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PubMed2003

Transposable elements and vertebrate protein diversity.

Interspersed repetitive sequences are major components of eukaryotic genomes. Repetitive elements comprise about 50% of the mammalian genome. They interact with the whole genome and influence its evolution. Repetitive elements may serve as recombination hot spots or acquire specific cellular functions such as RNA transcription control or become part of protein coding regions. The latter is a subject of presented analysis. We searched all currently available vertebrate protein sequences, including human proteome complement for the presence of transposable elements. It appears that insertion of TE-cassettes into open reading frames is a general phenomena. They can be found in all vertebrate lineages and originate in all types of transposable elements. It seems that genomes use those cassettes as 'ready to use' motifs in their evolutionary experiments. Most of TE-cassettes are used to create alternative forms of a message and usually the other form, without TE-cassette, is expressed in a cell. Tables listing vertebrate messages with TE-cassettes are available at http://warta.bio.psu.edu/ScrapYard/.

Animals↗

PubMed2003

[The relationship between proto-oncogene and testicular function].

Proto-oncogene, the fundamental component of cellular genome, is rarely or finitely expressed in normal conditions, and can regulate cellular proliferation, differentiation and information conduction. Many proto-oncogenes show the temporal and specific expression during spermatogenesis. The expression of some proto-oncogenes reinforces in the growth and development of Sertoli cells and Leydig cells. To explore the relationship between proto-oncogene and testicular function and that between proto-oncogene and regulative factors of testicular function helps to comprehend the regulation of the testicular function at the molecular level.

Animals↗

PubMed1990

Endogenous retroviral elements in human DNA.

Endogenous retroviruses and retroviral elements represent a substantial component of vertebrate genomes. They are inherited as stable Mendelian genes and may be activated spontaneously or by physical or chemical agents. In the human genome various retroviral elements have been detected by their relationship with mammalian endogenous and exogenous retroviruses. The structure of these elements resembles either full-length or truncated proviruses. The biological function of human retrovirus-related sequences is still unknown, but like other transposable elements, they may have contributed in shaping the eukaryotic genome. Furthermore, they exhibit a number of features giving them a potential for involvement in carcinogenesis. Expression of endogenous retroviral elements has been detected in various human tissues and cell lines and in some cases appears to be associated with human neoplasias.

DNA, Viral↗

PubMedDate not supplied

Treatment of mice bearing a Krebs ascitic tumor by means of a protocol based on radioactive copper (64Cu). IV. Consequences of the nature of cancer: tumor-resistant mice.

In the efficient treatment described (Anticancer Research 9: 941-946, 1989) some compounds (64Cu and thioproline) act against the malignant genomes, and other components (metal ions, amino acids, vitamin D2, thyroxine and chelating substances) act against the functioning of the host cells having the cancer functioning (cancer cells). The experiments described show that this treatment developed with mice injected on day zero with 5 x 10(5) Krebs ascitic cells, is also efficient for mice bearing a spontaneous malignant tumor even if it is not an ascitic tumor. After the decrease in weight due to the loss of the tumor, a typical weight evolution was observed characterized by a second weight increase followed by a decrease leading to normal weight. This last weight remained stable. This typical weight evolution in tumor-free mice (after spontaneous tumor or experimental Krebs ascitic tumor) was related to the age of the tumor at the beginning of the treatment, that is, according to our hypothesis (Anticancer Res 9:955-960, 1989) to the cancer evolution emphasizing the great importance of all physiological phenomena related to this cancer course. To test the consequence of this treatment, some of these tumor-free mice were injected with 5 x 10(5) ascitic cells. No tumor developed in these tumor-free mice meaning that they also were tumor-resistant. This last result is in agreement with the forecast of the systemic analysis on which the efficient treatment was based.

Animals↗

PubMedDate not supplied

Treatment of mice bearing a Krebs ascitic tumor by means of a protocol based on radioactive copper (64Cu). I. The "cancer animal": a new concept leading to an effective antitumoral treatment.

