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At least 1,135 records · Page 63Linked to original sources
PubMed1997

Regulation of mitochondrial transcription by mitochondrial transcription factor A.

In order to test the hypothesis that mitochondrial transcription factor A (mtTFA) regulates mitochondrial transcription in vivo, mtTFA was overexpressed in HeLa cells and imported into isolated rat liver mitochondria. Five hours after transfection with an eukaryotic expression vector, mitochondrial transcripts for cytochrome-c-oxidase subunit I and 12 S rRNA were increased over controls. In the presence of rat liver mitochondria, the 29 kDa mtTFA, generated by in vitro translation, was processed to a 24 kDa protein which was protected from protease digestion. This demonstrates that mtTFA was imported into the matrix. Incorporation of 32P-UTP into mitochondrial transcripts was stimulated following import of mTFA. We conclude that the intracellular and intramitochondrial concentration of mtTFA, respectively, indeed regulates mitochondrial transcription.

Animals↗
PubMed1998

Detection of the SYT-SSX fusion transcripts in formaldehyde-fixed, paraffin-embedded tissue: a reverse transcription polymerase chain reaction amplification assay useful in the diagnosis of synovial sarcoma.

Identification of the t(X;18)(p11.2;q11.2) translocation and detection of the resulting SYT-SSX1 or SYT-SSX2 fusion transcripts are useful diagnostic markers for synovial sarcoma. In this study, we developed a polymerase chain reaction (PCR) assay to amplify SYT-SSX fusion transcripts. The primer sequences were designed to generate small PCR products and to amplify sequences of all known SSX genes as fusion partners for the SYT gene. RNA was obtained from formaldehyde-fixed and paraffin-embedded tissues of 22 immunohistochemically characterized synovial sarcomas, 6 of them cytogenetically confirmed as t(X;18) positive. The SYT-SSX fusion transcripts were detected in 21 of the 22 analyzed cases. The type of the fusion was identified by the specific restriction enzyme digestion pattern as SYT-SSX1 in 13 cases and SYT-SSX2 in 7 cases; in 1 case, the type could not be assigned. None of the cases showed involvement of the SSX3, SSX4, or SSX5 genes, the other members of the SSX gene family. In seven cases, the SYT-SSX1 or SYT-SSX2 fusion transcripts were demonstrated in frozen tissue using a different PCR assay. The PCR products were confirmed as SYT-SSX sequences by sequencing in five randomly selected cases. Fifteen other sarcomas and related tumors were negative for SYT-SSX fusion transcripts. The PCR assay used in this study performs well in formaldehyde-fixed and paraffin-embedded tissue, and it shows a high specificity. This assay can be used as an adjunct test for diagnostically difficult cases or in retrospective studies to refine the diagnosis of synovial sarcoma in archival material.

Adolescent↗
PubMed1990

The cell type-specific octamer transcription factor OTF-2 has two domains required for the activation of transcription.

Many studies indicate that the cell type-specific transcription factor OTF-2 plays a central role in the lymphoid-specific transcription of immunoglobulin genes. In order to better understand the mechanisms regulating transcriptional selectivity, we have initiated a functional dissection of OTF-2. By mutagenesis of an OTF-2 cDNA and by subsequent transfection into non-lymphoid cells we have defined two domains that are required jointly for high levels of transcription from a lymphoid-specific target promoter. One of these domains, located at the extreme carboxy-terminus, is rich in proline. The other domain, which appears to represent a novel type, is located upstream of the POU-specific box and contains clusters of intermingled proline, glutamine and leucine residues. Point mutations that change either groups of glutamine or groups of leucine show that both types of amino acids are required for function. Our data indicate that a high content in a particular amino acid does not necessarily suffice to generate a potent activation domain but that severe structural constraints may also play a major role.

Amino Acid Sequence↗
PubMed2002

A second Zn(II)(2)Cys(6) transcriptional factor encoded by the YNA2 gene is indispensable for the transcriptional activation of the genes involved in nitrate assimilation in the yeast Hansenula polymorpha.

