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PubMed1999

Nutritional regulation of gene expression.

Genes are regulated by complex arrays of response elements that influence the rate of transcription. Nutrients and hormones either act directly to influence these rates or act indirectly through specialized signaling pathways. Metabolites of vitamins A and D, fatty acids, some sterols, and zinc are among the nutrients that influence transcription directly. Components of dietary fiber may influence gene expression indirectly through changes in hormonal signaling, mechanical stimuli, and metabolites produced by the intestinal microflora. In addition, consumption of water-soluble fibers may lead to changes in gene expression mediated through indirect mechanisms that influence transcription rates. In the large intestine, short-chain fatty acids, including butyric acid, are produced by microflora. Butyric acid can indirectly influence gene expression. Some sources of fiber limit nutrient absorption, particularly of trace elements. This could have direct or indirect effects on gene expression. Identification of genes in colonic epithelial cells that are differentially regulated by dietary fiber will be an important step toward understanding the role of dietary factors in colorectal cancer progression.

Animals↗

PubMed2000

Large-scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer.

Difficulties in the detection, diagnosis, and treatment of ovarian cancer result in an overall low survival rate of women with this disease. A better understanding of the pathways involved in ovarian tumorigenesis will likely provide new targets for early and effective intervention. Here, we have used serial analysis of gene expression (SAGE) to generate global gene expression profiles from various ovarian cell lines and tissues, including primary cancers, ovarian surface epithelia cells, and cystadenoma cells. The profiles were used to compare overall patterns of gene expression and to identify differentially expressed genes. We have sequenced a total of 385,000 tags, yielding >56,000 genes expressed in 10 different libraries derived from ovarian tissues. In general, ovarian cancer cell lines showed relatively high levels of similarity to libraries from other cancer cell lines, regardless of the tissue of origin (ovarian or colon), indicating that these lines had lost many of their tissue-specific expression patterns. In contrast, immortalized ovarian surface epithelia and ovarian cystadenoma cells showed much higher similarity to primary ovarian carcinomas than to primary colon carcinomas. Primary tissue specimens therefore appeared to be a better model for gene expression analyses. Using the expression profiles described above and stringent selection criteria, we have identified a number of genes highly differentially expressed between nontransformed ovarian epithelia and ovarian carcinomas. Some of the genes identified are already known to be overexpressed in ovarian cancer, but several represent novel candidates. Many of the genes up-regulated in ovarian cancer represent surface or secreted proteins such as claudin-3 and -4, HE4, mucin-1, epithelial cellular adhesion molecule, and mesothelin. Interestingly, both apolipoprotein E (ApoE) and ApoJ, two proteins involved in lipid homeostasis, are among the genes highly up-regulated in ovarian cancer. Selected serial analysis of gene expression results were further validated through immunohistochemical analysis of ApoJ, claudin-3, claudin-4, and epithelial cellular adhesion molecule in archival material. These experiments provided additional evidence of the relevance of our findings in vivo. The publicly available expression data reported here should stimulate and aid further research in the field of ovarian cancer.

Cell Transformation, Neoplastic↗

PubMed2006

Genetic variation in human gene expression.

Gene expression variation has been the focus of many studies in the past few years. The relevance of gene regulation and gene expression to disease and the development of the technologies used to screen large numbers of genes simultaneously have allowed this rapid development. In this review we discuss issues relating to the biological information one obtains from such studies and the biological significance and use of signals from mapping of gene expression variation.

Gene Expression Profiling↗

PubMed2003

DNA uptake and repair enzyme access to transfected DNA is under reported by gene expression.

Gene expression is the typical biological end point of interest following transfection. However, transcription may not accurately assess DNA uptake, or the ability of transfected DNA to be acted on by other enzymatic pathways. We have compared DNA uptake to gene expression and the unrelated enzymatic process of DNA double strand break (DSB) repair. Transfection efficiency (at limiting DNA concentration) was assessed as a function of DNA uptake and gene expression in the DSB repair proficient WI38VA13 and MO59K cell lines and the DSB repair defective cell line MO59J, by comparing eGFP expression from the pHygEGFP expression vector with uptake of rhodamine labeled linear pSP189 plasmid (3:1). Repair proficient cells expressed eGFP most efficiently, but never approached DNA uptake levels (>or=90%). Although transfected DNAs were stable in repair proficient cells and degraded in MO59J cells, most cells did not express eGFP, but in the repair proficient cells linear DNA did undergo DSB repair.

Blotting, Southern↗

PubMed2001

Protein kinase C control of gene expression.

