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PubMed2000

Chromosome structure and sequence organization between pathogenic and non-pathogenic Leishmania spp.

We have used a chromosome fragmentation strategy based on systematic genomic insertions of the rare cutting yeast I-SceI endonuclease to assess structure and sequence organization of homologous chromosomes between evolutionary divergent pathogenic and non-pathogenic Leishmania species. This method was combined to physical mapping and hybridization studies using a number of specific chromosomal markers as probes. Our studies have concentrated on two different chromosomes of Leishmania major (L. major), L. donovani and L. infantum and of the non-pathogenic species L. tarentolae. Specific chromosome fragmentation events at the level of multiple I-SccI genomic integrations indicated that very similar distances separated internal genomic sequences between homologous chromosomes and that distances from chromosome ends were more variable. The order and orientation of genes along the homologous chromosomes were also conserved between species. With only few exceptions, genome organization between pathogenic and non-pathogenic Leishmania species was found to be highly conserved. Genomic comparison of pathogenic and non-pathogenic species may be useful for depicting regions involved in species-specific related pathologies.

Animals↗
PubMed1999

Genomic structure, chromosomal mapping, and muscle-specific expression of a PH domain-associated intronless gene, cded/lior.

The aim of our study was to isolate novel gene(s) involved in cell differentiation and embryonic liver development. Mouse cded/lior was identified from subtraction hybridization of embryonic liver cDNA libraries as well as an adult mouse liver genomic DNA library. The full open reading frame of cded/lior encodes a 131-amino acid protein with 71.88% overall similarity to the PH domain of rat PLC-gamma1. A gapped search with the C-terminal region of CDED/LIOR revealed a 36-41% similarity to several proteins related to signal transduction and cell replication, such as ORC1 and KSR. Northern blot analysis of adult mouse tissues shows a strong 2.6-kb transcript restricted to heart and skeletal muscle. RT-PCR utilizing cded/lior-specific primers demonstrates cded/lior mRNAs in heart, brain, and liver tissue throughout mid-embryonic mouse gestation. cded/lior maps to the distal end of mouse Chromosome (Chr) 2. Analysis of the genomic structure for cded/lior demonstrated a single exon gene that is not an alternatively spliced isoform of PLC-gamma1. Analysis of the cded/lior promoter region revealed a high GC-content, high ratio of CpG/GpC, multiple GC-boxes, the lack of a TATA box, CTF/NFI element, and two MyoD-MCK binding sites. These characteristics are also found in several genes important in the regulation of cell growth or DNA synthesis, such as transforming growth factor-beta1, c-Ha-ras, nerve growth factor, epidermal growth factor receptor, and DNA polymerase beta. These results suggest that cded/lior is a mesoderm/muscle-specific transcript that may be involved in the mesodermal inductive and regulatory interactions required for liver formation and embryonic development.

Amino Acid Sequence↗
PubMed1997

Human estrogen receptor beta-gene structure, chromosomal localization, and expression pattern.

The estrogen receptor (ER) is a ligand-activated transcription factor that mediates the effects of the steroid hormone 17 beta-estradiol, in both males and females. Since the isolation and cloning of ER, the consensus has been that only one such receptor exists. The finding of a second subtype of ER (ER beta) has caused considerable excitement amongst endocrinologists. In this article, we present data regarding the genomic structure and chromosomal localization of the human ER beta gene, demonstrating that two independent ER genes do exist in the human. Furthermore, we present data regarding the tissue distribution of human ER beta, showing that this receptor is expressed in multiple tissues. For instance, ER beta is found in developing spermatids of the testis, a finding of potential relevance for the ongoing debate on the effects of environmental estrogens on sperm counts. In addition, we find ER beta in ovarian granulosa cells, indicating that estrogens also participate in the regulation of follicular growth in the human.

Amino Acid Sequence↗
PubMed1986

Nonrandom chromosome structural aberrations and oncogene loci in human malignant melanoma.

