Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genome Components”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,207 records · Page 67Linked to original sources
PubMed2001

Evolution of a 6-200 Mb long-range repeat cluster in the genus Mus.

By fluorescence in situ hybridization, we mapped the location of genes associated with the Sp100-rs cluster, a long-range repeat cluster in chromosome 1 of the house mouse, Mus musculus. The cluster comprises between 60 and 2000 repeats and extends over 6-200 Mb of the M. musculus genome, depending on the source of the cluster. The cluster evolved during the last two million years in the genus Mus in the lineage to which M. musculus belongs. The Asiatic mouse species M. caroli is not in this lineage and does not possess the cluster. M. caroli represents the ancestral genomic organization of the cluster source components Sp100, Csprs and Ifi75: they are located close to each other in the same chromosome band (1D). However, Sp100-rs, the principal gene of the cluster, is not present in the M. caroli genome. It is a chimeric M. musculus gene that arose by fusion of Csprs and the 5' part of Sp100. Sp100-rs and Ifi75 are homogeneously distributed throughout the cluster while Sp100 and Csprs in its original sequence context flank the cluster on opposite sides. Our results suggest a model for the origin and evolution of the long-range repeat cluster by duplication, gene fusion and amplification.

Animals↗
PubMed2001

Targeting silence: the use of site-specific recombination to introduce in vitro methylated DNA into the genome.

DNA methylation has emerged as an important component of transcriptional regulation. However, our understanding of how DNA methylation influences transcription, chromatin structure, replication timing, and imprinting has been limited by the lack of experimental systems that permit control of the methylation state of genes in a chromosomal context. Here, we describe a novel technique that allows for efficient introduction of methylated and unmethylated DNA into defined sites in the mammalian genome. This protocol utilizes bacterial CpG methyltransferases to methylate the DNA of interest in vitro, followed by site-specific targeting using Cre recombinase. Long-term maintenance of the methylation state in vivo allows analysis of the biological consequences of methylation by direct comparison of the methylated and unmethylated state in the same genomic position.

Animals↗
PubMed1982

The scattered distribution of actin genes in the mouse and human genomes.

A hamster actin cDNA probe was used to localize actin genes on the major components of mouse and human DNAs, namely on the four families of fragments forming the bulk of these genomes. Over 20 EcoRI fragments hybridizing the probe could be detected; a different subset of these fragments was found in each component. Since the fragment families forming the major components of the mouse and human DNAs derive from very long chromosomal segments, the isochores , the presence of actin genes on all components provides evidence for their dispersion in both genomes. In situ hybridization of 125I-labeled probe to metaphase chromosomes in the presence of dextran sulfate confirmed this dispersion by showing that the 29-30 actin gene sites so identified are distributed on almost all chromosomes. Moreover, some human actin genes could be mapped on specific chromosomal segments; in particular, one gene was localized on the long arm of the X chromosome. Finally, three different mouse actin genes were isolated from a recombinant DNA library and previously investigated interspersed repeated sequences were identified in the vicinity of these genes.

Actins↗
PubMed2002

[Genetic factors in myocardial infarction--Results from a candidate gene and a genome-wide approach between beta blockers].

