levels are developmentally regulated with a peak of expression in the developing fetus at day 15.5 of gestation, moderate levels during late gestation and in the neonate. In the adult, Fgf-6 mRNA can be detected in testis, heart and skeletal muscle.

Animals↗
PubMed1993

Human plastin genes. Comparative gene structure, chromosome location, and differential expression in normal and neoplastic cells.

Plastins are a family of actin-binding proteins that are conserved throughout eukaryote evolution and expressed in most tissues of higher eukaryotes. In humans, two ubiquitous plastin isoforms (L and T) have been identified. The L isoform is expressed only in hemopoietic cell lineages, while the T isoform has been found in all other normal cells of solid tissues that have replicative potential (fibroblasts, endothelial cells, epithelial cells, melanocytes, etc.). However, L-plastin has been found in many types of malignant human cells of non-hemopoietic origin suggesting that its expression is induced accompanying tumorigenesis in solid tissues. To learn more about the nature of plastin genes and their potential role in malignancy, the L- and T- plastin genes were cloned and sequenced to characterize their structure and mechanisms of regulation of expression. Each gene was found to be approximately 90 kilobases in size and was composed of 16 exons. All exon-intron junction sequences were identified and shown to conform to the canonical junction sequences. It was evident from their similar structure and coding homology that the two plastin genes have diverged from a common ancestor gene. L- and T-plastin genes were also mapped to chromosomes 13 and X, respectively, using polymerase chain reaction amplification with isoform-specific probes. An expanded survey of normal cell types and 50 tumor cell lines, demonstrated that 68% of carcinomas and 53% of other solid tumors of nonepithelial origin exhibited L-plastin expression, whereas the normal stem cell progenitors did not. Fibrosarcomas (n = 4), ovarian carcinomas (n = 9), breast carcinomas (n = 4), and choriocarcinomas (n = 2) combined exhibited the highest frequency and levels of L-plastin expression (95% frequency). In addition, 4 tumor cell lines that were L-plastin-negative exhibited evidence of defective T-plastin expression increasing the apparent co-incidence of plastin abnormalities associated with human tumorigenesis to 71%. Evidence is presented in support of a trans-activation mechanism for activation of L-plastin synthesis accompanying tumorigenesis. The induction of L-plastin expression accompanying SV40-mediated transformation of human embryonic lung MRC-5 fibroblasts was also confirmed. Finally, we present evidence that fimbrin is a third distinct plastin isoform which is specifically expressed at high levels in the small intestine.

Amino Acid Sequence↗
PubMed1988

[Cloning of the gpp gene of Escherichia coli and the use of recBC, sbcB cells for inserting its mutant allele into the chromosomal structure].

The gpp gene involved in the pppGpp conversion into ppGpp in Escherichia coli cells was cloned and localized within the multicopy pBR322 plasmid. Amplification of the gpp gene leads to the decline of the intracellular level of pppGpp, which implies enhanced activity of the corresponding enzyme, guanosine pentaphosphatase. To inactivate the cloned gene, a fragment of the pUC4K plasmid containing the kan gene was inserted within the gpp gene. The functional chromosomal allele of the gpp gene was replaced by its inactivated gpp::kan allele, taking advantage of homologous recombination during the transformation of recBC, sbcB cells with the intact hybrid plasmid. This procedure is accompanied by plasmid elimination and may be used for the replacement of other loci of bacterial chromosome with appropriate cloned alleles.

Alleles↗
PubMed1998

Characterisation of the mouse homologue of CD151 (PETA-3/SFA-1); genomic structure, chromosomal localisation and identification of 2 novel splice forms.

CD151 (PETA-3/SFA-1) is a member of the Transmembrane 4 Superfamily (TM4SF) of cell-surface proteins and, like other TM4SF members CD9 and CD63, is expressed by platelets, megakaryocytes and endothelial cells. The precise function of CD151 is unknown however complexes containing CD151 and beta1 integrins have been isolated from a number of cell systems and studies using anti-CD151 monoclonal antibodies have suggested a role in transmembrane signalling and cell adhesion. To further investigate the function of CD151 we have determined the genomic organisation of mouse CD151 (Cd151). Cd151 spans 4 kb and contains six coding region exons. Using 5' RACE and reverse transcriptase-polymerase chain reaction (RT-PCR) we have identified three 5' UTR splice variants which arise through alternate splicing of three exons. Splice variants were detected in a number of mouse tissues by RT-PCR. Analysis of the Cd151 genomic structure reveals a high degree of structural conservation with other TM4SF molecules supporting the theory that family members have arisen from gene duplication of a common ancestral gene. Cd151 maps to chromosome 7, in close linkage to the p gene (OCA2 in humans), and helps define a boundary in the human/mouse homology relationships.

Alternative Splicing↗
PubMed1999

Structure, chromosomal localization, and brain expression of human Cx36 gene.

Rat connexin-36 (Cx36) is the first gap junction protein shown to be expressed predominantly in neuronal cells of the mammalian central nervous system. As a prerequisite for studies devoted to the investigation of the possible role of this connexin in human neurological diseases, we report the cloning and sequencing of the human Cx36 gene, its chromosomal localization, and its pattern of expression in the human brain analyzed by radioactive in situ hybridization. The determination of the human gene sequence revealed that the coding sequence of Cx36 is highly conserved (98% identity at the protein level with the mouse and rat Cx36 and 80% with the ortholog perch and skate Cx35), and that the gene structure is that typical of the Cx35/36 subgroup observed in the other species (presence of a single intron located within the coding region, 71 bp after the translation initiation site). The distribution of Cx36 in several regions of the human central nervous system is similar to that previously observed in rat brain. The most intense signal among the cerebral areas examined by in situ hybridization was observed in the inferior olivary complex, both in principal and accessory nuclei. A moderate labeling was also observed in several myelencephalic nuclei, in specific cells of the the cerebellar cortex, in a relatively large subpopulation of cells in the cerebral cortex, in the hilus of the dentate gyrus, and in the strata radiatum and oriens of hippocampal subfields. Moreover, labeled cells were revealed in all the lamina of the spinal cord gray matter. The chromosomal localization of the human Cx36 gene was determined by fluorescence in situ hybridization. The results allowed assignment of the gene to band 15q14, thus making it a possible candidate gene for a form of familial epilepsy previously linked to the same chromosomal band. The knowledge of the human Cx36 gene sequence, of its chromosomal localization, and of its pattern of expression opens new avenues for the analysis of its possible involvement in human genetic and acquired neuropathology.