Gene expression is fashioned at multiple interconnected levels and is controlled by a complex interplay between nucleosomal assembly, the establishment of multifaceted transcriptional motifs, and the temporal and spatial organization of chromatin in loops and domains. Protein phosphorylation is one of the most versatile posttranslational modifications used in eukaryotic cells and plays a crucial role in the continuous remodeling of different transcriptional regulators. The protein kinase C (PKC) family of serine-threonine kinases encompasses 12 different isozymes that have been shown to transduce a myriad of signals mediated by phospholipid hydrolysis as a consequence of the activation of G protein-coupled receptors, tyrosine kinase receptors, and nonreceptor tyrosine kinases. Although the analysis of PKC activity in many systems has provided crucial insights to its biological function, unraveling the molecular mechanisms that underlie isozyme-specific modulation of gene expression within the complexity of genome structure and function remains a challenging issue. This review focuses on recent advances in PKC-dependent regulation of gene expression within the context of the dynamic linkages involving nuclear architecture and transcription. Implications of isozyme-specific phosphorylation of selected members of transcription factors are also discussed. Future perspectives disclosed by recently available methods for large-scale transcriptional profiling are also outlined.

Active Transport, Cell Nucleus↗

PubMed2002

Profiling gene expression using onto-express.

Gene expression profiles obtained through microarray or data mining analyses often exist as vast data strings. To interpret the biology of these genetic profiles, investigators must analyze this data in the context of other information such as the biological, biochemical, or molecular function of the translated proteins. This is particularly challenging for a human analyst because large quantities of less than relevant data often bury such information. To address this need we implemented an automated routine, called Onto-Express (http://vortex.cs.wayne.edu:8080), to systematically translate genetic fingerprints into functional profiles. Using strings of accession or cluster identification numbers, Onto-Express searches the public databases and returns tables that correlate expression profiles with the cytogenetic locations, biochemical and molecular functions, biological processes, cellular components, and cellular roles of the translated proteins. The profiles created by Onto-Express fundamentally increase the value of gene expression analyses by facilitating the translation of quantitative value sets to records that contain biological implications.

Gene Expression Profiling↗

PubMed2006

Gene expression and gene therapy imaging.

The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters.

Animals↗

PubMed2004

The flow of gene expression.

Gene expression is a highly interconnected multistep process. A recent meeting in Iguazu Falls, Argentina, highlighted the need to uncover both the molecular details of each single step as well as the mechanisms of coordination among processes in order to fully understand the expression of genes.

Alternative Splicing↗

PubMed1999

On-line monitoring of gene expression.

Gene expression in cultures of Escherichia coli has been determined in situ and on-line by the use of an electrochemical sensor. Intact bacteria were used to monitor the induction of the lacZ gene; the onset of stationary phase was also monitored, using a reporter gene fused to the RpoS-dependent promoter of the osmY gene. The technique described can in principle be used to determine the activity of any promoter, with a variety of reporter genes. This technology is non-intrusive, allows real-time monitoring of gene expression, and will be useful in the study of growth regulation and development.

Biosensing Techniques↗

PubMedDate not supplied

Novel NMR platform for detecting gene transfection: synthesis and evaluation of fluorinated phenyl beta-D-galactosides with potential application for assessing LacZ gene expression.

Gene therapy holds great promise for the treatment of diverse diseases, but widespread implementation is hindered by difficulties in assessing the success of transfection. The development of noninvasive reporter techniques based on appropriate molecules and imaging modalities may help to assay gene expression. Fluorophenyl-beta-d-galactopyranosides provide a novel class of NMR active molecules, which are highly responsive to the action of beta-galactosidase (beta-gal), the product of the lacZ gene. The reporter molecules are stable in solution and with respect to wild-type cells, but the enzyme causes liberation of the aglycon, a fluorophenol, accompanied by distinct color formation and a (19)F NMR chemical shift of 5-10 ppm, depending on pH. Synthetic strategy, experimental methods, and molecular and (19)F NMR characteristics are reported for a series of molecules in solution, blood, and tumor cells. This class of molecules presents a new strategy for assaying gene expression with a highly versatile molecular structural platform.

Animals↗

PubMed1994

ADP-ribosylation and gene expression.

Gene expression can be defined as the conversion of information existing in a molecule of DNA into a mature RNA or protein product and each step in the process, which requires the concerted action of several macromolecules for completion, may be perturbed by the post-translational modification of specific proteins with ADP-ribose. The participation of poly(ADP-ribose) in the regulation of transcription initiation was examined using cell-free systems for both ribosomal RNA and ribosomal proteins. The presence or absence of poly(ADP-ribose) polymerase did not influence the transcription process. Similarly, under conditions optimal for poly(ADP-ribose) polymerase activity, no change in transcription was observed. A direct contribution of poly(ADP-ribosyl)ation to gene transcription thus could not be detected. In contrast, the addition of 3-aminobenzamide to quiescent hepatoma cells treated with insulin inhibited the stimulation of rRNA synthesis. The high concentrations necessary for this effect suggest that a mono(ADP-ribosyl)ation event participates in the cellular action of insulin. A role in the signal transduction pathway leading to activation of rRNA gene expression has been proposed.