BACKGROUND: Coronary artery disease and myocardial infarction are the most frequent causes of death in the Western societies. Even nowadays, every second myocardial infarction is lethal and hits the patients unexpectedly without previous signs or symptoms. In order to install preventive measures most efficiently, it is necessary to have a detailed knowledge on the pathophysiology of the disease. The identification of patients who are at high risk for suffering from myocardial infarction can be done with epidemiological methods, such as the determination of "traditional" risk factors, like arterial hypertension, hypercholesterolemia, diabetes mellitus or smoking), or eventually in the future using molecular genetic testing. This is of great importance especially for asymptomatic siblings and children from myocardial infarction patients. POLYMORPHISMS: Although traditional risk factors occur frequently in families, they explain only in part the familial accumulation of coronary artery disease. Furthermore, stron genetic effects on the development of coronary artery disease and myocardial infarction have been demonstrated in several studies. These genetic effects can be examined by 1. a candidate gene approach, or 2. a systematic screening of the whole genome. In the first step, several polymorphisms (sequence variations) wee examined in several candidate genes in which a significant influence on a cardiovascular risk factor or intermediate phenotype (such as atherogeneic lipid profile or arterial hypertension) has been shown in the literature. We thus examined in a large population of patients with myocardial infarction and a sample of the general population the effects of the HindIII polymorphism in the lipoproteinlipase gene, of the -344T/C promoter polymorphism in the aldosterone synthase gene and of the 825C/T polymorphism in the gene of the beta3 subunit of the G protein gene (GNB3). In the general population, we could show an association with unfavorable lipid levels in men and in postmenopausal (but not premenopausal) women for the H2H2 genotype of the HindIII lipoproteinlipase polymorphism. However, the theoretical increase in risk for this genotype is not large enough to demonstrate a significant association with myocardial infarction in the population examined. With the promoter polymorphism in the aldosterone synthase gene, anthropometrical and echocardiographical data did not suggest that the polymorphism is a risk factor for myocardial infarction nor for left ventricular remodeling after myocardial infarction, which was observed in earlier studies. Furthermore, we could show an association with arterial hypertension in our general population sample with the polymorphism in the GNB3 gene. However, no association could be demonstrated for this polymorphism with myocardial infarction. AFFECTED SIB-PAIR APPROACH: In a systematic screening of the genome for genes that are relevant in the pathogenesis of coronary artery disease or myocardial infarction, an affected sib-pair approach was followed. 1,261 families were identified in which at least two brothers or sisters were affected with myocardial infarction or severe coronary artery disease, such as percutaneous coronary intervention or coronary after bypass grafting. In a subpopulation of 513 families and 1,407 individuals, we performed a total genome screening. The analyses using the variance component method and the SOLAR program revealed a susceptibility locus for myocardial infarction of chromosome 14q32 with a lod score of 3.89 (genome-wide p < 0.05). This locus comprises a region of about seven centi-Morgan and contains approximately 150 genes. Furthermore, a comprehensive analysis including the cardiovascular risk factors showed that 1. this myocardial infarction locus is unique and does not overlap with chromosomal loci for well-established risk factors, 2. cardiovascular risk factors, such as Lp(a), diabetes mellitus, serum lipids, or arterial hypertension have strong genetic components. CONCLUSION: These findings do not exclude a role of cardiovascular s do not exclude a role of cardiovascular risk factors or candidate genes in the pathogenesis of myocardial infarction, but rather demonstrate that risk factors may act as surrogates of specific underlying disease mechanisms. It is thus necessary to perform a comprehensive analysis of complex polygenic diseases, such as myocardial infarction, including both, established cardiovascular risk factors and genomic data.

Adrenergic beta-Antagonists↗
PubMed1998

Mutational analysis of the role of nucleoside triphosphatase P4 in the assembly of the RNA polymerase complex of bacteriophage phi6.

Bacteriophage phi6 is a complex enveloped double-stranded RNA virus with a segmented genome and replication strategy quite similar to that of the Reoviridae. An in vitro packaging and replication system using purified components is available. The positive-polarity genomic segments are translocated into a preformed polymerase complex (procapsid) particle. This particle is composed of four proteins: the shell-forming protein P1, the RNA polymerase P2, and two proteins active in packaging. Protein P7 is involved in stable packaging, and protein P4 is a homomultimeric potent nucleoside triphosphatase that provides the energy for the RNA translocation event. In this investigation, we used mutational analysis to study P4 multimerization and assembly. P4 is assembled onto a preformed particle containing proteins P2 and P7 in addition to P1. Only simultaneous production of P1 and P4 in the same cell leads to P4 assembly on P1 alone, whereas the P1 shell is incompetent for accepting P4 if produced separately. The C-terminal part of P4 is essential for particle assembly but not for multimerization or enzymatic activity. Altering the P4 nucleoside triphosphate binding site destroys the ability to form multimers.

