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PubMed1995

Structure, chromosomal location, and expression pattern of three mouse genes homologous to the human MAGE genes.

The human MAGE1 gene directs the expression of an antigen recognized on a melanoma by autologous cytolytic T lymphocytes. MAGE1 belongs to a family of genes that are expressed in a number of tumors of various histological types but not in normal tissues except testis. The MAGE genes are arranged in two groups that are located within two different regions of the human X chromosome (Xq26-qter and Xp21.3). By hybridizing mouse genomic libraries with a MAGE1 probe, we identified three homologous genes. Two of these mouse genes, Smage1 and Smage2, are more than 99% identical to each other and encode the same protein of 330 aa. The 5' noncoding region of Smage2 provides the potential for regulating the expression of the gene through several different promoters located in front of alternative first exons. The third gene, Smage3, has the structure of a processed transcript. It codes for a protein with only 11 aa substitutions with respect to the Smage1/2 product. Somatic cell hybrids and interspecific backcross analysis showed that Smage3 is autosomal and that Smage1 and Smage2 are located between the Dmd and the Ar loci on the mouse X chromosome. Since this region is syntenic to the human Xp21.1-p22.1 region, we conclude that Smage1 and Smage2 are homologous to the MAGE-Xp rather than to the MAGE-Xq genes. Smage1/2 transcripts were detected in several tumor and embryonal cell lines but not in normal mouse tissues with the exception of testis. Expression of Smage3 was found in embryos from Day 11 to Day 15.

Amino Acid Sequence↗
PubMed2000

Gene structure, chromosomal localization, and expression pattern of Capn12, a new member of the calpain large subunit gene family.

We report the identification of mouse Capn12, a new member of the calpain large subunit gene family. It possesses potential protease and calcium-binding domains, features typical of the classical calpains. In situ hybridization and Northern blot analysis demonstrate that during the anagen phase of the hair cycle the cortex of the hair follicle is the major expression site of Capn12. The gene was sequenced in its entirety and consists of 21 exons spanning 13 kb with an exon-intron structure typical of the calpain gene family. The last exon of the mouse Actn4 gene overlaps the 3' end of Capn12 but in the opposite orientation. This overlap between the two genes is conserved in the human genome. Three versions of the Capn12 mRNA transcript were identified. They occur as a result of alternative splicing, and two of these encode a protein lacking the C-terminal calmodulin-like domain. Radiation hybrid mapping localized Capn12 to mouse chromosome 7, closely linked to a marker positioned at 10.4 cM. Refined mapping of Capn5, also previously localized to chromosome 7, indicated that it was not closely linked to Capn12, mapping tightly linked to a marker positioned at 48.5 cM.

Actinin↗
PubMed1998

Proviral structure, chromosomal location, and expression of HERV-K-T47D, a novel human endogenous retrovirus derived from T47D particles.

We previously described that type B retrovirus-like particles released from the human mammary carcinoma cell line T47D are pseudotypes and package retroviral RNA of different origins (W. Seifarth, H. Skladny, F. Krieg-Schneider, A. Reichert, R. Hehlmann, and C. Leib-Mösch, J. Virol. 69:6408-6416, 1995). One preferentially packaged retroviral sequence, ERV-MLN, has now been used to isolate the corresponding full-length provirus from a human genomic library. The 9,315-bp proviral genome comprises a complete retroviral structure except for a 3' long terminal repeat (LTR) truncation. A lysine tRNA primer-binding site and phylogenetic analyses assign this human endogenous retroviral element, now called HERV-K-T47D, to the HML-4 subgroup of the HERV-K superfamily. The gag, prt, pol, and env genes exhibit 40 to 60% amino acid identity to HERV-K10. HERV-K-T47D is located on human chromosome 10, with five closely related elements on chromosomes 8, 9, 15, 16, and 19 and several hundred HERV-K-T47D-related solitary LTRs dispersed over the human genome. HERV-K-T47D-related sequences are detected in the genomes of higher primates and Old World monkeys but not in those of New World monkeys. High HERV-K-T47D transcription levels were observed in human placenta tissue, whereas transcription in T47D cells was strictly steroid dependent.

Amino Acid Sequence↗
PubMed1980

Action of short-term cycloheximide administration associated with colchicine on nuclear and chromosome structure in cleaving Newt eggs. Reappearance of chromomeres?