Previous experiments have shown that 64Cu transmutation was inefficient to cure mice which had been injected 6 days earlier with 5 x 10(5) Krebs ascitic cells. The experiments were repeated with 64CuCl2 administered only 1 day after the injection of 5 x 10(5) Krebs ascitic cells when no developing tumor existed. The results reported showed that, even in this case, only a delay in death could be observed. These negative results revealed that malignant cells injected 24 hours previously in a mouse (in vivo conditions) differ from a malignant cell suspension in a tube (in vitro conditions) where the lethal effect of 64Cu transmutation was clearly evidenced. We concluded that some kind of collaboration was established between the few accepted malignant cells and the host. Based on this collaboration we introduced a new concept, "the cancer mouse", in which in addition to the malignant cells some cells in the host, even though non - malignant, nonetheless feature a slightly modified functioning: "the cancer functioning". In this view, an efficient antitumor treatment must act at the same time and in a coordinated manner on the malignant cells and on the host cells which now feature "the cancer functioning". In the efficient treatment described (Anticancer Res 9: 947-954, 1989) some compounds (64Cu and thioproline) act against the malignant genomes, and other components (metal ions, amino acids, vitamin D2, thyroxine and chelating substances) act against the functioning of the host cells by taking into account certain characteristics of living systems. This treatment was efficient in curing mice injected 1 or 6 days previously with 5 x 10(5) Krebs ascitic cells.

Animals↗

PubMed1984

Type C influenza virus.

According to the morphology, type and function of its structural components the segmented genome of type C influenza virus is similar to that of influenza viruses A and B. However, type C influenza virus differs from them by the reticular structure of virion surface, absence of the surface glycoprotein neuraminidase, the presence of unusual for Orthomyxoviridae cell receptors and the ability to induce an essentially moderate respiratory illness.

Antigens, Viral↗

PubMedDate not supplied

Immunohistochemistry of medulloepithelioma and neural tube.

Immunohistochemistry profiles of medulloepithelioma (from two 2 1/2-year-old girls who had cerebral medulloepitheliomas and a 35-week postconceptional female infant with congenital posterior fossa tumor) and neural tube are compared. Microscopically, the tumors contained a medulloepitheliomatous component, manifested as tubular epithelial structures lined by pseudostratified columnar epithelium delineated by well-defined basement membranes. In all cases, glial and neuronal differentiation were noted to differing extents. The medulloepitheliomatous components did not exhibit glial fibrillary acidic protein, neuron-specific enolase, or S-100 protein reactivity. Neurofilament, cytokeratin, and epithelial membrane antigen were focally present in one case. Extensive nestin immunopositivity was confined to the basal cell layer of the epithelium, leaving the luminal surface unreactive or slightly reactive. These cells also displayed a reactivity to vimentin and to microtubule-associated protein type 5 similar to that of cells of the primitive neural tube. The similarity between the immunohistochemical profile of medulloepithelioma and that of neural tube epithelium suggests a possible reexpression of that component of the genome responsible for neural tube growth and differentiation in medulloepithelioma.

Central Nervous System Neoplasms↗

PubMed1997

About the origin of retroviruses and the co-evolution of the gypsy retrovirus with the Drosophila flamenco host gene.

The gypsy element of Drosophila melanogaster is the first retrovirus identified so far in invertebrates. According to phylogenetic data, gypsy belongs to the same group as the Ty3 class of LTR-retrotransposons, which suggests that retroviruses evolved from this kind of retroelements before the radiation of vertebrates. There are other invertebrate retroelements that are also likely to be endogenous retroviruses because they share with gypsy some structural and functional retroviral-like characteristics. Gypsy is controlled by a Drosophila gene called flamenco, the restrictive alleles of which maintain the retrovirus in a repressed state. In permissive strains, functional gypsy elements transpose at high frequency and produce infective particles. Defective gypsy proviruses located in pericentromeric heterochromatin of all strains seem to be very old components of the genome of Drosophila melanogaster, which indicates that gypsy invaded this species, or an ancestor, a long time ago. At that time, Drosophila melanogaster presumably contained permissive alleles of the flamenco gene. One can imagine that the species survived to the increase of genetic load caused by the retroviral invasion because restrictive alleles of flamenco were selected. The characterization of a retrovirus in Drosophila, one of the most advanced model organisms for molecular genetics, provides us with an exceptional clue to study how a species can resist a retroviral invasion.

Animals↗

PubMed1997

Molecular domestication of mobile elements.