Adolescent↗
PubMed2000

Structure, chromosomal localization, and promoter analysis of the human elastin microfibril interfase located proteIN (EMILIN) gene.

Elastin microfibril interfase-located protein (EMILIN) is an extracellular matrix glycoprotein abundantly expressed in elastin-rich tissues such as the blood vessels, skin, heart, and lung. It occurs with elastic fibers at the interface between amorphous elastin and microfibrils. In vitro experiments suggested a role for EMILIN in the process of elastin deposition. This multimodular protein consists of 995 amino acids; the domain organization includes a C1q-like globular domain at the C terminus, a short collagenous stalk, a region containing two leucine zippers, and at least four heptad repeats with a high potential for forming coiled-coil alpha-helices and, at the N terminus, a cysteine-rich sequence characterized by a partial epidermal growth factor-like motif and homologous to a region of multimerin. Here we report the complete characterization of the human and murine EMILIN gene, their chromosomal assignment, and preliminary functional data of the human promoter. A cDNA probe corresponding to the C terminus of EMILIN was used to isolate two genomic clones from a human BAC library. Sequencing of several derived subclones allowed the characterization of the whole gene that was found to be about 8 kilobases in size and to contain 8 exons and 7 introns. The internal exons range in size from 17 base pairs to 1929 base pairs. All internal intron/exon junctions are defined by canonical splice donor and acceptor sites, and the different domains potentially involved in the formation of a coiled-coil structure are clustered in the largest exon. The 3'-end of the EMILIN gene overlaps with the 5'-end of the promoter region of the ketohexokinase gene, whose chromosomal position is between markers D2S305 and D2S165 on chromosome 2. A 1600-base pair-long sequence upstream of the translation starting point was evaluated for its promoter activity; five deletion constructs were assayed after transfection in primary chicken fibroblasts and in a human rhabdomyosarcoma cell line. This analysis indicates the existence of two contiguous regions able to modulate luciferase expression in both cell types used, one with a strong activatory function, ranging from positions -204 to -503, and the other, ranging from positions -504 to -683, with a strong inhibitory function.

5' Untranslated Regions↗
PubMed2001

Budding yeast chromosome structure and dynamics during mitosis.

Using green fluorescent protein probes and rapid acquisition of high-resolution fluorescence images, sister centromeres in budding yeast are found to be separated and oscillate between spindle poles before anaphase B spindle elongation. The rates of movement during these oscillations are similar to those of microtubule plus end dynamics. The degree of preanaphase separation varies widely, with infrequent centromere reassociations observed before anaphase. Centromeres are in a metaphase-like conformation, whereas chromosome arms are neither aligned nor separated before anaphase. Upon spindle elongation, centromere to pole movement (anaphase A) was synchronous for all centromeres and occurred coincident with or immediately after spindle pole separation (anaphase B). Chromatin proximal to the centromere is stretched poleward before and during anaphase onset. The stretched chromatin was observed to segregate to the spindle pole bodies at rates greater than centromere to pole movement, indicative of rapid elastic recoil between the chromosome arm and the centromere. These results indicate that the elastic properties of DNA play an as of yet undiscovered role in the poleward movement of chromosome arms.

Anaphase↗
PubMed2002

Mouse cytosolic and mitochondrial deoxyribonucleotidases: cDNA cloning of the mitochondrial enzyme, gene structures, chromosomal mapping and comparison with the human orthologs.

Two of the five known mammalian 5'-nucleotidases show a preference for the dephosphorylation of deoxynucleoside-5'-phosphates. One is a cytoplasmic enzyme (dNT-1), the other occurs in mitochondria (dNT-2). The human mitochondrial enzyme, recently discovered and cloned by us, is encoded by a nuclear gene located on chromosome 17 p11.2 in the critical region deleted in the Smith-Magenis syndrome (SMS), a genetic disease of unknown etiology. Looking for a model system to study the possible involvement of dNT-2 in the disease, we have cloned the cDNA of the mouse ortholog. The deduced protein sequence is 84% identical to the human ortholog, has a very basic NH(2)-terminus, a very high calculated probability of being imported into mitochondria and contains the DXDXT/V motif conserved among nucleotidases. Expression in Escherichia coli of the predicted processed form of the protein produced an active deoxyribonucleotidase. We also identified in genomic sequences present in the data base the structures of the murine genes for the cytosolic and mitochondrial deoxyribonucleotidases (Nt5c and Nt5m). PAC clones for the two loci were isolated from a library and used for chromosomal localization by fluorescent in situ hybridization. Both genes map on chromosome 11: Nt5c at 11E and Nt5m at 11B, demonstrating the presence of the dNT-2 locus in the mouse shaker-2 critical region, the murine counterpart of the human SMS region. We performed pair-wise dot-plot and PIP (percent identity plot) analyses of mouse and human deoxyribonucleotidase genes, and found a strong conservation that extends also to some intronic sequences of possible regulatory significance.

5'-Nucleotidase↗