Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: DrugBank:BIOD00017 (IFN-gamma)
 28,919 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The promoters of two interferon-induced genes (the ISG54 and guanylate-binding protein [GBP] genes) have been analyzed in whole cells and in isolated nuclei by using a new genomic sequencing technique. The ISG54 gene contains an interferon-simulating response element (ISRE), earlier shown to be necessary and sufficient for alpha interferon (IFN-alpha) induction, that appeared complexed with proteins in both transcribing and nontranscribing cells. However, the extent of protection and hypersensitivity to DNase I or dimethyl sulfate within the ISRE region was changed upon transcriptional induction, suggesting the binding of different factors in different transcriptional states. In addition to the ISRE, the GBP gene needs a newly recognized DNA element, called the GAS, that partly overlaps the ISRE for full induction by either IFN-alpha or IFN-gamma. This GAS element was transiently protected against DNase I in the nuclei of interferon-treated cells but was not protected at later times when transcription reached maximal levels. Thus, the GAS-binding activity may be necessary only transiently for the initial assembly of a transcription initiation complex on the GBP promoter. Dimethyl sulfate methylation of genomic DNA performed on intact cells showed a characteristic sensitivity over the GAS that correlated with transcription levels and that persisted longer than did DNase I protection over the GAS. These results demonstrate the involvement of the GAS in IFN-alpha and -gamma induction of GBP and suggest the presence of an altered DNA conformation or a small protein in the major groove of the GAS associated with ongoing GBP transcription.
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PMID:Interferon induction of gene transcription analyzed by in vivo footprinting. 172 91

The class II (Ia) MHC Ag are integral membrane proteins whose expression is limited to specific cell types. A pair of consensus sequences, X and Y, is found upstream from all class II genes and deletion of each of these sequences eliminates expression of transfected genes. Cells that express Ia demonstrate a coordinate response to lymphokines and other stimuli. These conserved sequences might, therefore, play a role in tissue specificity or lymphokine inducibility of Ia gene expression. The X box sequence of the murine class II A alpha gene diverges much more substantially from the X consensus than does the Y box motif of this gene. We demonstrate that this X box motif is nonetheless recognized by sequence-specific DNA-binding proteins, as is the more closely conserved Y box. Gel retardation assays and DNase I footprints were compared for a panel of Ia+ and Ia- cells as well as for cells stimulated with the Ia-inducing lymphokines IL-4 and IFN-gamma. The level, retardation pattern and region of DNA contact were comparable in all instances. Thus the availability of active DNA-binding X and Y box factors cannot alone account for the regulation of A alpha expression. To test whether the same set of proteins binds all class II MHC conserved motifs, oligonucleotide probe binding and cross-competition experiments with X box sequences from A alpha, E alpha, and E beta genes were performed. These studies demonstrated A alpha, E alpha, and E beta DNA-protein complexes with unique mobilities and specificities. In addition, all three X box oligonucleotide probes generated one faint complex with an affinity profile of E beta greater than E alpha much greater than A alpha. These three complexes comigrated and thus may represent a communal binding protein. The data are most consistent with the conclusion that multiple proteins bind class II MHC X boxes. For A alpha, the predominant complexes represent different specificities from the predominant E alpha and E beta X box binding proteins.
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PMID:Differences in DNA sequence specificity among MHC class II X box binding proteins. 249 26

MHC class I antigens play a crucial role in immunological functions, e.g. transplant and tumor rejection and antigen presentation. Whereas class I antigens are normally expressed on most adult tissues, albeit in varying amounts, embryonic as well as many tumor cells are characterized by the absence of major histocompatibility complex class I antigens on their cell surfaces. In this study the mechanism controlling the lack of class I expression was analyzed at the level of the chromatin structure. Five DNase I hypersensitive sites were determined at the H-2 D-locus of cell lines constitutively expressing class I genes. Two of them (DH1, located at the TATA box/transcription start site, and DH2, located at the enhancer/interferon response sequence) were absent in the fibrosarcoma IC9 in which expression of the silent Dk class I gene was not inducible. DH1 and DH2 remained absent even after fusion with class-I-positive cells. However, transfected Dk genes were expressed in IC9, and both DH1 and DH2, which were probably derived from the transfected gene, became detectable. In tumor cells expressing class I genes only after treatment with IFN-gamma (e.g. the lung carcinoma CMT64.5) or after in vitro differentiation (F9 embryonal carcinoma cells), DH1 and DH2 were already present before induction of class I expression. However, the intensity of the band indicative of DH2 was reduced in undifferentiated and differentiated F9 cells and in untreated CMT cells.
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PMID:Altered regulation of MHC class I genes in different tumor cell lines is reflected by distinct sets of DNase I hypersensitive sites. 250 17