ADP Ribose Transferases↗

PubMed2005

Stochastic simulations of the origins and implications of long-tailed distributions in gene expression.

Gene expression noise results in protein number distributions ranging from long-tailed to Gaussian. We show how long-tailed distributions arise from a stochastic model of the constituent chemical reactions and suggest that, in conjunction with cooperative switches, they lead to more sensitive selection of a subpopulation of cells with high protein number than is possible with Gaussian distributions. Single-cell-tracking experiments are presented to validate some of the assumptions of the stochastic simulations. We also examine the effect of DNA looping on the shape of protein distributions. We further show that when switches are incorporated in the regulation of a gene via a feedback loop, the distributions can become bimodal. This might explain the bimodal distribution of certain morphogens during early embryogenesis.

Animals↗

PubMed2005

Tetracycline-inducible gene expression and gene deletion in Candida albicans.

The genetic analysis of Candida albicans, the major fungal pathogen of humans, is hampered by its diploid genome, the absence of a normal sexual cycle, and a nonstandard codon usage. Although effective methods to study gene function have been developed in the past years, systems to control gene expression in C. albicans are limited. We have established a system that allows induction of gene expression in C. albicans by the addition of tetracycline (Tet). By fusing genetically modified versions of the reverse Tet repressor from Escherichia coli and the transcription activation domain of the Gal4 protein from Saccharomyces cerevisiae, a C. albicans-adapted reverse Tet-dependent transactivator (rtTA) was created that was expressed from the constitutive ADH1 or the opaque-specific OP4 promoter. To monitor Tet-inducible gene expression, the caGFP reporter gene was placed under the control of a Tet-dependent promoter, obtained by fusing a minimal promoter from C. albicans to seven copies of the Tet operator sequence. Fluorescence of the cells demonstrated that gene expression could be efficiently induced by the addition of doxycycline in yeast, hyphal, and opaque cells of C. albicans. The Tet-inducible gene expression system was then used to manipulate the behavior of the various growth forms of C. albicans. Tet-induced expression of a dominant-negative CDC42 allele resulted in growth arrest as large, multinucleate cells. Filamentous growth was efficiently inhibited under all tested hyphal-growth-promoting conditions by Tet-inducible expression of the NRG1 repressor. Tet-induced expression of the MTLa1 gene in opaque cells of an MTLalpha strain forced the cells to switch to the white phase, whereas Tet-induced expression of the MTLa2 transcription factor induced shmooing. When the ecaFLP gene, encoding the site-specific recombinase FLP, was placed under the control of the Tet-dependent promoter, Tet-inducible deletion of genes which were flanked by the FLP target sequences was achieved with high efficiency to generate conditional null mutants. In combination with the dominant selection marker caSAT1, the Tet-inducible gene expression system was also applied in C. albicans wild-type strains, including drug-resistant clinical isolates that overexpressed the MDR1, CDR1, and CDR2 multidrug efflux pumps. This system, therefore, allows a growth medium-independent, Tet-inducible expression and deletion of genes in C. albicans and provides a convenient, versatile new tool to study gene function and manipulate cellular behavior in this model pathogenic fungus.

Alleles↗

PubMed2006

Differential expression of genes encoding CD30L and P-selectin in cattle with Johne's disease: progress toward a diagnostic gene expression signature.

Mycobacterium avium subspecies paratuberculosis (Mycobacterium paratuberculosis), the causative agent of paratuberculosis (paraTB) or Johne's disease in ruminants, is a health problem for the global cattle industry with significant economic losses related to decreased milk production and reduced fertility. Commonly paraTB in cattle is diagnosed by antibody detection by serum enzyme-linked immunosorbent assay (ELISA), by detection of the pathogen by cultivation of individual faecal samples, or by in vitro measurement of cell mediated immune responses using the IFN-gamma test. There is an ongoing need for developing new diagnostic approaches as all currently available diagnostic tests for paraTB may fail to detect sub-clinical infection. We used cDNA microarrays to simultaneously measure expression of over 1300 host genes to help identify a subset of gene expression changes that might provide a unique gene expression signature for paraTB infection. In the present study, non-stimulated leukocytes isolated from 10 sub-clinical paraTB infected cows were examined for genes being expressed at significantly different levels than in similar cells from control cows with the same herd background. We included cattle (Holstein) from two locations (Denmark and USA) for the microarray experiment. Our results indicate that expression profiles of at least 52 genes are different in leukocytes from M. paratuberculosis infected cattle compared to control cattle. Gene expression differences were verified by quantitative real-time reverse transcriptase polymerase chain reactions (qRT-PCR) on the same group of cattle (Holstein) used for the microarray experiment. In order to assess the generality of the observed gene expression, a second and different group of cattle (Jersey) was also examined using qRT-PCR. Out of the seven genes selected for qRT-PCR, CD30 ligand (CD30L) and P-selectin were consistently differentially expressed in freshly isolated leukocytes from paraTB infected and control animals of both breeds of cattle. Although further work is clearly needed to develop a more complete gene expression signature specific for paraTB, our results demonstrate that a subset of genes in leukocytes are consistently expressed at different levels, depending upon M. paratuberculosis infection status.