Short-term cultures of 10 malignant melanomas derived from 8 patients were analyzed cytogenetically. The chromosome composition of the tumors was found to be similar in terms of modal number and structural and numerical aberrations, especially the nonrandom nature of breakpoints. Six chromosomes were consistently involved in marker formation. Aberrations of chromosomes #1 and #9 were identified in every tumor, whereas structural alterations of chromosome #2 were found in 9 tumors. In contrast, aberrations of chromosomes #6, #3, and #7 were identified in 7, 7, and 8 of the tumors, respectively. The nonrandom breakpoints on these chromosomes frequently coincided with known oncogenic loci and resulted in morphologically identical marker chromosomes. Consecutive lesions were obtained for two patients. Common markers were identified in both cases, indicating the clonal origin of the tumors. In addition, many marker chromosomes characteristic of the individual lesions were also identified. The presence of these lesion-specific markers indicates the nonrandom selective nature of the metastatic process and suggests the possible heterogeneity of the original tumor cell population.

Adult↗
PubMed1998

First steps in eukaryogenesis: physical phenomena in the origin and evolution of chromosome structure.

Our present understanding of the origin and evolution of chromosomes differs considerably from current understanding of the origin and evolution of the cell itself. Chromosome origins have been less prominent in research, as the emphasis has not shifted so far appreciably from the phenomenon of primeval nucleic acid encapsulation to that of the origin of gene organization, expression, and regulation. In this work we discuss some reasons why preliminary steps in this direction are being taken. We have been led to examine properties that have contributed to raise the ancestral prokaryotic programmes to a level where we can appreciate in eukaryotes a clear departure from earlier themes in the evolution of the cell from the last common ancestor. We shift our point of view from evolution of cell morphology to the point of view of the genes. In particular, we focus attention on possible physical bases for the way transmission of information has evolved in eukaryotes, namely, the inactivation of whole chromosomes. The special case of the inactivation of the X chromosome in mammals is discussed, paying particular attention to the physical process of the spread of X inactivation in monotremes (platypus and echidna). When experimental data is unavailable some theoretical analysis is possible based on the idea that in certain cases collective phenomena in genetics, rather than chemical detail, are better correlates of complex chemical processes.

Animals↗
PubMedDate not supplied

[Electron microscopic study of changes in chromosomal structural organization under the effect of formamide].

Isolated human metaphase chromosomes were treated with formamide at different (0-70%) concentrations and examined electronmicroscopically by protein monolayer technique. At increasing formamide concentration chromosomes gradually decondense, the scaffold becomes more clearly visible, the loops of chromatin fibres coming off the central part of chromosomes lose their nucleosomal appearance. Electrophoretic analysis of chromosomal proteins data show that formamide-treated chromosomes have approximately the same histone content as those before treatment, although chromosomes treated with 70% formamide look very similar to histone-depleted ones described elsewhere.

Chromosomes, Human↗
PubMed2000

Genomic structure, chromosomal localization and identification of mutations in the xeroderma pigmentosum variant (XPV) gene.

The xeroderma pigmentosum variant (XP-V) is one of the most common forms of this cancer-prone syndrome. XP groups A through G are characterized by defective nucleotide excision repair, whereas the XP-V phenotype is proficient in this pathway. The XPV gene encodes DNA polymerase eta, which catalyzes an accurate translesion synthesis, indicating that the XPV gene contributes tumor suppression in normal individuals. Here we describe the genomic structure and chromosomal localization of the XPV gene, which includes 11 exons covering the entire coding sequence, lacks a TATA sequence in the upstream region of the transcription-initiation, and is located at the chromosome band 6p21.1-6p12. Analyses of patient-derived XP-V cell lines strongly suggested that three of four cell lines carried homozygous mutations in the XPV gene. The fourth cell line, XP1RO, carried heterozygous point mutations in the XPV gene, one of which was located at the splice acceptor site of exon 2, resulting in the omission of exon 2 from the mature mRNA. These findings provide a basis for diagnosis and therapy of XP-V patients.

Alleles↗
PubMed1971

Influence of chromosome structure on the frequency of tonB trp deletions in Escherichia coli.