The analysis of the carcinoembryonic antigen (CEA) promoter in the colon carcinoma lines HT-29 and SW403, using HeLa as a control, was performed using gel mobility shift assays and in vitro and in vivo footprinting before and after IFN-gamma treatment. Using a 332-bp probe extending from the start of translation (+1 to -331), we detected 4-5 specific complexes that increased with intensity with IFN-gamma treatment as measured by a gel mobility shift assay. In contrast, no complexes were observed for probes covering the regions -500 to -1000 and -1000 to -1500. DNase I in vitro footprinting with the 332-bp probe revealed three footprints, FP-I to FP-III, none of which changed during the course of IFN-gamma treatment. Using probes corresponding to each footprint, 6-7 specific complexes were observed by gel mobility shift assays. Although minor changes were observed on IFN-gamma treatment, no consistent pattern was observed for all cell lines tested. Several of the proteins involved in the promoter complexes were identified by antibody super shifts, UV cross-linking, and Southwestern blotting. FP-I bound an Sp1-like protein, binding to a GT box sequence, and USF (upstream regulatory factor). FP-II and FP-III bound Sp1, binding through the consensus sequence for a GC box. Lower molecular weight complexes of an unknown nature were observed with sequence specificity for both single- and double-stranded DNA. DNase I in vivo footprints confirmed the boundaries of FP-I to FP-III and revealed a fourth but weaker footprint, FP-IV. The strongest in vivo footprints were observed for SW403 cells, with weaker and no footprints observed for HeLa cells, thus correlating with the degree of CEA transcriptional activity (HeLa cells make no CEA mRNA). DNase I hypersensitive sites correlated well with the boundaries of the footprints and also revealed activity around the start of transcription (-110). The specific pattern for DNase I hypersensitivity for Sp1 in the CEA promoter was the same as observed for the SV40 early promoter. In vivo footprinting with dimethyl sulfate revealed protein binding at the Sp1 consensus sequences in FP-II and FP-III and at the USF consensus sequence in FP-I. We conclude that in vivo footprinting is the most accurate predictor of the state of transcriptional activity of the CEA gene. It is also likely that Sp1 and USF play a major role in CEA transcriptional activation and that the majority of IFN-gamma effects are at the posttranscriptional level.
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PMID:In vitro and in vivo footprint analysis of the promoter of carcinoembryonic antigen in colon carcinoma cells: effects of interferon gamma treatment. 764 Dec 7

To further elucidate the potential role of mitogens and cytokines in regulation of the kappa immunoglobulin light-chain locus, we have characterized the activation of transcription factor binding, kappa germ line transcription, DNase I hypersensitivity, and Vkappa-to-Jkappa recombination upon induction of model pre-B-cell lines. We find that both lipopolysaccharide (LPS) and gamma interferon (IFN-gamma) are capable of activating germ line transcription, DNase I hypersensitivity, and recombination of the kappa locus. We also find that transforming growth factor beta is capable of completely inhibiting LPS activation of transcription and recombination but has no apparent effect on activation of transcription factor binding, including activation of NF-kappaB. To address the functional role of NF-kappaB in LPS and IFN-gamma induction of these events, we blocked the nuclear translocation of NF-kappaB by overexpression of a dominant negative mutant of IkappaB-alpha (IkappaB deltaN). Overexpression of the IkappaB deltaN protein results in an inhibition of LPS but not IFN-gamma activation of germ line transcription, DNase I hypersensitivity, and Vkappa-to-Jkappa recombination. Our results demonstrate that activation of NF-kappaB is necessary but not sufficient for LPS activation of transcription and recombination at kappa. These results also suggest that NF-kappaB is not required for IFN-gamma activation of transcription or recombination. These results are important in establishing that there are multiple independent pathways of activation of both transcription and recombination.
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PMID:Coordinate transcription and V(D)J recombination of the kappa immunoglobulin light-chain locus: NF-kappaB-dependent and -independent pathways of activation. 919 83

