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G C Overton

Publications and source records attributed to G C Overton.

30 records · Page 2Linked to original sources
PubMed1988

Expression of SPARC/osteonectin transcript in murine embryos and gonads.

A cDNA clone, p2-4, was isolated from mouse teratocarcinoma-derived parietal endoderm-like cells and used to analyze expression of the corresponding transcript during mouse embryogenesis. Nucleotide-sequence analysis revealed extensive homology between this clone and SPARC/osteonectin cDNA cloned from mouse parietal endoderm and bovine bone cells. The SPARC/osteonectin transcript became more abundant when embryonal carcinoma (EC) cells differentiated into parietal endoderm-like cells. In embryos, the transcript began to appear in the embryo proper on day 11 and continued to be expressed throughout the gestation period. The transcript was also present in extraembryonic membranes and placenta from days 9 and 11 onward, respectively. Thus, expression of the transcript was regulated during differentiation of EC cells and during embryogenesis. In adult mice, several non-bone tissues, including testis, also expressed the transcript. Analysis of germ-cell-deficient mice indicated that non-germ-cell components of the testis expressed the transcript. Analysis of mouse testicular cell lines further suggested that the transcript was abundant in Sertoli cells and Leydig cells. Cumulus oophorus cells that envelope the ovulated egg also expressed high levels of the transcript.

Animals↗
PubMed1986

Expression of the intracisternal A-particle is elevated during differentiation of embryonal carcinoma cells.

Three cDNA clones coding for the 3' region of the intracisternal A-particle (IAP), a mouse endogenous retrovirus, were isolated during screening of a library for genes whose expression was modulated during the retinoic acid-induced differentiation of the embryonal carcinoma cell line F9 into parietal endoderm-like (PE-like) cells. In contrast to previously reported results, no IAP transcripts were detected in either F9 cells or two pluripotent cell lines tested. Instead, IAP transcripts as well as IAPs were abundant in the PE-like cells PYS-2 and F9AcCl 9 and in retinoic acid-induced F9 cells but not in the other differentiated cell types of teratocarcinoma origin which were examined. A comparison of the nucleotide sequences of the three IAP cDNA clones with a genomically integrated proviral sequence (MIA14) demonstrated heterogeneity in both length and sequence among the clones. The position of the poly(A) addition site was determined to be 15 nucleotides from the proposed poly(A) addition signal and to occur after the sequence CAGA, not CA, as previously proposed. Length heterogeneity was greatest in a region of TC repeats 80 base pairs 5' to the poly(A) addition site. Additionally, the putative TATAA box found in MIA14 was deleted in the cDNA clones and in the long terminal repeat regions from two other genomic clones examined. The heterogeneity evident among the cDNA clones further demonstrated that at least two distinct IAP genes are activated during differentiation. An analysis of the rate of transcription in isolated nuclei indicated that the activation of expression of IAP genes in PE-like cells is the result of transcriptional regulation. Together, these observations suggest that the modulation of IAP transcription is regulated autonomously rather than by the fortuitous integration of an IAP sequence adjacent to a developmentally regulated cellular gene.

Animals↗
PubMed1984

Post-transcriptional regulation of the abundance of mRNAs encoding alpha-tubulin and a 94,000-dalton protein in teratocarcinoma-derived stem cells versus differentiated cells.