The frequency of tonB trp deletions varies in different strains and substrains of Escherichia coli. Studies with chromosomal hybrids constructed by transducing various segments of the cysB-trp-suIII region from K-12(Ymel) into K-12(W3110) indicate that the characteristic low deletion frequency of K-12(Ymel) is determined largely by the (genetic) structure of the trp-suIII region of the chromosome. Transduction of the trp region from K-12(W3110) or K-12(Ymel) into strain B has little effect on the frequency of tonB trp deletions in that strain. When tonB trp deletions occur at 42 C rather than at 37 C, there is a significant reduction in the frequency of deletions in all strains examined except K-12(Ymel) and hybrids exhibiting a Ymel deletion pattern. The magnitude of this temperature effect in different K-12 strains increases proportionally with the frequency of tonB trp deletions at 37 C. At 42 C the frequency of tonB trp deletions in all K-12 strains approaches the low frequency observed for Ymel at 37 or 42 C. In contrast, spontaneous deletions in another region of the genome which simultaneously result in resistance to phages T7 and lambda and in proline auxotrophy (tfrA pro deletions) occur at a constant frequency regardless of growth temperature or the structure of the chromosome in the trp region. Two mutants of strain KB30 obtained after treatment with nitrosoguanidine show very low tonB trp deletion frequencies. The alterations in both mutants map in the trp region of the chromosome. These studies indicate that the structure of the cysB-trp-suIII region is responsible for many of the characteristic deletion frequencies observed.

Chromosome Aberrations↗
PubMed1998

The human glycine receptor subunit alpha3. Glra3 gene structure, chromosomal localization, and functional characterization of alternative transcripts.

The neuronal glycine receptor is a ligand-gated chloride channel composed of ligand binding alpha and structural beta polypeptides. Homology screening of a human fetal brain cDNA library resulted in the identification of two alternative splice variants of the glycine receptor alpha3 subunit. The amino acid sequence predicted for the alpha3L variant was largely identical to the corresponding rat subunit. In contrast, the novel splice variant alpha3K lacked the coding sequence for 15 amino acids located within the cytoplasmic loop connecting transmembrane spanning region 3 (TM3) and TM4. Using P1 artificial chromosome (PAC) clones, the structure of the GLRA3 gene was elucidated and its locus assigned to human chromosomal bands 4q33-q34 by fluorescence in situ hybridization. Two transcripts of 2.4 and 9 kilobases, corresponding to alpha3L and alpha3K, respectively, were identified and found to be widely distributed throughout the human central nervous system. Structural analysis of the GLRA3 gene revealed that the alpha3K transcript resulted from a complex splice event where excision of the novel exon 8A comprising the alternative sequence of 45 base pairs coincides with the persistence of a large intronic sequence in the 3'-untranslated region. Functional expression in HEK 293 cells of alpha3L and alpha3K subunits resulted in the formation of glycine-gated chloride channels that differed significantly in desensitization behavior, thus defining the cytoplasmic loop as an important determinant of channel inactivation kinetics.

Alternative Splicing↗
PubMed1975

[Action of aurantin on the chromosomal structure of continuous cultures of human amniotic cells (line A-1)].

When transplantable cultures of human amniotic cells, line A-1 were treated with auranthin in concentrations of 0.1 and 0.5 gamma/ml for 48 hours of their growth, the chromosomes in the methaphase proved to be not evently spiralized longitudinally and acquired the appearance of segmented structures. All the chromosomes in the set possessed the capacity for such segmentation. It was most pronounced near the centromers and at the ends of the meta- and submetacentric chromosomes. The acrocentric chromosomes were segmented longitudinally more evenly. Loose segments of the chromosomes most probably corresponded to the areas, in which auranthin binding with DNA occurred. The effect of auranthin on differentiation of the chromosomes longitudinally may be used, as it was indicated for actnomycin D, in identification of homological chromosomes in the karyotype, as well as in studies on the temporal sequence of DNA synthesis in the chromosomes.

Amniotic Fluid↗
PubMed2001

Genomic structure, chromosomal localization and expression profile of a novel melanoma differentiation associated (mda-7) gene with cancer specific growth suppressing and apoptosis inducing properties.