Transposable elements are ubiquitous in all organisms and represent a dynamic component of their genomes, causing mutations and thereby genetic variation. Because of their independent and expansive replication strategy, these elements are called selfish and were thought to have no impact on the adaptive evolution of their host organisms. Although most TE-induced mutations seem to exert only negative effects on the fitness of their carrier, recent evidence indicates that in the course of evolution at least some TE-mediated changes have become established features of the host genome. For example, the insertion of TEs may provide novel cis-regulatory regions to preexisting host genes or TE-derived trans-acting factors may undergo a molecular transition into novel host genes through a process described as molecular domestication. The stationary P element related gene clusters of D. guanche, D. madeirensis and D. subobscura provide an excellent model system to study the evolutionary impact of TEs on genome evolution. Each cluster unit consists of a cis-regulating section composed of different insertion sequences followed by the first three exons of a P element that are coding for a 66 kDa 'repressor-like' protein.

Animals↗

PubMed2003

A QTL genome scan of the metabolic syndrome and its component traits.

BACKGROUND: Because high blood pressure, altered lipid levels, obesity, and diabetes so frequently occur together, they are sometimes collectively referred to as the metabolic syndrome. While there have been many studies of each metabolic syndrome trait separately, few studies have attempted to analyze them combined, i.e., as one composite variable, in quantitative trait linkage or association analysis. We used genotype and phenotype data from the Framingham Heart Study to perform a full-genome scan for quantitative trait loci underlying the metabolic syndrome. RESULTS: Heritability estimates for all of the covariate-adjusted and age- and gender-standardized individual traits, and the composite metabolic syndrome trait, were all fairly high (0.39-0.62), and the composite trait was among the highest at 0.61. The composite trait yielded no regions with suggestive linkage by Lander and Kruglyak's criteria, although there were several noteworthy regions for individual traits, some of which were also observed for the composite variable. CONCLUSION: Despite its high heritability, the composite metabolic syndrome trait variable did not increase the power to detect or localize linkage peaks in this sample. However, this strategy and related methods of combining correlated individual traits deserve further investigation, particularly in settings with complex causal pathways.

Adult↗

PubMed2000

Retroelements contribute to the excess low-copy-number DNA in pine.

Excess DNA in the single-copy component is rarely recognized as a contributor to the C-value paradox yet the single-copy component of the pine genome is reported to comprise over 3000 Mb of DNA, in large excess over the estimated 100 Mb required for gene expression. Two hypotheses regarding the factors that might contribute to the excess low-copy-number DNA were tested. The first hypothesis proposes that the excess low-copy kinetic component is actually overestimated by reassociation data analysis. To test this, a previously published C0t curve for Pinus strobus was reanalyzed using a new estimate of genome size based on laser flow cytometry. Part of the excess low-copy-number DNA in the pine genome could be attributed to the choice of parameters used in the analysis of the reassociation data. The second hypothesis holds that diverged retrotransposons contribute to the excess low-copy DNA. Sequences randomly sampled from single-copy and low-repetitive kinetic components of the P. taeda genome were characterized. Twelve of 46 fragments cloned from these fractions were found to show sequence similarity to retroelements: hence diverged retroelements contribute to the excess low-repetitive kinetic component in the pine genome. Similarity search was shown to be a conservative method for identifying retroelements, and thus the number of retroelements in the low-copy component was actually underestimated. Most of the retroelements in this fraction were nonfunctional. divergent from known retroelement families and previously reported only for flowering plants. Divergent retrotransposons are thus a major factor contributing to the expansion of the low-repetitive DNA component in higher plants.

Amino Acid Sequence↗

PubMed2005

BLAP75, an essential component of Bloom's syndrome protein complexes that maintain genome integrity.

Bloom's syndrome (BS) is a rare human genetic disorder characterized by dwarfism, immunodeficiency, genomic instability and cancer predisposition. We have previously purified three complexes containing BLM, the helicase mutated in this disease. Here we demonstrate that BLAP75, a novel protein containing a putative OB-fold nucleic acid binding domain, is an integral component of BLM complexes, and is essential for their stability in vivo. Consistent with a role in BLM-mediated processes, BLAP75 colocalizes with BLM in subnuclear foci in response to DNA damage, and its depletion impairs the recruitment of BLM to these foci. Depletion of BLAP75 by siRNA also results in deficient phosphorylation of BLM during mitosis, as well as defective cell proliferation. Moreover, cells depleted of BLAP75 display an increased level of sister-chromatid exchange, similar to cells depleted of BLM by siRNA. Thus, BLAP75 is an essential component of the BLM-associated cellular machinery that maintains genome integrity.