Nitrate assimilation genes encoding a nitrate transporter (YNT1), nitrite reductase (YNI1), a Zn(II)(2)Cys(6) transcriptional factor involved in nitrate induction (YNA1) and the nitrate reductase (YNR1) are clustered in the yeast Hansenula polymorpha. A second gene, termed YNA2 (yeast nitrate assimilation), was located seven nucleotides away from the 3' region of YNR1 gene. The cluster is flanked by an ORF encoding a protein with similarity to glutathione-S-transferase on the YNT1 side and an ORF with similarity to Saccharomyces cerevisiae Rad3p on the YNA2 side. The disruption of YNA2 confers the resulting null mutant strain with inability to grow in nitrate. The YNA2 gene encodes a putative protein of 618 residues bearing in the N-terminus the consensus sequence Cys-X(2)-Cys-X(6)-Cys-X(5-16)-Cys-X(2)-Cys-X(6-8)-Cys characteristic of the Zn(II)(2)Cys(6) transcriptional factors. YNA2 is therefore a member of the H. polymorpha nitrate assimilation gene cluster which is transcribed in the opposite direction to the rest of the members. Yna2p shares about 27% similarity with the H. polymorpha Yna1p Zn(II)(2)Cys(6) transcriptional factor involved in nitrate induction. Unlike the wild-type, the yna2::URA3 strain showed no expression of the nitrate assimilation genes when incubated in nitrate for 2 h. With regard to YNA2 expression, similar YNA2 transcript levels were observed in ammonium and in ammonium plus nitrate, but about a four-fold higher expression was observed in nitrate. However, this induction by nitrate of the YNA2 gene was not observed in the Deltayna1::URA3 strain. On the contrary, the pattern of YNA1 expression was the same in the wild-type as in the yna2::URA3 strain, indicating that YNA2 does not affect YNA1 expression.

Amino Acid Sequence↗
PubMed1999

HIF1A gene transcription is dependent on a core promoter sequence encompassing activating and inhibiting sequences located upstream from the transcription initiation site and cis elements located within the 5'UTR.

Hypoxia inducible factor-1 (HIF-1) is a transcription factor composed of two subunits, HIF-1alpha and ARNT, which is activated under hypoxia. HIF-1alpha mRNA is expressed constitutively in a wide variety of cell types, whereas in some others HIF1A gene expression is upregulated by hypoxia. In this report, we show that in endothelial cells (HMEC-1) the HIF-1alpha mRNA expression level is the same in both normoxia and hypoxia. Deletion analysis experiments of the HIF1A promoter showed that in hypoxia HIF1A gene expression is upregulated through a short sequence located next to the transcription initiation site. We also show that in hypoxia another sequence located upstream from the +1 initiation site plays an inhibitory role on HIF1A transcription in HMEC-1 but not in hepatoma cells and brings back this expression level to that observed in normoxia. Finally, we demonstrate that HIF1A gene transcription is dependent on Sp1 binding sites and that the 5'UTR sequence also contains other important cis-acting elements.

5' Untranslated Regions↗
PubMedDate not supplied

ATF/CREB elements in the herpes simplex virus type 1 latency-associated transcript promoter interact with members of the ATF/CREB and AP-1 transcription factor families.

The herpes simplex virus type 1 (HSV-1) latency-associated transcript (LAT) promoter 1 (LP1) is an inducible and cell type-specific promoter involved in regulating the production of an 8.3-kb primary LAT transcript during acute and latent infection of peripheral sensory neurons and during subsequent virus reactivation. A number of cis-acting regulatory elements have been identified in LP1, including two cyclic-AMP (cAMP) response element (CRE)-like sequences, designated CRE-1 and CRE-2. CRE-1 has previously been shown to confer cAMP responsiveness to LP1 and to regulate reactivation of HSV-1 from latency in vivo. A role for CRE-2 in modulating inducible activity is not yet as clear; however, it has been shown to support basal expression in neuronal cells in vitro. Electrophoretic mobility shift (EMS) analyses demonstrate that the LP1 CRE-like elements interact with distinct subsets of neuronal ATF/CREB and Jun/Fos proteins including CREB-1, CREB-2, ATF-1, and JunD. The factor-binding properties of each LP1 CRE element distinguish them from each other and from a highly related canonical CRE binding site and the TPA response element (TRE). LP1 CRE-1 shares binding characteristics of both a canonical CRE and a TRE. LP1 CRE-2 is more unusual in that it shares more features of a canonical CRE site than a TRE with two notable exceptions: it does not bind CREB-1 very well and it binds CREB-2 better than the canonical CRE. Interestingly, a substantial proportion of the C1300 neuroblastoma factors that bind to CRE-1 and CRE-2 have been shown to be immunologically related to JunD, suggesting that the AP-1 family of transcription factors may be important in regulating CRE-dependent LP1 transcriptional activity. In addition, we have demonstrated the two HSV-1 LP1 CRE sites to be unique with respect to their ability to bind neuronal AP1-related factors that are regulated by cAMP. These studies suggest that both factor binding and activation of bound factors may be involved in cAMP regulation of HSV-1 LP1 through the CRE elements, and indicate the necessity of investigating the expression and posttranslational modification of a variety of ATF/CREB and AP-1 factors during latency and reactivation.