Association of short-term cycloheximide (CHM) administration (1/3, 1/2 or 1 cycle) with long-term treatment by colchicine (Co) confirms the results obtained by CHM alone under similar conditions, namely the striking relationship between the starting-time of treatment and the type of nuclei obtained (centred telophasic or non-centred prophasic). This relationship is highly significant. Various nuclear structures were observed: they correspond to a special evolution of the abnormal nuclei during telophase, telo-prophase and prophase which is very different from that in untreated ones. A difference in evolution of the central and peripheral parts of the same nucleus explains their centred structure. On the contrary, this difference disappears at prophase. The association CHM-Co favours the unveiling of beads which are interpreted as prophasic chromomeres. These beads are of different size, spacing and form according to the moment of the prophasic evolution attained. Electron microscopy study confirms the strong dispersion of chromatin by CHM and the beaded appearance of chromosomes by CHM and Co. Simultaneously, many dense bodies are accumulated in the centrospheres, as after quinoline and glutaraldehyde administration. The mechanisms of production of centred nuclei and of the beaded appearance of chromosomes are discussed.

Animals↗
PubMed1993

Chromosomal structure of Rhodobacter capsulatus strain SB1003: cosmid encyclopedia and high-resolution physical and genetic map.

A combination of cosmid genome walking and pulsed-field gel electrophoresis was used to construct a high-resolution physical and genetic map of the 3.8-megabase (Mb) genome of Rhodobacter capsulatus SB1003. The mapping was done by hybridization of pulsed-field gel blots and by grouping and further mapping of the cosmids and bacteriophages from genomic libraries. Cosmid clones formed two uninterrupted and ordered groups, one corresponding to the chromosome of R. capsulatus, the other to its 134-kb plasmid. Cos site end-labeling and partial EcoRV digestion of cosmids were used to construct a high-resolution EcoRV map of the genome. Overlapping of the cosmids was confirmed by the resemblance of the cosmid restriction maps and by direct end-to-end hybridization with SP6- and T7-specific transcripts. Twenty-three previously cloned genes and eight groups of repeated sequences, revealed in this work, were located in the ordered gene library and mapped with an accuracy of 1-10 kb. Blots of a minimal set of 192 cosmids, covering the chromosome and the plasmid with the known map position of each cosmid, give to R. capsulatus the same advantages that the Kohara phage panel gives to E. coli.

Chromosome Mapping↗
PubMed1999

Genetic monitoring of the human population from high-level natural radiation areas of Kerala on the southwest coast of India. II. Incidence of numerical and structural chromosomal aberrations in the lymphocytes of newborns.

Cytogenetic studies using cord blood samples from newborns from high-level natural radiation areas of the Kerala coast in Southwest India have been in progress since 1986. A total of 963,940 metaphases from 10,230 newborns have been screened for various types of chromosomal aberrations. Comparison of 8,493 newborns (804,212 cells) from high-level natural radiation areas (dose rate >1.5 mGy/year) and 1,737 newborns (159,728 cells) from normal-level natural radiation areas (</=1.5 mGy/year) did not show any significant difference in the frequency of dicentrics, translocations, inversions or other types of aberrations known to be associated with radiation exposure. The cytogenetic studies were continued for constitutional anomalies using karyotype analysis, and scoring of 16,169 newborns has been completed. The overall frequency of constitutional anomalies was 4.95 +/- 0.55 per 1,000 newborns, which is comparable to the incidence reported in the literature. Within the limitations of sample size, the frequencies of total autosomal and sex aneuploids as well as structural anomalies were comparable between the high-level and normal-level natural radiation areas. A striking observation was the presence of rogue cells, the rarely occurring metaphases with a high level of chromosomal damage, which have not been reported previously among newborns.

Chromosome Aberrations↗
PubMed1988

Platelet-derived growth factor A chain: gene structure, chromosomal location, and basis for alternative mRNA splicing.

Genomic clones encoding the A chain of platelet-derived growth factor (PDGF) have been isolated. The gene contains seven exons spanning about 24 kilobases of DNA. The positions of intervening sequences closely match those of the related B-chain (c-sis) gene on chromosome 22. In situ hybridization was used to localize the PDGF A-chain gene to the distal portion of the short arm of chromosome 7 (7p21-p22). Within the (G + C)-rich 5' region, a single transcriptional start site was identified approximately equal to 36 base pairs downstream of a TATAA consensus promoter element. The three size classes of A-chain mRNA probably arise by selection of alternative poly(A) sites in exon 7, but only a single consensus AATAAA signal was identified in this region. Two functionally different A-chain precursors, which differ by the presence or absence of a basic C terminus, are generated as a result of alternative mRNA splicing events, which include or exclude exon 6. This and other structural features of the A-chain gene suggest that PDGF expression may be modulated at transcriptional and post-transcriptional levels.