Animals↗

PubMed2006

Tumor-specific gene expression patterns with gene expression profiles.

Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues. First, a variation of the Relief algorithm, "RFE_Relief algorithm" was proposed to learn the relations between genes and tissue types. Then, a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts. After tissue-specific genes were removed, cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues. The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues, and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper.

Algorithms↗

PubMed2003

Myometrial effects of selective estrogen receptor modulators on estradiol-responsive gene expression are gene and cell-specific.

We examined in vivo effects of selective estrogen receptor modulators (SERMs) 4-OH-tamoxifen (Tam), GW 5638 (GW) and EM-800 (EM) on myometrial gene expression. The uteri of ovariectomized ewes were infused with 10(-7)M of one SERM via indwelling catheters for 24h preceding hysterectomy. Half of the ewes in each SERM group received an intramuscular injection of 50 microg 17beta-estradiol (E2) 18 h prior to hysterectomy. Northern blot analysis and in situ hybridization demonstrated that E2 increased estrogen receptor (ER), progesterone receptor (PR) and cyclophilin (CYC) gene expression in the cells of both inner layer of myometrium (IM) and outer layer of myometrium (OM) as well as glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene expression in OM. Tam also increased ER mRNA levels in OM. EM appeared to increase ER gene expression, but antagonized E2's up-regulation of PR and CYC gene expression in both IM and OM. Tam and GW also antagonized E2 up-regulation of PR gene expression in OM but not IM. No SERM affected GAPDH gene expression with or without E2. Immunohistochemistry indicated that E2 increased nuclear ER and PR protein levels in both IM and OM. EM was unique in up-regulating ER protein levels, opposite to its effects in endometrial cells. All SERMs tested antagonized this increase in PR immunostaining preferentially in OM compared to the IM layer. These results illustrate gene and cell layer-specific effects of SERMs in sheep myometrium.

Animals↗

PubMed2002

Intrinsic and extrinsic contributions to stochasticity in gene expression.

Gene expression is a stochastic, or "noisy," process. This noise comes about in two ways. The inherent stochasticity of biochemical processes such as transcription and translation generates "intrinsic" noise. In addition, fluctuations in the amounts or states of other cellular components lead indirectly to variation in the expression of a particular gene and thus represent "extrinsic" noise. Here, we show how the total variation in the level of expression of a given gene can be decomposed into its intrinsic and extrinsic components. We demonstrate theoretically that simultaneous measurement of two identical genes per cell enables discrimination of these two types of noise. Analytic expressions for intrinsic noise are given for a model that involves all the major steps in transcription and translation. These expressions give the sensitivity to various parameters, quantify the deviation from Poisson statistics, and provide a way of fitting experiment. Transcription dominates the intrinsic noise when the average number of proteins made per mRNA transcript is greater than approximately 2. Below this number, translational effects also become important. Gene replication and cell division, included in the model, cause protein numbers to tend to a limit cycle. We calculate a general form for the extrinsic noise and illustrate it with the particular case of a single fluctuating extrinsic variable-a repressor protein, which acts on the gene of interest. All results are confirmed by stochastic simulation using plausible parameters for Escherichia coli.

Biophysical Phenomena↗

PubMed1999

Differential display competitive polymerase chain reaction: an optimal tool for assaying gene expression.

Gene discovery, i.e. detection of genes whose expression is affected in diseases or by different treatments of cells or animals, has become the focus of much genetic research. The technologies that are used to detect changes in expression level include polymerase chain reaction (PCR)-based subtraction methods, arrays of cDNA clones on chips or filters, serial analysis of gene expression, and differential display. In this paper we show that differential display can be used to investigate global gene expression in situations where a few genes change expression levels such as exposure of MCF7 cells to estradiol, and in more complex situations such as neuronal differentiation of human NTERA2 cells which affects a large number of genes. Furthermore, we show that differential display can replace Northern blotting and RNase protection as a tool to study the expression level of a specific gene in many samples. Results obtained by differential display can be stored in databases, where the identity of a band (gene or mRNA name) can be linked with information about the primer combination displaying the band and a gel image showing the band pattern, which is all the information that is needed to compare the expression level of this gene in other samples.

Base Sequence↗