Previous work has demonstrated that inducible NO synthase (iNOS) can be expressed in cardiac myocytes. In this study, we investigated transcriptional regulation of the iNOS gene in these cells. Lipopolysaccharide (LPS) induced iNOS mRNA and protein in cultured neonatal rat cardiac myocytes. H-89, dexamethasone, herbimycin, genistein, staurosporine, or pyrrolidine dithiocarbamate (PDTC) attenuated the iNOS induction by LPS. Forskolin, interleukin (IL)-6, tumor necrosis factor (TNF)-alpha, or interferon (IFN)-gamma enhanced the LPS-induced iNOS expression. Combined stimulation of IL-6 and TNF-alpha also induced iNOS. The 5'-upstream sequence of the rat iNOS gene contains the nuclear factor-kappa B (NF-kappa B) site, CAAT box, IFN-gamma activation site (GAS), and IFN regulatory factor (IRF) site. DNase I footprinting assay revealed that the nuclear factors binding to these elements were increased by LPS exposure. Transient transfection assay suggested that these elements were indispensable for transcriptional regulation of the iNOS induction. Electrophoretic mobility shift assay revealed that LPS or TNF-alpha increased binding activity for the NF-kappa B site. A slower-migrating complex binding to the CAAT box gave rise after exposure to LPS or forskolin. Competition assay suggested that this slower-migrating complex consisted of a heterodimer between a member of CAAT box/enhancer binding (C/EBP) protein family and cAMP responsive element binding protein (CREB). LPS or IL-6 increased binding complexes for the IRF site, which was compatible with induction of IRF-1. LPS, IL-6, or IFN-gamma induced a novel binding complex for GAS, which also existed in the 5'-flanking region of the IRF-1 gene. These data suggest that (1) iNOS induction simultaneously requires both NF-kappa B activation and IRF-1 induction, and (2) the heterodimer between C/EBP and CREB has synergistic effects on the iNOS induction via the CAAT box.
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PMID:Transcriptional regulation of inducible nitric oxide synthase in cultured neonatal rat cardiac myocytes. 940 Mar 71

Cell-type specific transcription of the myelin basic protein (MBP) gene in primary oligodendrocytes (OL) is regulated by cis-acting regulatory elements located at both upstream and downstream of the TATA-box region of the MBP promoter. To identify cell-type specific factors that bind to the downstream regulatory elements, we utilised DNase I footprinting analysis and gel retardation assays with nuclear extracts from myelin-forming OL as well as a non-myelin forming cell line, C6 glioma (C6) cells. Several regions of DNA were protected from DNAse I digestion by nuclear extracts of both cell types. However, two regions, from -17 to +17 and from +47 to +58 were protected specifically in OL, while three regions, from + 17 to + 22, from +43 to +49 and from +58 to +64 were protected only with C6 nuclear extracts. Inspection of the protected regions for homology with known transcription factor binding sites revealed that sequences at from +47 to +58 and from +56 to +68 showed extensive homology to the negative regulatory element (NRE1), of the mouse renin gene and to the interferon (IFN) consensus sequence of major histocompatibility complex class I genes (MHC I-ICS), respectively. Gel retardation assays using a MHC I-ICS oligonucleotide and transient transfection assays using MBP-CAT constructs were used to study the effect of IFNs on MBP promoter activity in OL and C6 cells. In OL, IFN-alpha/beta caused little induction of CAT activity, but IFN-gamma resulted in a 2-3.5-fold decrease in CAT activity. In contrast, in C6 cells both IFN-alpha/beta and IFN-gamma induced a 1.5-2.5-fold increase in CAT activity. The cooperative effects of factors binding to NREs and ICS may be responsible for the cell-type specific regulation of MBP gene transcription.
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PMID:Cell-type specific factors bind to regulatory elements located downstream of the TATA-box element in the mouse myelin basic protein (MBP) gene promoter. 947 27