Base Sequence↗
PubMed1991

Structure, chromosome location, and expression of the human smooth muscle (enteric type) gamma-actin gene: evolution of six human actin genes.

Recombinant phages that carry the human smooth muscle (enteric type) gamma-actin gene were isolated from human genomic DNA libraries. The amino acid sequence deduced from the nucleotide sequence matches those of cDNAs but differs from the protein sequence previously reported at one amino acid position, codon 359. The gene containing one 5' untranslated exon and eight coding exons extends for 27 kb on human chromosome 2. The intron between codons 84 and 85 (site 3) is unique to the two smooth muscle actin genes. In the 5' flanking region, there are several CArG boxes and E boxes, which are regulatory elements in some muscle-specific genes. Hybridization with the 3' untranslated region, which is specific for the human smooth muscle gamma-actin gene, suggests the single gene in the human genome and specific expressions in enteric and aortic tissues. From characterized molecular structures of the six human actin isoform genes, we propose a hypothesis of evolutionary pathway of the actin gene family. A presumed ancestral actin gene had introns at least sites 1, 2, and 4 through 8. Cytoplasmic actin genes may have directly evolved from it through loss of introns at sites 5 and 6. However, through duplication of the ancestral actin gene with substitutions of many amino acids, a prototype of muscle actin genes had been created. Subsequently, striated muscle actin and smooth muscle actin genes may have evolved from this prototype by loss of an intron at site 4 and acquisition of a new intron at site 3, respectively.

Actins↗
PubMed2006

Modelling gene flow between oilseed rape and wild radish. I. Evolution of chromosome structure.

The assessment of gene flow from crop species to weeds has found a new emphasis over the last years because of the marketing of transgenic crops and the possible selective advantage that crop (trans)gene may confer to the weeds. Several studies focused on the F1 interspecific hybrid production but few data are available on the factors affecting the genetic structure of advanced generations. It depends on the genomic structure of the species concerned as well as on the degree of their genome homology that affect the occurrence of intergenomic recombination. Oilseed rape (Brassica napus, AACC, 2n = 38)-wild radish (Raphanus raphanistrum, RrRr, 2n = 18), a distantly related weed, is a good model to address such questions. From seven male sterile oilseed rape lines carrying an herbicide tolerance transgene, F1 interspecific hybrids and four advanced generations were produced under field conditions with wild radish as pollinator. Observation of hybrid chromosome numbers across four generations revealed a high variability, especially in the "BC1" generation. A regression model was fitted in order to describe the relationship between parent and offspring chromosome numbers. The effects of generation, transgenic line and selection pressure on the mean relationship were investigated. The first two factors had an influence on the rate of decrease of chromosome numbers, whereas selection pressure resulted in the presence of an additional chromosome in the herbicide treated plants. The model provided a convenient framework for analysing how chromosome numbers evolve over successive hybridization events and it may prove useful as a basis for simulation-based approaches.

Biological Evolution↗
PubMed1990

Human neutrophil cytochrome b light chain (p22-phox). Gene structure, chromosomal location, and mutations in cytochrome-negative autosomal recessive chronic granulomatous disease.

A membrane-bound cytochrome b, a heterodimer formed by a 91-kD glycoprotein (heavy chain) and a 22-kD polypeptide (light chain), is an essential component of the phagocyte NADPH-oxidase responsible for superoxide generation. Cytochrome b is absent in two subgroups of chronic granulomatous disease (CGD), an inherited disorder characterized by the lack of oxidase activity. Mutations in the cytochrome heavy chain gene, encoded by the CYBB locus in Xp21.1, result in the X-linked form of CGD. A rare subgroup of autosomal recessive CGD also lacks cytochrome b (A- CGD), but the genetic defect has not previously been identified. In order to search for possible mutations in the cytochrome light chain locus, CYBA, the structure of this gene was characterized. The CYBA locus was localized to 16q24, and the approximately 600-bp open reading frame determined to be encoded by six exons that span approximately 8.5 kb. Three unrelated patients with A- CGD were studied for evidence of mutations in the light chain gene. One patient, whose parents were first cousins, was homozygous for a large deletion that removed all but the extreme 5' coding sequence of the gene. The other two patients had a grossly normal light chain transcript on Northern blot of mononuclear cell RNA. The light chain transcript was amplified by the polymerase chain reaction and sequenced. One patient was a compound heterozygote for two alleles containing point mutations in the open reading frame that predict a frame shift and a nonconservative amino acid replacement, respectively. The second patient, whose parents were second cousins, was homozygous for a different single-base substitution resulting in another nonconservative amino acid change. These results indicate that A- CGD can results from defects in the gene encoding the 22-kD light chain of the phagocyte cytochrome b.

