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Epidermal growth factor and Ras regulate gene expression in GH4 pituitary cells by separate, antagonistic signal transduction pathways.

We have previously demonstrated that epidermal growth factor (EGF) produces activation of the rat prolactin (rPRL) promoter in GH4 neuroendocrine cells via a Ras-independent mechanism. This Ras independence of the EGF response appears to be cell rather than promoter specific. Oncogenic Ras also produces activation of the rPRL promoter when transfected into GH4 cells and requires the sequential activation of Raf kinase, mitogen-activated protein (MAP) kinase, and c-Ets-1/GHF-1 to mediate this response. In these studies, we have investigated the interaction between EGF and Ras in stimulating rPRL promoter activity and the role of Raf and MAP kinases in mediating the EGF response. We have also examined the role of several transcription factors and used various promoter mutants of the rPRL gene in order to better define the trans- and cis-acting components of the EGF response. EGF treatment of GH4 cells inhibits activation of the rPRL promoter produced by transfection of V12Ras from 24- to 4-fold in an EGF dose-dependent manner. This antagonistic effect of EGF and Ras is mutual in that transfection of V12Ras also blocks EGF-induced activation of the rPRL promoter in a Ras dose-dependent manner, from 5.5- to 1.6-fold. Transfection of a plasmid encoding the dominant-negative Raf C4 blocks Ras-induced activation by 66% but fails to inhibit EGF-mediated activation of the rPRL promoter. Similarly, transfection of a construct encoding an inhibitory form of MAP kinase decreases the Ras response by 50% but does not inhibit the EGF response. Previous studies have demonstrated that c-Ets-1 is necessary and that GHF-1 acts synergistically with c-Ets-1 in the Ras response of the rPRL promoter. In contrast, overexpression of neither c-Ets-1 nor GHF-1 enhanced EGF-mediated activation of the rPRL promoter, and dominant-negative forms of these transcription factors failed to inhibit the EGF response. Using 5' deletion and site-specific mutations, we have mapped the EGF response to two regions on the proximal rPRL promoter. One region maps between -255 and -212, near the Ras response element, and a second maps between -125 and -54. The latter region appears to involve footprint 2, a previously identified repressor site on the rPRL promoter. Neither footprint 1 nor 3, known GHF-1 binding sites, appears to be crucial to RGF-mediated rPRL promoter activation. The results of these studies indicate that in GH4 neuroendocrine cells, rPRL gene regulation by EGF is mediated by a signal transduction pathway that is separate and antagonistic to the Ras pathway. Hence, the functional role of the Ras/Raf/MAP kinase pathway in mediating transcriptional responses to EGF and other receptor tyrosine kinase may differ in highly specialized cell types.

Animals↗

CDNA microarray analysis of nerve growth factor-regulated gene expression profile in rat PC12 cells.

Nerve growth factor (NGF)-driven differentiation of PC12 cells into neuronal-like cells provides a representative model system for studying neuronal differentiation processes. Despite of extensive research, gene regulation associated with the differentiation program in PC12 cells still needs to be elucidated. We used cDNA microarray analysis to characterize the response of PC12 cells to NGF at mRNA expression. Forty-six genes were reproducibly influenced by 2-fold or more after NGF treatment for 5 days. Twenty-five of the regulated transcripts were matched to genes which have known functions. Among the microarray results confirmed with real-time reverse transcriptase assay, several genes have not previously known to be modulated by NGF. The results mostly reflected changes in molecules regulating neural plasticity, cytoskeletal organization, and lipid metabolism, which include neuritin, PDZ protein Mrt1, lipoprotein lipase, tropomodulin 1 and rhoB. These observed genetic changes may provide new information about molecular mechanisms underlying NGF-promoted differentiation of PC12 cells.

Animals↗

Role of covalent modifications of histones in regulating gene expression.

DNA is organized into a hierarchy of structures, resulting in the level of compaction required to pack 2m of DNA into a nucleus with a diameter of 10 micrometer. The orderly packaging of DNA in the nucleus plays an important role in the functional aspects of gene regulation. A small percentage of chromatin is made available to transcription factors and the transcription machinery, while the remainder of the genome is in a state that is essentially invisible to the RNA polymerases. Modification of histones has a key role in altering chromatin higher order structure and function. In this review, we will present the latest developments in the study of histone modifications (ubiquitination, acetylation, methylation, and phosphorylation) and the enzymes involved in these processes.