Bacteriophage phi 6↗
PubMed2006

Kaposi's sarcoma-associated herpesvirus-encoded latency-associated nuclear antigen induces chromosomal instability through inhibition of p53 function.

Kaposi's sarcoma-associated herpesvirus (KSHV) is predominantly associated with three human malignancies, KS, primary effusion lymphoma, and multicentric Castleman's disease. These disorders are linked to genomic instability, known to be a crucial component of the oncogenic process. Latency-associated nuclear antigen (LANA), encoded by open reading frame 73 of the KSHV genome, is a latent protein consistently expressed in all KSHV-associated diseases. LANA is important in viral genome maintenance and is associated with cellular and viral proteins to regulate viral and cellular gene expression. LANA interacts with the tumor suppressor genes p53 and pRb, indicating that LANA may target these proteins and promote oncogenesis. In this study, we generated cell lines which stably expressed LANA to observe the effects of LANA expression on cell phenotype. LANA expression in these stable cell lines showed a dramatic increase in chromosomal instability, indicated by the presence of increased multinucleation, micronuclei, and aberrant centrosomes. In addition, these stable cell lines demonstrated an increased proliferation rate and as well as increased entry into S phase in both stable and transiently transfected LANA-expressing cells. Additionally, p53 transcription and its transactivation activity were suppressed by LANA expression in a dose-dependent manner. LANA may therefore promote chromosomal instability by suppressing the functional activities of p53, thereby facilitating KSHV-mediated pathogenesis and cancer.

Animals↗
PubMed2004

Sample introduction techniques for microfabricated separation devices.

A great deal of progress has been made toward the development of the micro total analysis system (micro-TAS) since its inception in 1990. A wide variety of applications, including genomics, proteomics and drug discovery, have prompted the development of analytical methods capable of very high throughput while maintaining low cost. The micro-TAS concept addresses both of these requirements. Electrophoresis has been a key element in the development of the micro-TAS. Most chemical and biochemical assays utilize a separation component at some point during analysis. Genomics, in particular, depends almost exclusively on electrophoresis for size-based separations of DNA. This review examines sample introduction into microfabricated electrophoretic devices, or chips, primarily for DNA analysis. Sample introduction is an important component of these systems and is an essential process for making chip electrophoresis a widely applicable analytical technique. Specific issues, such as automation, the delivery of large numbers of samples to microfabricated devices and injection of picoliter-sized sample plugs into a separation lanes on chips, are presented.

DNA↗
PubMed1981

Interspersed repeated sequences in the African green monkey genome that are homologous to the human Alu family.

The dominant family of interspersed repetitive DNA sequences in the human genome has been termed the Alu family. We have found that more than 75% of the lambda phage in a recombinant library representing an African green monkey genome hybridize with a human Alu sequence under stringent conditions. A group of clones selected from the monkey library with probes other than the Alu sequence were analyzed for the presence and distribution of Alu family sequences. The analyses confirm the abundance of Alu sequences and demonstrate that more than one repeat unit is present in some phages. In the clones studied, the Alu units are separated by an average of 8 kilobase pairs of unrelated sequences. The nucleotide sequence of one monkey Alu sequence is reported and shown to resemble the human Alu sequences closely. Hence, the sequence, dispersion pattern, and copy number of the Alu family members are very similar in the African green monkey and human genomes. Among the clones investigated were two that contain segments of the satellite DNA term alpha-component joined to non alpha-component DNA. The experiments indicate that in the monkey genome Alu sequences can occur close to regions of alpha-component DNA.

Animals↗
PubMed2004

The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes.