The lymphocyte activation gene-3 (LAG-3), a major histocompatibility complex (MHC) class II ligand evolutionarily related to CD4, is expressed exclusively in activated T and NK lymphocytes and seems to play a role in regulating the evolving immune response. We first determined that surface LAG-3 expression on activated human T cells is upregulated by certain cytokines (IL-2, IL-7, IL-12) and not by others (IL-4, IL-6, IL-10, TNF-alpha, TNF-beta, IFN-gamma). Surface LAG-3 expression correlated with intracellular IFN-gamma production in both CD4+ and CD8+ T-cell subsets. We then analyzed the 5' transcription control sequences of LAG-3. A DNase I hypersensitive site induced in T cells following cellular activation was found in the region including the transcriptional start site, showing that DNA accessibility is a mechanism which restricts LAG-3 expression to activated T cells. Transcription is initiated at three sites. A GC box, 80 base pairs (bp) upstream of the major transcription start site, forms a minimal promoter which is regulated by two upstream regions containing positive and negative regulatory elements with multiple protein binding sites as shown by footprinting analysis. In particular, a GATA/c-Ets motive was identified in a short segment homologous to the mouse CD4 distal enhancer, suggesting that LAG-3, which is embedded in the CD4 locus, may be controlled by some CD4 regulatory elements. Finally, a 100 bp region downstream of the transcription start site was shown to be involved in the cell-specific control of LAG-3 expression. Understanding this highly regulated expression may help to determine the intriguing role of this activation-induced MHC class II ligand.
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PMID:Regulation of expression of the human lymphocyte activation gene-3 (LAG-3) molecule, a ligand for MHC class II. 963 75

We have previously shown that iron regulates the transcription of inducible nitric oxide synthase (iNOS). To elucidate the underlying mechanisms we performed a series of transient transfections of murine fibroblast (NIH-3T3) and macrophage-like cells (J774.A1) with reporter plasmids containing the iNOS promoter and deletions thereof. By means of this and subsequent DNase I footprinting analysis we identified a regulatory region between -153 and -142 bp upstream of the transcriptional start site of the iNOS promoter that was sensitive to regulation by iron perturbation. Gel shift and supershift assays revealed that the responsible protein for this observation is NF-IL6, a member of the CCAAT/enhancer binding protein family of transcription factors. Binding of NF-IL6 to its consensus motif within the iNOS promoter was inducible by IFN-gamma and/or LPS, was reduced by iron, and was enhanced by the iron chelator desferrioxamine. Introduction of a double mutation into the NF-IL6 binding site (-153/-142) of an iNOS promoter construct resulted in a reduction of IFN-gamma/LPS inducibility by >90% and also impaired iron mediated regulation of the iNOS promoter. Our results provide evidence that this NF-IL6 binding site is of central importance for maintaining a high transcriptional rate of the iNOS gene after IFN-gamma/LPS stimulation, and that NF-IL6 may cooperate with hypoxia inducible factor-1 in the orchestration of iron-mediated regulation of iNOS.
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PMID:Central role of transcription factor NF-IL6 for cytokine and iron-mediated regulation of murine inducible nitric oxide synthase expression. 1022 61

We have previously reported that in vitro treatment with interferons of MA891, a spontaneous mouse mammary tumor capable of metastasizing to the lungs upon subcutaneous inoculation, could modulate its metastatic potential. IFN-gamma increases while IFN-alpha decreases lung metastasis. Identifying the genes differentially expressed in MA891 cells separately treated with IFN-alpha and IFN-gamma. MA891 cells were treated in vitro with 200 U/ml IFN-alpha or IFN-gamma respectively for 48 h. Total RNA was isolated with the single step method of acid guanidinium thiocyanate. After being digested by DNase I, the two RNA samples were differentially displayed with T12MA/T/C/G x 20 arbitrary primer pairs. Most of the RT-PCR were done twice. The differentially expressed cDNA bands were isolated, reampliated and cloned. Ten differentially expressed cDNA bands were identified: T2 alpha, T2 gamma, C4 alpha, T6 alpha, T11 gamma, G15 gamma, T16 gamma, T5 alpha 1, T5 alpha 2, T17 alpha, T15 alpha, T15 gamma, named according to the type of IFN and primer pairs used. The total RNA samples of MA891 cells treated by IFN-alpha and IFN-gamma were differentially displayed with T12MA/T/C/G x 20 arbitrary primer pairs. Theoretically they can cover 95% mRNAs. It is anticipated that one or more of the ten cDNA clones may be related to the metastatic potential of MA891 cells.
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PMID:[Preliminary application of mRNA differential display technique in the isolation of genes possibly associated with tumor metastasis]. 1045 26


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