Amino Acid Sequence↗
PubMedDate not supplied

[Chromosomal structures of Pseudomonas testosteroni. IV. Effect of testosterone on RNA-synthesis (author's transl)].

Testosterone degrading enzymes are synthesized de novo by bacterium P. testosteroni to utilize testosterone-like steroids as the only source of carbon. RNA-synthesis of the whole lysate of testosterone-induced bacteria was found to be 15% reduced compared to the control, suggesting a cytoplasmatic factor which modulates chromatin associated RNA-polymerase activity.

Chromosomes, Bacterial↗
PubMed1988

A birefringence, electron microscopy, and histochemical survey of chromosomal structure in the sperm nuclei of an echinothurid sea urchin, Araeosoma owstoni.

The mature sperm head of Araeosoma owstoni, an echinothurid sea urchin, showed positive birefringence reflecting that the overall orientation of DNA molecules was semiperpendicular toward the nuclear axis of the sperm head. Transmission electron microscopical observation of sperm in this species revealed a highly electron-dense cylindrical coil with an empty central core extending along the major axis of the sperm head. This coil had seven to eight turns along its entire length of 3.5 micron. The maximum width was 0.35 micron near the distal end of the nucleus, and the minimum width was 0.17 micron near the apical end. Lamellar substructures were also present in the sperm nucleus, appearing at the periphery of the electron-dense cylinder in a radial manner. Staining with Feulgen's reaction and acid-orcein indicated that the coil was probably composed of sperm chromosomes.

Animals↗
PubMed2001

Regulation of initiation of S phase, replication checkpoint signaling, and maintenance of mitotic chromosome structures during S phase by Hsk1 kinase in the fission yeast.

Hsk1, Saccharomyces cerevisiae Cdc7-related kinase in Shizosaccharomyces pombe, is required for G1/S transition and its kinase activity is controlled by the regulatory subunit Dfp1/Him1. Analyses of a newly isolated temperature-sensitive mutant, hsk1-89, reveal that Hsk1 plays crucial roles in DNA replication checkpoint signaling and maintenance of proper chromatin structures during mitotic S phase through regulating the functions of Rad3 (ATM)-Cds1 and Rad21 (cohesin), respectively, in addition to expected essential roles for initiation of mitotic DNA replication through phosphorylating Cdc19 (Mcm2). Checkpoint defect in hsk1-89 is indicated by accumulation of cut cells at 30 degrees C. hsk1-89 displays synthetic lethality in combination with rad3 deletion, indicating that survival of hsk1-89 depends on Rad3-dependent checkpoint pathway. Cds1 kinase activation, which normally occurs in response to early S phase arrest by nucleotide deprivation, is largely impaired in hsk1-89. Furthermore, Cds1-dependent hyperphosphorylation of Dfp1 in response to hydroxyurea arrest is eliminated in hsk1-89, suggesting that sufficient activation of Hsk1-Dfp1 kinase is required for S phase entry and replication checkpoint signaling. hsk1-89 displays apparent defect in mitosis at 37 degrees C leading to accumulation of cells with near 2C DNA content and with aberrant nuclear structures. These phenotypes are similar to those of rad21-K1 and are significantly enhanced in a hsk1-89 rad21-K1 double mutant. Consistent with essential roles of Rad21 as a component for the cohesin complex, sister chromatid cohesion is partially impaired in hsk1-89, suggesting a possibility that infrequent origin firing of the mutant may affect the cohesin functions during S phase.

Cell Cycle Proteins↗
PubMed2000

[The study of chromatin and chromosome structure on preparations of interphase nucleus derivatives resulting from nuclear wall removal.III Structural heterogeneity of chromatin and argyrophilic zone of the nucleolus in stretched membrane-free nuclei and chromatin bodies from human peripheral lymphocytes].