This paper first introduces our present knowledge of the origin of mitochondria and chloroplasts, and the organization and inheritance patterns of their genomes, and then carries on to review the evolutionary processes influencing mitochondrial and chloroplast genomes. The differences in evolutionary phenomena between the nuclear and cytoplasmic genomes are highlighted. It is emphasized that varying inheritance patterns and copy numbers among different types of genomes, and the potential advantage achieved through the transfer of many cytoplasmic genes to the nucleus, have important implications for the evolution of nuclear, mitochondrial and chloroplast genomes. Cytoplasmic genes transferred to the nucleus have joined the more strictly controlled genetic system of the nuclear genome, including also sexual recombination, while genes retained within the cytoplasmic organelles can be involved in selection and drift processes both within and among individuals. Within-individual processes can be either intra- or intercellular. In the case of heteroplasmy, which is attributed to mutations or biparental inheritance, within-individual selection on cytoplasmic DNA may provide a mechanism by which the organism can adapt rapidly. The inheritance of cytoplasmic genomes is not universally maternal. The presence of a range of inheritance patterns indicates that different strategies have been adopted by different organisms. On the other hand, the variability occasionally observed in the inheritance mechanisms of cytoplasmic genomes reduces heritability and increases environmental components in phenotypic features and, consequently, decreases the potential for adaptive evolution.

Animals↗
PubMed1995

5' proximal potyviral sequences mediate potato virus X/potyviral synergistic disease in transgenic tobacco.

The interaction of potato virus X (PVX) and potato virus Y (PVY) in tobacco causes a synergistic disease characterized by a dramatic increase in symptom severity, a change in the regulation of PVX RNA replication, and an increase in accumulation of PVX. In this study we demonstrate that PVX also interacts synergistically with three other members of the potyvirus group of plant viruses, tobacco vein mottling virus (TVMV), tobacco etch virus (TEV), and pepper mottle virus. These synergisms resemble the classic PVX/PVY synergism with respect to both the increase in host response and the change in PVX replication. To determine if the induction of PVX/potyviral synergism requires potyviral genome replication per se or if the response is mediated by expression of one or more potyviral genes, we used tobacco plants stably transformed with various subsets of the TVMV genome. PVX infections of transgenic plants expressing the 5'-proximal region of the TVMV genome, including the protease-1, helper component protease, and protein-3 genes, result in symptoms resembling those of PVX/potyviral synergism. A similar synergistic-like response occurs when transgenic tobacco plants expressing the analogous but smaller region from the 5'-proximal region of the TEV genome were infected with PVX. Replication of PVX RNA is altered in transgenic plants expressing 5'-proximal sequences of either TVMV or TEV, and in a manner similar to that observed in double infections. These results indicate that replication of the potyviral genome is not required for PVX/potyviral synergism and that the response is mediated by expression of potyviral sequences which have been localized to the 5'-proximal third of the genomic RNAs of both TVMV and TEV.

Genome, Viral↗
PubMed1999

A two-component enhancer-inhibitor transposon mutagenesis system for functional analysis of the Arabidopsis genome.

A modified Enhancer-Inhibitor transposon system was used to generate a series of mutant lines by single-seed descent such that multiple I insertions occurred per plant. The distribution of original insertions in the population was assessed by isolating transposon-flanking DNA, and a database of insertion sites was created. Approximately three-quarters of the identified insertion sites show similarity to sequences stored in public databases, which demonstrates the power of this regimen of insertional mutagenesis. To isolate insertions in specific genes, we developed three-dimensional pooling and polymerase chain reaction strategies that we then validated by identifying mutants for the regulator genes APETALA1 and SHOOT MERISTEMLESS. The system then was used to identify inserts in a class of uncharacterized genes involved in lipid biosynthesis; one such insertion conferred a fiddlehead mutant phenotype.

Arabidopsis↗
PubMed1975

Mouse immunoglobulin genes: studies on the reiteration frequency of light-chain genes by hybridisation procedures.

The partially purified immunoglobulin light chain messenger RNA fraction from P3K (MOPC 21) mouse myeloma tissue-culture cells has been employed in hybridisation studies. Fragments of the messenger RNA were generated by alkali hydrolysis. 6-S fragments not containing poly(A) showed the characteristic biphasic hybridisation profile seen with the intact RNA fraction. 12-S and 6-S poly(A)-containing fragments, however, showed single transitions lacking the rapidly hybridising component. Complementary DNA copies of the intact messenger RNA fraction were prepared with RNA-dependent DNA polymerase and the DNA populations fractionated on acrylamide gels. Hybridisation experiments with complementary DNA fractions up to 800 bases in length showed annealing to single (or a few) genes. A rapidly hybridising component (about 200 copies) appears in the cDNA fraction containing the largest transcripts. We conclude that the kappa constant region gene and the MOPC 21 variable region gene are present as one or a few copies in the haploid genome and that the rapidly hybridising component is not due to variable region genes.