Adenosine Triphosphatases↗

PubMed1983

Examination of the mitochondrial genome of revertant progeny from S cms maize with cloned S-1 and S-2 hybridization probes.

We have examined the molecular rearrangement of mitochondrial DNAs in each of several fertile revertants that arose spontaneously from S-type cytoplasmically male-sterile maize. Cloned segments of S-1 and S-2 DNAs (plasmid-like DNAs characteristic of the mitochondrial DNAs of S-type lines) were hybridized to untreated and restriction endonuclease-treated mitochondrial DNAs from fertile plants carrying normal cytoplasm, from cytoplasmically male-sterile plants, and from plants that had cytoplasmically reverted to fertility. The relative intensity of hybridization with S-1 and S-2 probes was different among the fertile, sterile, and revertant lines. The sizes of some restriction endonuclease fragments from the fertile revertant lines that hybridize with the S-2 probe differ from those of the sterile parental lines. Preferential synthesis of high molecular weight components of the mitochondrial genome carrying S-1 and S-2 sequences, concomitant with cessation in apparent autonomous replication of discrete S-1 and S-2 DNAs and their replicative intermediates (described here), could accommodate the hybridization data. The results suggest but do not prove that S-2 sequences are transposed coincident with the sterile plant's reversion to fertility. The inserted segments could arise from sequences already present in the high molecular weight DNA or from the lower molecular weight linear components of the mitochondrial genome. Putative target sites of insertion of S-1 and S-2 sequences would be multiple and separate for each. Reversion of S-type cytoplasmically male-sterile plants to fertility does not restore the organization of the mitochondrial genome to that of a normal fertile plant.

Base Sequence↗

PubMed1988

Inversion events in the HSV-1 genome are directly mediated by the viral DNA replication machinery and lack sequence specificity.

The bacterial transposable element Tn5 was observed to undergo high-frequency sequence inversion when integrated into the herpes simplex virus type 1 (HSV-1) genome. Deletion analysis of the IS50 elements through which this recombination event occurred demonstrated the absence of cis-acting signals involved in the inversion process. Several observations suggested an intimate association of the recombination mechanism with HSV-1 DNA replication, including the ability of the seven viral genes that are essential for HSV-1 DNA synthesis to mediate Tn5 inversion in the absence of any other viral functions. Comparable results were obtained by using duplicate copies of the L-S junction of the HSV-1 genome. Thus inversion of the L and S components of the HSV-1 genome during productive infection does not appear to be a site-specific process, but rather is the result of generalized recombination mediated by the complex of gene products that replicate the viral DNA.

Animals↗

PubMed2000

Genome scan of human systemic lupus erythematosus by regression modeling: evidence of linkage and epistasis at 4p16-15.2.

Systemic lupus erythematosus (SLE) is a complex autoimmune disorder involving at least hormonal, environmental, and genetic factors. Familial aggregation, a 2%-3% sibling recurrence rate, monozygotic twin concordance >20%, association with several candidate genes, as well as the results of five genome scans support a genetic component. We present here the results of a genome scan of 126 pedigrees multiplex for SLE, including 469 sibling pairs (affected and unaffected) and 175 affected relative pairs. Using the revised multipoint Haseman-Elston regression technique for concordant and discordant sibling pairs and a conditional logistic regression technique for affected relative pairs, we identify a novel linkage to chromosome 4p16-15.2 (P=.0003 and LOD=3.84) and present evidence of an epistatic interaction between chromosome 4p16-15.2 and chromosome 5p15 in our European American families. We confirm the evidence of linkage to chromosome 4p16-15.2 in European American families using data from an independent pedigree collection. In addition, our data support the published results of three independent studies for nine purportedly linked regions and agree with the previously published results from a subset of these data for three regions. In summary, results from two new analytical techniques establish and confirm linkage with SLE at 4p16-15.2, indicate epistasis between 4p16-15.2 and 5p15, and confirm other linkage effects with SLE that have been reported elsewhere.

Africa↗

PubMed1980

Melting fine structure of filamentous fungus nuclear DNA.