Viewed by light microscopy, the majority of lymphocytes in smears of human peripheral blood display a deep staining (with any chromatin- or DNA-specific dye) of the nucleus consisting of densely aggregated chromatin in addition to one or several small nucleoli with a dot- or spot-like argyrophilic zone. Amembraneous nuclei and "free chromatin" structures were isolated from intact lymphocytes gently treated with Triton X-100. Surface stretching of both these nuclei and structures, shortly fixed in methanol--glacial acetic acid (3:1), resulted in spatial separation of thin and thick chromatin or argyrophilic fibres, nucleoli, intranuclear bodies, polymorphous aggregations of chromatin or argyrophilic fibres and incidentally observed splitted or beaded thick chromatin fibres and the chromocenter. The light microscopic pattern of chromatin fibres of stretched amembraneous nuclei, isolated from peripheral lymphocytes, well compares with that of deconvolved images of intact lymphocyte nucleus obtained with optical tomography.

Cell Nucleus↗
PubMed1985

Analysis of inactive X chromosome structure by in situ nick translation.

Nick translation assays of fixed interphase female fibroblasts with tritiated nucleotides demonstrated a characteristic absence of label over sex chromatin. The chromatin bodies were nearly always peripheral in location and a ribbon of nick translatable DNA was detected between the sex chromatin and the nuclear envelope. High voltage electron microscopy indicated the possibility of a special nuclear envelope attachment region. The apparent resistance of sex chromatin to nick translation did not appear to be due to resistance to DNase I attack.

Cells, Cultured↗
PubMed1981

Position-effect variegation and chromosome structure of a heat shock puff in Drosophila.

Position-effect variegation was studied in Drosophila melanogaster using a rearrangement that places the 87C heat shock puff locus next to heterochromatin. After heat shock, the translocated 87C region failed to puff or to accumulate RNA in some nuclei, but puffed normally in other nuclei from the same individual. In situ hybridization experiments showed that the level of polyteny was not greatly affected at the inactive gene site. Therefore, the variable ability of a gene to be transcriptionally induced, rather than its dosage, is the basis of the position effect phenomenon. These experiments also showed that heat shock gene sequences are single-stranded in puffs under relatively gentle specimen preparation conditions, in contrast to the same sequences in unpuffed sites.

Animals↗
PubMed2006

Changes in chromosome structure, mitotic activity and nuclear DNA content from cells of Allium Test induced by bark water extract of Uncaria tomentosa (Willd.) DC.

The influence of water extract of Uncaria tomentosa (Willd.) DC bark on the meristematic cells of the root tips of Allium cepa L., e.g. cells of Allium Test, was investigated. The experiment was carried out in two variants: (1) continuous incubation at different concentrations (2, 4, 8 and 16 mg/ml) of the extract for 3, 6, 12, 24, 48 and 72h; and (2) 24-h incubation in three concentrations of the extract (4, 8 or 16 mg/ml), followed by post-incubation in distilled water for 3, 6, 12, 24 and 48h. During the continuous incubation, the mitotic activity was reduced (2 and 4 mg/ml) or totally inhibited (8 and 16 mg/ml), depending on the concentration of the extract. All the concentrations resulted in gradual reduction of the mitotic activity. In the concentration of 2 mg/ml, the mitotic activity reached its lowest value after 12h (2 mg/ml) and after 24h in 4 mg/ml, followed by spontaneous intensification of divisions during further incubation. Instead, in higher concentrations of the extracts (8 and 16 mg/ml), the mitotic activity was totally inhibited within 24h and did not resume even after 72h. Incubation caused changes in the phase index, mainly as an increase in the number of prophases. After 24h of incubation, in all phases, condensation and contraction of chromosomes were observed. During post-incubation, divisions resumed in all concentrations, reaching even higher values than the control. Cytometric analysis showed that the extract caused inhibition of the cell cycle at the border between gap(2) and beginning of mitosis (G(2)/M).

Antimitotic Agents↗
PubMed2006

In vivo DNase I sensitivity of the Streptomyces coelicolor chromosome correlates with gene expression: implications for bacterial chromosome structure.

For a bacterium, Streptomyces coelicolor A3(2) contains a relatively large genome (8.7 Mb) with a complex and adaptive pattern of gene regulation. We discovered a correlation between the physical structure of the S.coelicolor genome and the transcriptional activity of the genes therein. Twelve genes were surveyed throughout 72 h of growth for both in vivo sensitivity to DNase I digestion and levels of transcription. DNase I-sensitivity correlated positively with transcript levels, implying that it was predictive of gene expression, and indicating increased accessibility of transcribed DNA. The genome was fractionated based on the sensitivity to DNase I digestion, with the low molecular weight (frequently cut) fraction highly enriched for actively transcribed sequences when compared to the infrequently cut fraction, which was representative of the entire genome. This approach will allow comparison of nucleoid proteins, and any modifications thereof, associated with transcriptionally active and inactive regions of the bacterial genome.

Chromosomes, Fungal↗