Abnormalities in cellular differentiation are frequent occurrences in human cancers. Treatment of human melanoma cells with recombinant fibroblast interferon (IFN-beta) and the protein kinase C activator mezerein (MEZ) results in an irreversible loss in growth potential, suppression of tumorigenic properties and induction of terminal cell differentiation. Subtraction hybridization identified melanoma differentiation associated gene-7 (mda-7), as a gene induced during these physiological changes in human melanoma cells. Ectopic expression of mda-7 by means of a replication defective adenovirus results in growth suppression and induction of apoptosis in a broad spectrum of additional cancers, including melanoma, glioblastoma multiforme, osteosarcoma and carcinomas of the breast, cervix, colon, lung, nasopharynx and prostate. In contrast, no apparent harmful effects occur when mda-7 is expressed in normal epithelial or fibroblast cells. Human clones of mda-7 were isolated and its organization resolved in terms of intron/exon structure and chromosomal localization. Hu-mda-7 encompasses seven exons and six introns and encodes a protein with a predicted size of 23.8 kDa, consisting of 206 amino acids. Hu-mda-7 mRNA is stably expressed in the thymus, spleen and peripheral blood leukocytes. De novo mda-7 mRNA expression is also detected in human melanocytes and expression is inducible in cells of melanocyte/melanoma lineage and in certain normal and cancer cell types following treatment with a combination of IFN-beta plus MEZ. Mda-7 expression is also induced during megakaryocyte differentiation induced in human hematopoietic cells by treatment with TPA (12-O-tetradecanoyl phorbol-13-acetate). In contrast, de novo expression of mda-7 is not detected nor is it inducible by IFN-beta+MEZ in a spectrum of additional normal and cancer cells. No correlation was observed between induction of mda-7 mRNA expression and growth suppression following treatment with IFN-beta+MEZ and induction of endogenous mda-7 mRNA by combination treatment did not result in significant intracellular MDA-7 protein. Radiation hybrid mapping assigned the mda-7 gene to human chromosome 1q, at 1q 32.2 to 1q41, an area containing a cluster of genes associated with the IL-10 family of cytokines. Mda-7 represents a differentiation, growth and apoptosis associated gene with potential utility for the gene-based therapy of diverse human cancers.

Antigens, Neoplasm↗
PubMedDate not supplied

Minibands and chromosome structure. A theory.

Bright and dark field microscopy were used to examine interphase nuclei and RBG-banded human chromosomes. In dark field microscopy both chromosomes and interphase chromatin appeared to be composed of similar independent structures alternating between bright and dull light intensity. The position, colour, and number of these structures may support the theory that the transition from interphase chromatin to metaphase chromosomes, takes place without any dramatic changes in local chromatin structure. Although the resolution power of bright and dark field microscopy prevent a direct proof for the miniband model, our observations in combination with other data may add further support to this particular model of chromosome organization.

Cells, Cultured↗
PubMed1983

Insights on plant chromosome structure provided by the FPG technique.

The high resolution afforded by the fluorescence plus Giemsa (FPG) labelling method has allowed us to visualize three main features in BrdU-substituted A. cepa chromosomes. These are (1) exchanged segments smaller than the width of the chromatid detected after BrdU substitution for two S periods; (2) late-replicated chromosome segments (LRS) of similar characteristics; (3) discontinuous or 'step-wise' exchanges (SWE). A variation in longitudinal dimension has not been observed in any case; all these features have a roughly constant longitudinal dimension of about 0.5 microns. These results suggest that arrangements of the chromatin fibres having a diameter detectable under the light microscope following a longitudinal pattern can be ignored. In addition, our observations seem to support the model of a coiled structure of metaphase chromosomes. On the other hand, the analysis of the morphological pattern shown by the SWE along a chromatid and in sister chromatids has provided us with what could be evidence of a direction of the hypothetical gyres.

Azure Stains↗
PubMed1979

Quantitative conservation of chromatin-bound RNA polymerases I and II in mitosis. Implications for chromosome structure.

RNA synthesis almost ceases in mitosis. It is ambiguous whether this temporal, negative control of RNA synthesis is solely because of the nature of chromosomes per se, (i.e., their condensed state), or to a physical loss of RNA polymerases along with other nuclear proteins which have been shown to pass into the cytoplasm in mitosis, or to their combined feature. Aside from such regulatory considerations, a question has also been raised as to whether RNA polymerases are constituents of metaphase chromosomes. To clarify these aspects of RNA polymerase-chromatin interaction in mitosis, the enzymes in chromosomes were quantitated and their levels compared to those in interphase nuclei and cells at various phases of the cell cycle. The results show that the amounts of form I, form II, and probably form III enzymes bound to a genome-equivalent of chromatin stay constant during the cell cycle. Thus, the mechanism for the negative control of RNA synthesis in mitosis appears to exist in the chromosomes per se, but not to be directly related to the RNA polymerase levels. This quantitative conservation of chromatin-bound RNA polymerases implies that they may persist as structural components of the chromosomes in mitosis.

Animals↗