Acetylation↗

Self-regulating gene: an exact solution.

An exact steady-state solution of the stochastic equations governing the behavior of a gene regulated by a self-generated proteomic atmosphere is presented. The solutions depend on an adiabaticity parameter measuring the relative rate of DNA-protein unbinding and protein degradation. The steady-state solution reveals deviations from the commonly used Ackers et al approximation based on the equilibrium law of mass action, allowing anticooperative behavior in the "nonadiabatic" limit of slow binding and unbinding rates. Noise from binding and unbinding events dominates the shot noise of protein synthesis and degradation up to quite high values of the adiabaticity parameter.

Animals↗

Gene regulation in reverse transformation: cyclic AMP-induced actin homolog in CHO cells.

Reverse transformation (RT) presents a challenge in understanding of the role of protein-genome interaction in regulating gene expression in normal and transformed cells. Early during RT of CHO-K1 cells by cyclic AMP a new protein, mol wt = 43,000 and pI = 5.3 +/- 0.2, was rapidly and specifically induced. This cAMP-induced protein (CIP) is a phosphorylated actin homolog. Induction required new protein synthesis. Actinomycin D treatment failed to inhibit CIP induction, suggesting the existence of an untranslated or sequestered mRNA in untreated cells. Expression of CIP was not dependent upon cell shape or cytoskeletal integrity as are other steps in RT. CIP was detectable only in cAMP-treated cells, whether transformed or nontransformed, and cAMP treatment inhibited growth of both cell types. CIP was associated with soluble cell fractions and not with F-actin. We propose that CIP plays an early role in RT, that is necessary but not sufficient for the complete RT process, and that it participates in the cAMP signaling pathway of cells through changes in the cytoskeleton. This pathway inhibits cell growth as required in the differentiated phenotype. A molecular model is presented for the RT reaction in CHO-K1, which also explains cAMP effects on transformed cells such as the S49 lymphoma and other malignancies.

Actins↗

Expression profiling of human breast cancers and gene regulation by progesterone receptors.

Even the first expression profiling studies of breast cancers have generated new insights. They suggest for example, that information about tumor aggressiveness, prognosis, metastatic potential, or treatment outcome is encoded in, and can be deduced from, the primary tumor. On the other hand no clinical genomic array data have yet been published that deal with hormonal aspects of breast tumorigenesis, tumor progression, or therapeutics. Rather, studies have focused on experimental model systems. We review below the currently published data on array profiling in clinical breast cancer, then describe our studies in breast cancer cell lines and xenograft models dealing with progesterone receptors (PRs) and the role of progesterone. We demonstrate that the two PR isoforms, PR-A and PR-B, have mostly nonoverlapping molecular signatures when liganded by progesterone, with PR-B the more active form. Additionally, we document the surprising finding that unliganded PRs can regulate gene transcription, with PR-A the more active form. In ovariectomized mice supplemented with estradiol but lacking measurable progesterone, PR-B-expressing tumors grow to twice the size of PR-A-expressing ones. We conclude that in breast cancers, PRs are more than simple markers of estrogen receptor function. Rather, presence of PRs and the ratio of the two isoforms directly influence tumor phenotype, even in the absence of ligand.

Animals↗

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.

The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match and Patch provides increased functionality for TRANSFAC. The list of databases which are linked to the common GENE table of TRANSFAC and TRANSCompel has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD and TRANSPRO. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.

Animals↗

Novel PAX6 binding sites in the human genome and the role of repetitive elements in the evolution of gene regulation.