Changes in the expression of the genes encoding alpha-tubulin and a 94,000-dalton protein (p94) specified by a cDNA clone, p4-30, were examined in a differentiated teratocarcinoma-derived parietal endoderm cell line, PYS-2, and an undifferentiated teratocarcinoma stem cell line, F9. Relative to other proteins or mRNA species, the synthesis rate of the alpha-tubulins and of p94, as well as the levels of their corresponding cytoplasmic mRNAs, were lower in PYS-2 than in F9 cells. The decrease was greater for the relative abundance of cytoplasmic alpha-tubulin mRNA than for p94 mRNA. Similarly, induction of differentiation of F9 cells by simultaneous exposure to retinoic acid (RA) and dibutyryl cyclic AMP resulted in reduced relative levels of the cytoplasmic mRNAs for these proteins. The reduction in abundance of the two RNA species was not due to a decrease in growth rate since the differentiated cells, PYS-2, RA-treated F9, and RA plus dibutyryl cyclic AMP-treated F9 cells, grew at a rate similar to that of undifferentiated F9 cells. However, induction of differentiation of F9 cells by treatment with RA alone did not cause down-regulation of the two RNA species. The relative levels of total cellular RNA encoding alpha-tubulin and p94 in PYS-2 cells were also lower than those in F9 cells to an extent comparable to the decrease in the cytoplasmic RNAs. Since the apparent relative rates of RNA transcription were similar in both cell types, we conclude that the reduction in relative levels of the alpha-tubulin and p94 RNAs in the cell depends largely on the relative stability of the two RNAs and not on the relative rates of transcription. The faster disappearance of the two RNA species relative to other cellular RNAs from actinomycin D-treated PYS-2 compared with F9 cells is consistent with this interpretation.

Animals↗
PubMed1978

Length and sequence heterogeneity of the histone gene repeat unit of the sea urchin, S. purpuratus.

Histone gene repeats in S. purpuratus are shown to be of variable length and sequence. Two recombinant plasmids containing the full-length 6.3 kb histone repeat unit are found to differer in length at two sites in the repeating structure and in the occurrence of two restriction enzyme recognition sites. Variation in repeat length is also demonstrated in the unfractionated DNA of five sea urchins and in a sample of DNA enriched for histone gene sequences by density gradient methods. The repeats in each individual are of a very limited number of major classes, which may differ from one another in overall length or in distribution and presence of particular restriction enzyme sites. Variations are found to occur at many regions of the repeat; some have been mapped specifically to spacer regions. Repeats may differ dramatically from individual to individual since there is no one type of repeat class common to all, although the absolute length differences of the repeats that are found are small.

Base Sequence↗
PubMed1975

Histone gene arrangement in the sea urchin, Strongylocentrotus purpuratus.

The DNA coding for histones from Strongylocentrotus purpuratus, purified up to 100-fold with the use of Hg+2-CS2-SO4 and actinomycin-CsC1 equilibrium density gradients, has been used to study the clustering of genes coding for different histones and the size of the repeating multigene cluster. When digested with EcoRI restriction endonuclease, the histone DNA is identified in two classes of fragments with molecular weights of 1.15 X 106 and 2.8 X 106, whereas after treatment of the DNA with HindIII restriction endonuclease, histone gene sequences can be identified only in a fragment of 3.95 X 106. Treatment of the DNA with both enzymes simultaneously shows that there is a HindIII site within the smaller EcoRI fragment. Partial digests with HindIII give fragment sizes that appear to be simple multiples of a 3.95 X 106 repeat. Individual histone mRNAs all hybridize to the 3.95 X 106 fragment but only to one or the other EcoRI fragments. The evidence strongly suggests a repeating unit of 3.95 X 106 containing the genes for most, if not all, the histonrs.

Animals↗
PubMedDate not supplied

Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.

MOTIVATION: Recognition of functional sites remains a key event in the course of genomic DNA annotation. It is well known that a number of sites have their own specific oligonucleotide content. This pinpoints the fact that the preference of the site-specific nucleotide combinations at adjacent positions within an analyzed functional site could be informative for this site recognition. Hence, Web-available resources describing the site-specific oligonucleotide content of the functional DNA sites and applying the above approach for site recognition are needed. However, they have been poorly developed up to now. RESULTS: To describe the specific oligonucleotide content of the functional DNA sites, we introduce the oligonucleotide alphabets, out of which the frequency matrix for a given site could be constructed in addition to a traditional nucleotide frequency matrix. Thus, site recognition accuracy increases. This approach was implemented in the activated MATRIX database accumulating oligonucleotide frequency matrices of the functional DNA sites. We have demonstrated that the false-positive error of the functional site recognition decreases if the oligonucleotide frequency matrixes are added to the nucleotide frequency matrixes commonly used. AVAILABILITY: The MATRIX database is available on the Web, http://wwwmgs.bionet.nsc.ru/Dbases/MATRIX/ and the mirror site, http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.