Animals↗
PubMed1995

Requirement for HC-Pro processing during genome amplification of tobacco etch potyvirus.

The helper component-proteinase (HC-Pro) of tobacco etch potyvirus (TEV) is a multifunctional protein with several known activities. The N-terminal region is required for aphid transmission and efficient genome amplification, the central region is required for long-distance movement in plants, and the C-terminal domain is a cysteine-type proteinase that autocatalytically cleaves between itself and the P3 protein. To investigate the requirement for HC-Pro-mediated proteolysis during viral replication, a variety of mutations resulting in amino acid substitutions and insertions in the proteolytic domain and cleavage site motif were introduced into the viral genome. Mutations affecting the active site residues, His722 and Cys649, or the cleavage site P1' residue, Gly764, inhibited proteolytic activity of HC-Pro. Mutant genomes containing these modifications were amplification-defective in protoplasts and plants. Mutants with substitutions affecting several conserved, but non-active site, residues (Ser610, Cys694, and Asp715) within the proteinase domain encoded active HC-Pro proteinases and were similar to parental virus in protoplasts and plants. To determine if the replication defect of the proteinase-debilitated mutants was due to inactivation of HC-Pro proteolytic activity or simply to the inability of HC-Pro and P3 protein to separate, a sequence coding for a heterologous cleavage site recognized by the TEV NIa proteinase was inserted between the HC-Pro and P3 coding regions of an active site mutant. This cleavage site was functional in vitro using purified NIa proteinase. However, this modification was insufficient to restore amplification activity to the mutant. In addition, the active site mutant was not complemented by wild-type HC-Pro supplied in trans by transgenic plants. These results suggest that an active HC-Pro proteinase is required in cis for TEV genome amplification.

Chromosome Mapping↗
PubMed1997

The critical active-site amine of the human 8-oxoguanine DNA glycosylase, hOgg1: direct identification, ablation and chemical reconstitution.

BACKGROUND: Base-excision DNA repair (BER) is the principal pathway responsible for the removal of aberrant, genotoxic bases from the genome and restoration of the original sequence. Key components of the BER pathway are DNA glycosylases, enzymes that recognize aberrant bases in the genome and catalyze their expulsion. One major class of such enzymes, glycosylase/lyases, also catalyze scission of the DNA backbone following base expulsion. Recent studies indicate that the glycosylase and lyase functions of these enzymes are mechanistically unified through a common amine-bearing residue on the enzyme, which acts as both the electrophile that displaces the aberrant base and an electron sink that facilitates DNA strand scission through imine (Schiff base)/conjugate elimination chemistry. The identity of this critical amine-bearing residue has not been rigorously established for any member of a superfamily of BER glycosylase/lyases. RESULTS: Here, we report the identification of the active-site amine of the human 8-oxoguanine DNA glycosylase (hOgg1), a human BER superfamily protein that repairs the mutagenic 8-oxoguanine lesion in DNA. We employed Edman sequencing of an active-site peptide irreversibly linked to substrate DNA to identify directly the active-site amine of hOgg1 as the epsilon-NH2 group of Lys249. In addition, we observed that the repair-inactive but recognition-competent Cys249 mutant (Lys249-->Cys) of hOgg1 can be functionally rescued by alkylation with 2-bromoethylamine, which functionally replaces the lysine residue by generating a gamma-thia-lysine. CONCLUSIONS: This study provides the first direct identification of the active-site amine for any DNA glycosylase/lyase belonging to the BER superfamily, members of which are characterized by the presence of a helix-hairpin-helix-Gly/Pro-Asp active-site motif. The critical lysine residue identified here is conserved in all members of the BER superfamily that exhibit robust glycosylase/lyase activity. The ability to trigger the catalytic activity of the Lys249-->Cys mutant of hOgg1 by treatment with the chemical inducer 2-bromoethylamine may permit snapshots to be taken of the enzyme acting on its substrate and could represent a novel strategy for conditional activation of catalysis by hOgg1 in cells.