Pax6 is a critical transcription factor in the development of the eye, pancreas, and central nervous system. It is composed of two DNA-binding domains, the paired domain (PD), which has two helix-turn-helix (HTH) motifs, and the homeodomain (HD), made up from another HTH motif. Each HTH motif can bind to DNA separately or in combination with the others. We identified three novel binding sites that are specific for the PD and HD domains of human PAX6 from single-copy human genomic DNA libraries using cyclic amplification of protein binding sequences (CAPBS) and electrophoretic mobility shift assays (EMSAs). One of the binding sites was found within sequences of repetitive Alu elements. However, most of the Alu sequences were unable to bind to PAX6 because of a small number of mismatches (mostly in CpG dinucleotide hot spots) in the consensus Alu sequences. PAX6 binding Alu elements are found primarily in old and intermediate-aged Alu subfamilies. These data along with our previously identified B1-type Pax6 binding site showed that evolutionarily conserved Pax6 has target sites that are disparate in primates and rodents. This difference indicates that human and mouse Pax6-regulated gene networks may have evolved through these lineage-specific repeat elements.

Alu Elements↗

Chromatin and gene regulation in archaea.

The chromatinisation of DNA by nucleoid-associated proteins (NAPs) in archaea 'formats' the genome structure in profound ways, revealing both striking differences and analogies to eukaryotic chromatin. However, the extent to which archaeal NAPs actively regulate gene expression remains poorly understood. The dawn of quantitative chromatin mapping techniques and first NAP-specific occupancy profiles in different archaea promise a more accurate view. A picture emerges where in diverse archaea with very different NAP repertoires chromatin maintains access to regulatory motifs including the gene promoter independently of transcription activity. Our re-analysis of genome-wide occupancy data of the crenarchaeal NAP Cren7 shows that these chromatin-free regions are flanked by increased Cren7 binding across the transcription start site. While bacterial NAPs often form heterochromatin-like regions across islands with xenogeneic genes that are transcriptionally silenced, there is little evidence for similar structures in archaea and data from Haloferax show that the promoters of xenogeneic genes remain accessible. Local changes in chromatinisation causing wide-ranging effects on transcription restricted to one chromosomal interaction domain (CID) in Saccharolobus islandicus hint at a higher-order level of organisation between chromatin and transcription. The emerging challenge is to integrate results obtained at microscale and macroscale, reconciling molecular structure and function with dynamic genome-wide chromatin landscapes.

Chromatin↗

[MicroRNAs: novel class of gene regulators involved in endocrine function and cancer].

MicroRNAs (miRNAs) represent a novel class of endogenous approximately 22-nucleotide RNAs that negatively regulate gene expression by inhibiting translation of target RNAs. Discovered just over a decade ago in Caenorhabditis elegans, miRNAs are now recognized as one of the major regulatory gene families in plants and animals. In the human genome, 462 miRNA genes have been discovered and the estimated number of miRNAs is as high as 1000. Bioinformatics analysis indicated that a unique miRNA acts on several mRNA, influencing multiple signaling pathways concomitantly, thus presenting enormous regulatory potential. Although the biology of miRNAs is not well understood, recent evidences have linked these molecules to diverse biological processes. Moreover, aberrant expression of miRNAs has been associated to human disease, including that related to the endocrine system and cancer.

Adipocytes↗

Promoter competition assay for analyzing gene regulation in joint tissue engineering.

We describe a new biochemical technique, "promoter competition assay," for examining the role of cis-acting DNA elements in tissue cultures. Recent advances in tissue engineering permit the culture of a variety of cells. Many tissues are engineered, however, without an appropriate understanding of molecular machinery that regulates gene expression and cellular growth. For elucidating the role of cis-acting regulatory elements in cellular differentiation and growth, we developed the promoter competition assay. This assay uses a transient transfer into cells of double-stranded DNA fragments consisting of cis-acting regulatory elements. The transferred DNA fragments act as a competitor and titrate the function of their genomic counterparts. Using synovial cells derived from a rheumatoid arthritis patient, we examined a role of NF-kappa B binding sites in the regulation of the expression of matrix metalloproteinase (MMP) genes. The results support a stimulatory role of NF-kappa B in transcriptional regulation of MMP-1 and MMP-13.

Arthritis, Rheumatoid↗

Regulator genes affecting red cell antigens.