Melting fine structure of the nuclear DNA isolated from the filamentous fungus Fusarium graminearum Schwabe is presented. Optical melting profiles of nuclear DNA were analyzed by using a combination of curve fitting and derivative techniques. The "melting components" were obtained from the derivative curve by a simple decomposition technique. Differential optical melting curves of unsheared nuclear DNA indicate the presence of 15 "melting components" in filamentous fungus nuclear genome. It should be emphasized that the "melting components" observed here are different from the "thermalites" which can be observed in bacteriophage DNA. The "melting components" reported here represent the separately melting of large "blocks" of fungus nuclear DNA.

Base Composition↗

PubMed2026

Access to Guideline-Concordant Oncology Genomic Testing: A Qualitative Study of Black Cancer Patients and Oncology Providers.

Genomic testing is a key component of precision oncology; however, Black patients receive genomic testing at lower rates. The purpose of this qualitative study was to identify individual and health system drivers of genomic testing disparities at a National Cancer Institute-designated comprehensive cancer center. We conducted interviews with 15 oncology providers and 11 Black cancer patients between September 2023 and October 2024. These patients were eligible for genomic testing based on National Comprehensive Cancer Network (NCCN) guidelines, being diagnosed within last 10 years (2014-2023), at least 18 years old, and English-speaking. Providers included oncologists and oncology patient navigators. Topics included motivators, barriers, and knowledge of genomic testing and factors influencing decision-making. The Penchansky and Thomas theoretical framework of healthcare access (e.g., availability, accessibility, accommodation, affordability, and acceptability) guided thematic analysis. Among patients eligible for genomic testing, most participants (n = 7) received genomic testing as part of their cancer treatment based on EMRs, however many patients (n = 7) could not recall discussing genomic testing with their oncologist. Most patients and all providers highlighted affordability as a challenge: patients were concerned about unexpected costs associated with testing, while providers were concerned about costs of matched molecular targeted therapy. Both patients and providers highlighted patient-centered communication to mitigate mistrust and promote patient engagement in care. Despite limited awareness, Black patients view genomic testing positively. Addressing multiple dimensions of access is key to improving system-level processes and ensuring that more patients benefit from lifesaving targeted therapy.

Humans↗

PubMed2006

Interactions among genomic structure, function, and evolution revealed by comprehensive analysis of the Arabidopsis thaliana genome.

The genome in a higher organism consists of a number of types of nucleotide sequence-specialized components, with each having tens of thousands of members or elements. It is crucial for our understanding of how a genome as an entity is organized, functions, and evolves to determine how these components are organized in the genome and how they relate with each other; however, no such knowledge is available. Here, we report a comprehensive analysis of the organization and interaction of all 40 components constituting the genome of the plant model species, Arabidopsis thaliana, at the whole-genome and chromosome levels. The 40 components include (i) 6 genome structural components consisting of GC%, genes, retrotransposons, DNA transposons, simple repeats, and low complex repeats; (ii) 3 evolutionarily critical features consisting of recombination rate, nucleotide substitutions, and nucleotide insertions/deletions; and (iii) 31 categories of genes with different functions and numbers of functions. We show that the distributions of 39 of the 40 components of the genome (excepting GC%) deviate significantly from the random distribution model and different types of the genome components are significantly correlated. These results remained to be true even when the genomic regions, such as centromeric regions, where transposable and repeat elements are abundant were excluded from the analyses. These findings suggest that DNA molecules contained in the Arabidopsis genome are each organized and structured from their constituting components in an unambiguous manner and that different types of the components that constitute or characterize the genome interact. The analysis also showed that each chromosome consists of a similar set of the components at similar densities, suggesting that the unique organization and interaction pattern of the components in each chromosome may represent, at least in part, the identity of a chromosome or a genome at the genome level, thus partly accounting for the phenotypic variation among different species. The data also provide comprehensive and new insights into many phenomena significant in genome biology, with which we particularly discuss the variation of genetic recombination. The variation of genetic recombination rate along a chromosomal arm is shaped, not only by the distribution of simple repeats, retrotransposons, DNA transposons, and nucleotide substitutions, but also by the functions of genes contained, especially those with multiple functions, suggesting that variation of genetic recombination along a chromosomal arm is the result of interactions among the components constituting local genome structure, function, and evolution.

Arabidopsis↗