Amines↗
PubMed2005

The Human Genome Diversity Project: past, present and future.

The Human Genome Project, in accomplishing its goal of sequencing one human genome, heralded a new era of research, a component of which is the systematic study of human genetic variation. Despite delays, the Human Genome Diversity Project has started to make progress in understanding the patterns of this variation and its causes, and also promises to provide important information for biomedical studies.

Chromosome Mapping↗
PubMed2003

A genomewide survey of developmentally relevant genes in Ciona intestinalis. X. Genes for cell junctions and extracellular matrix.

Cell junctions and the extracellular matrix (ECM) are crucial components in intercellular communication. These systems are thought to have become highly diversified during the course of vertebrate evolution. In the present study, we have examined whether the ancestral chordate already had such vertebrate systems for intercellular communication, for which we have searched the genome of the ascidian Ciona intestinalis. From this molecular perspective, the Ciona genome contains genes that encode protein components of tight junctions, hemidesmosomes and connexin-based gap junctions, as well as of adherens junctions and focal adhesions, but it does not have those for desmosomes. The latter omission is curious, and the ascidian type-I cadherins may represent an ancestral form of the vertebrate type-I cadherins and desmosomal cadherins, while Ci-Plakin may represent an ancestral protein of the vertebrate desmoplakins and plectins. If this is the case, then ascidians may have retained ancestral desmosome-like structures, as suggested by previous electron-microscopic observations. In addition, ECM genes that have been regarded as vertebrate-specific were also found in the Ciona genome. These results suggest that the last common ancestor shared by ascidians and vertebrates, the ancestor of the entire chordate clade, had essentially the same systems of cell junctions as those in extant vertebrates. However, the number of such genes for each family in the Ciona genome is far smaller than that in vertebrate genomes. In vertebrates these ancestral cell junctions appear to have evolved into more diverse, and possibly more complex, forms, compared with those in their urochordate siblings.

Animals↗
PubMed2004

Characterization of simian virus 40 on its infectious entry pathway in cells using fluorescence correlation spectroscopy.

SV40 (simian virus 40) is a double-stranded DNA virus and is strongly oncogenic in experimental animals. SV40 enters cells by atypical endocytosis mediated by caveolae, transporting the virus to its usual destination, namely the endoplasmic reticulum. The cellular mechanisms of capsid disassembly (uncoating) and deliverance of the viral genome into the cellular nucleus remain unknown. Here, we study (i) the formation of caveolae after viral infection and the diffusion of caveosome vesicles in the cytoplasm and (ii) the capsid disassembly and the mobility of the viral genome on its way to the nucleus, using fluorescence correlation spectroscopy. To follow the viral genome and capsids separately, the histone components of SV40 minichromosomes were labelled with enhanced yellow fluorescent protein and the capsid was labelled with a fluorescent red dye, Alexa568. We characterized the diffusion of caveosomes, the capsid disassembly process in the cytoplasm and the mobility of the viral genome in the nucleus, using two kinds of permissive cells.

Animals↗
PubMed1993

Replication of the retroviral terminal repeat sequence during in vivo reverse transcription.

There is a copy of a short terminal repeat segment, r, at each end of the retroviral RNA genome. During reverse transcription, r is copied from the genomic RNA to form the R component of the long terminal repeat in viral DNA. Although our current model for reverse transcription suggests that the 5' r is copied, it is not known whether the 5' copy, the 3' copy, or part of each r in the genomic RNA serves as the template for the R region in the progeny viral DNA. To assess the relative contribution of the 5' and 3' r templates, we examined the effect of mutations located at the center of the 5' or 3' r of spleen necrosis virus and determined the sequence of the R region in the progeny proviruses after a single round of retroviral replication. In approximately 90% of the proviruses, the 5' r marker was copied, whereas 10% of the proviruses had derived the R marker from the 3' r.

Base Sequence↗