Several mechanisms may be involved to explain the action of genes that regulate the expression of red cell antigens. When carbohydrate antigens are involved, lack of an enzyme in the biochemical pathway prevents formation of the precursor for the next and following steps of that path, or, alternatively, addition of an extra sugar to the immuno-dominant sugar may produce a new structure in which the expression of the expected antigen is masked. Thinking of genetic rather than biochemical interference, a regulator gene may "switch-off" the action of a structural gene, and this mechanism could involve the upset of repressor and/or derepressor genes. The mechanisms for the regulator genes described in this article are unknown. The effect of XGR is limited to red cells: the expression of 12E7 antigen on other tissues and cells, other than red cells, is invariable. The reported effects of XOr and XQ are for red cells, but it is unlikely that other cells and tissues have been studied intensively; propositi with these regulator genes are much rarer than people informative for XGR and In(Lu). The effects of In(Lu) are not limited to red cells but have been shown to regulate the expression of p80 on some white cells. Most of the abnormalities in Rhnull cells appear to be associated with the lack of the Rh antigens and lack of Rh proteins. The hypothesis of a functional complex involving Rh, lack of which affects incorporation of apparently unrelated proteins into the red cell membrane, is an attractive idea. Studies of the similar phenotype, Rhmod, suggest that some Rh specificities can be present in cells that appear to be as abnormal, serologically and morphologically, as Rhnull cells. Perhaps some polypeptides are functionally more important than others and perhaps all polypeptides required for the functional efficiency of the Rh complex have not yet been identified. Lack of Lutheran antigens is not always accompanied by modification of other red cell antigens. As suggested by Telen and green, if In(Lu) acts via a single mechanism, then that mechanism differs from that of XS2. Certainly the mechanisms of In(Lu) and XS2 differ in their action on the expression of CD44 or p80 antigens. The red cell surface is well charted territory, familiar to serologists, immunologists, biochemists, and geneticists. It still provides an excellent model for study of cell surface antigens and for the regulator genes described above that modify expression of some red cell antigens.(ABSTRACT TRUNCATED AT 400 WORDS)

Antigens, Surface↗

A genome-wide identification of E2F-regulated genes in Arabidopsis.

The completion of the Arabidopsis genomic sequence offers the possibility to extract global information about regulatory mechanisms. Here, we describe a data mining strategy in combination with gene expression analysis to identify bona fide genes regulated by the E2F transcription factor. Starting with a genome-wide search of chromosomal sites containing E2F-binding sites, we studied in depth two of the most abundant E2F-binding sites within the Arabidopsis genome and identified over 180 potential E2F target genes. Among them and in addition to cell cycle-related genes, we have also identified genes belonging to other functional categories, e.g. transcription, stress and defense or signaling. We have determined the expression levels of genes selected from different categories under two experimental situations. Using cultured cells partially synchronized with aphidicolin, we found that most potential E2F targets identified in silico show a cell cycle-regulated expression pattern with a peak in early/mid S-phase. In addition, we used Arabidopsis transgenic plants expressing a DP gene containing a truncated DNA-binding domain, which likely has a dominant-negative effect on AtE2Fa, b and c (also named AtE2F3, 1 and 2, respectively), which require DP for efficient DNA binding. Contrary to the up-regulation observed in early/mid S-phase-cultured cells, the expression of a large number of potential E2F targets was decreased in the transgenic plants. Our results strongly support that the RBR/E2F pathway plays a crucial role in regulating the expression of the genes identified in this study.

Amino Acid Sequence↗

The chicken Ig light chain 3'-enhancer is essential for gene expression and regulates gene conversion via the transcription factor E2A.

Expression of the rearranged chicken immunoglobulin light chain (IgL) gene is regulated by a V gene promoter, a matrix attachment region (MAR) in the J-C intron and an enhancer downstream of the Ig constant region. Using knockout analysis, we demonstrate that the 3'-enhancer is not only required for gene activation but is also essential for the maintenance of gene expression. Deletion of the MAR on the other hand increases IgL transcription, indicating that the MAR acts as negative regulator. We demonstrate that Id1 and Id3, dominant-negative regulators of basic-region helix-loop-helix (bHLH) transcription factors, are able to reduce chicken IgL 3'-enhancer activity in transient assays and strongly reduce the rate of gene conversion (GC) in DT40 clone 18 cells. Conversely, overexpression of avian E47, a bHLH transcription factor, leads to a dramatic increase in GC rates independent of IgL or activation-induced cytidine deaminase RNA levels. Thus, E47 is the first transcription factor to activate GC without an apparent increase in transcription.