Algorithms↗
PubMedDate not supplied

Conformational and physicochemical DNA features specific for transcription factor binding sites.

MOTIVATION: A reliable recognition of transcription factor binding sites is essential for analysis of regulatory genomic sequences. The experimental data make evident an important role of DNA conformational features for site functioning. However, Internet-available tools for revealing conformational and physicochemical DNA features significant for the site functioning and subsequent use of these features for site recognition have not been developed up to now. RESULTS: We suggest an approach for revealing significant conformational and physicochemical properties of functional sites implemented in the database B-DNA-VIDEO. This database is designed to study the sets of various transcription factor binding sites, providing evidence that transcription factor binding sites are characterized by specific sets of significant conformational and physicochemical DNA properties. For a fixed site, by using the B-DNA features selected for this site recognition, the C-program recognizing this site may be generated, control tested and stored in the database B-DNA-VIDEO. Each B-DNA-VIDEO entry links to the Web-applet recognizing the site, whose significant B-DNA features are stored in this entry as the 'site recognition programs'. The pairwise linked entry-applet pairs are compiled within the B-DNA-VIDEO system, which is simultaneously the database and the program tools package applicable immediately for recognizing the sites stored in the database. Indeed, this is the novelty. Hence, B-DNA-VIDEO is the Web resource of both 'searching for static data' and 'active computation' type, that is why it was called an 'activated database'. AVAILABILITY: B-DNA-VIDEO is available at http://wwwmgs.bionet.nsc.ru/systems/BDNAVideo/ and the mirror site at http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.

Base Sequence↗
PubMedDate not supplied

Integrated databases and computer systems for studying eukaryotic gene expression.

MOTIVATION: The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. RESULTS: The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. AVAILABILITY: GeneExpress is available at http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.

Algorithms↗
PubMedDate not supplied

Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.

MOTIVATION: The commonly accepted statistical mechanical theory is now multiply confirmed by using the weight matrix methods successfully recognizing DNA sites binding regulatory proteins in prokaryotes. Nevertheless, the recent evaluation of weight matrix methods application for transcription factor binding site recognition in eukaryotes has unexpectedly revealed that the matrix scores correlate better to each other than to the activity of DNA sites interacting with proteins. This observation points out that molecular mechanisms of DNA/protein recognition are more complicated in eukaryotes than in prokaryotes. As the extra events in eukaryotes, the following processes may be considered: (i) competition between the proteins and nucleosome core particle for DNA sites binding these proteins and (ii) interaction between two synergetic/antagonist proteins recognizing a composed element compiled from two DNA sites binding these proteins. That is why identification of the sequence-dependent DNA features correlating with affinity magnitudes of DNA sites interacting with a protein can pinpoint the molecular event limiting this protein/DNA recognition machinery. RESULTS: An approach for predicting site activity based on its primary nucleotide sequence has been developed. The approach is realized in the computer system ACTIVITY, containing the databases on site activity and on conformational and physicochemical DNA/RNA parameters. By using the system ACTIVITY, an analysis of some sites was provided and the methods for predicting site activity were constructed. The methods developed are in good agreement with the experimental data. AVAILABILITY: The database ACTIVITY is available at http://wwwmgs.bionet.nsc.ru/systems/Activity/ and the mirror site, http://www.cbil.upenn.edu/mgs/systems/acti vity/.

Algorithms↗
PubMedDate not supplied

[Averaging results of site recognition can increase the accuracy of annotating the human genome].

A systemic approach is proposed, which makes it possible to increase the accuracy of recognition of functional sites in arbitrary DNA sequences. The approach is based on the Central limit theorem and consists in the averaging of a large number of recognitions of a particular site. To obtain a rather large number of recognitions within the framework of conventional methods of recognition, consensus, and frequency matrix, 20 novel oligonucleotide alphabets were used. The approach was used to study the binding sites of GATA-1 and C/EBP transcription factors. It was found that the averaged recognition of these sites is more precise than each of specific recognitions, which just follows from the Central limit theorem.

Base Sequence↗