Animals↗

Gene regulation in cancer gene therapy strategies.

Regulation of expression in gene therapy is considered to be a very desirable goal, preventing toxic effects and improving biological efficacy. A variety of systems have been reported in an ever widening range of applications, this paper describes these systems with specific reference to cancer gene therapy.

Animals↗

Identification of estrogen-regulated genes during fracture healing, using DNA microarray.

Estrogen deficiency impairs fracture healing, while estrogen treatment of ovariectomized rats accelerates fracture healing. To identify genes regulated by estrogen during fracture healing, we evaluated gene expression in calluses from three groups of rats: sham-operated, ovariectomized, and ovariectomized and treated with estrogen. RNA from calluses harvested 10 days after fracture was subjected to DNA microarray-based analysis of 5147 genes. In total, 52 genes were identified whose mRNA expressions were found to be downregulated by ovariectomy but restored with estrogen. Differential mRNA expression of 4 genes (collagen type 2, extracellular superoxide dismutase, urokinase-type plasminogen activator [ u-PA], and ptk-3) was confirmed by reverse transcription polymerase chain reaction. Further, chondrocytes and chondroclasts were positive for u-PA in the junction between cartilage and bone, implying its importance in resorption and remodeling of callus. Identification of these genes is a prerequisite to understanding the mechanism by which estrogen influences the complex metabolic process of fracture repair.

Animals↗

Streptogramin-based gene regulation systems for mammalian cells.

Here we describe repressible (PipOFF) as well as inducible (PipON) systems for regulated gene expression in mammalian cells, based on the repressor Pip (pristinamycin-induced protein), which is encoded by the streptogramin resistance operon of Streptomyces coelicolor. Expression of genes placed under control of these systems was responsive to clinically approved antibiotics belonging to the streptogramin group (pristinamycin, virginiamycin, and Synercid). The versatility of these systems was demonstrated by streptogramin-regulated expression of mouse erythropoietin (EPO), human placental secreted alkaline phosphatase (SEAP), or green fluorescent protein (GFP) in diverse cell lines (BHK, CHO, HeLa, and mouse myoblasts). Analysis of isogenic constructs in CHO cells demonstrated the PipOFF system gave lower background and higher induction ratios than the widely used tetracycline-repressible (TetOFF) expression systems. The streptogramin-based expression technology was functionally compatible with the TetOFF system, thus enabling the selective use of different antibiotics to independently control two different gene activities in the same cell.

Alkaline Phosphatase↗

The role of nuclear factor-kappa B in cytokine gene regulation.

Transcription factors are DNA-binding proteins that regulate gene expression. Nuclear factor-kappa B (NF-kappa B) is a critical transcription factor for maximal expression of many cytokines that are involved in the pathogenesis of inflammatory diseases, such as adult respiratory distress syndrome (ARDS) and sepsis syndrome. Activation and regulation of NF-kappa B are tightly controlled by a group of inhibitory proteins (I kappa B) that sequester NF-kappa B in the cytoplasm of immune/inflammatory effector cells. NF-kappa B activation involves signaled phosphorylation, ubiquitination, and proteolysis of I kappa B. Liberated NF-kappa B migrates to the nucleus, where it binds to specific promoter sites and activates gene transcription. The activation of NF-kappa B initiates both extracellular and intracellular regulatory events that result in autoregulation of the inflammatory cascade through modulation of NF-kappa B activation. Recently, activation of NF-kappa B has been linked to ARDS and has been shown to be a critical proximal step in the initiation of neutrophilic inflammation in animal models. Activation of NF-kappa B can be inhibited in vivo by treatment with antioxidants, corticosteroids, and the induction of endotoxin tolerance. Identification of more specific and efficacious inhibitors of NF-kappa B activation might prove beneficial for the treatment of cytokine-mediated inflammatory diseases.

Adult↗