Activating Transcription Factor 1↗
PubMed2005

CSF-1 induces fos gene transcription and activates the transcription factor Elk-1 in mature osteoclasts.

Mice with targeted deletion of the fos gene fail to develop mature osteoclasts, reflecting an absolute requirement for the c-Fos proto-oncogene in osteoclast precursors. C-Fos is also expressed in mature osteoclasts; however, the regulation of fos in these cells has not been studied. By using cultured murine osteoclast-like cells (OCLs) we found that treatment with colony-stimulation factor 1 (CSF-1) induced a 3.9-fold increase in c-Fos rnRNA at 30 minutes and a 2.6-fold increase at 60 minutes. With use of mature osteoclasts isolated from transgenic mice expressing the bacterial Lac-Z gene under the control of the murine fos promoter, we were able to directly demonstrate transcriptional activation of fos by CSF-1 in these cells. Transcriptional activation was 2.6-fold greater at 5 minutes and 2.8-fold greater at 15 minutes in CSF-1-treated cells than in vehicle-treated cells. CSF-1 induced nuclear protein binding to the fos serum response element that was significantly attenuated by antibodies to the transcription factor Elk-1 but not by Sap-1a. Treatment of mature osteoclasts with CSF-1 for 2 hours resulted in a significant increase in the levels of nuclear c-Fos protein. These data demonstrate that CSF-1 upregulates c-fos expression in mature osteoclasts at least in part via transcriptional activation of fos. CSF-1 induced binding of Elk-1 to the fos gene serum response element appears to be part of the molecular mechanism by which this occurs.

Animals↗
PubMed1991

A Pit-1 binding site 3' to the transcription start site inhibits transcription elongation in vitro.

The transcription factor Pit-1 can autoregulate its own expression by interacting with binding sites associated with the Pit-1 gene. One of these binding sites is located within the transcribed region of the gene and appears to be responsible for negatively regulating Pit-1 transcription. Using unique constructions in an in vitro transcription system, we show here that binding of Pit-1 to its recognition element can impede the progress of transcription elongation through the occupied site. We propose that this is a viable mechanism for Pit-1 autoregulation.

Animals↗
PubMed1996

Trans-synaptic control of NGFI-A and jun-B expression: contrasting transcriptional and post-transcriptional mechanisms directed by common receptors.

Previous studies have demonstrated that of the multiple primary response gene products which are induced in the rat pineal gland through a nocturnally activated adrenoceptor-linked mechanism. JunB is the principal component of a dark phase-specific activator protein-1 DNA binding complex. JunB is therefore implicated as a nuclear component of the mechanisms that determine nocturnal changes in pineal function. It is now shown that the marked increase in jun-B mRNA expression following norepinephrine stimulation in vitro, is mediated through a post-transcriptional mechanism that involves mRNA stabilization. This mode of regulation is contrasted with that controlling the expression of other primary response genes. In the case of NGFI-A, a co-regulated primary response gene which is controlled through a pharmacologically similar pathway, nuclear run-on transcription assays have shown that pineal mRNA levels are elevated through an increase in transcription rate that can be measured both in vitro and in vivo. These results show that multiple molecular mechanisms are engaged to effect the genomic consequences of adrenoceptor stimulation, and that rhythmic changes in gene expression may be controlled by post-transcriptional mechanisms involving mRNA stability.

Adrenergic Agents↗
PubMed2003

Transcriptional activation of mouse mast cell protease-9 by microphthalmia-associated transcription factor.

We explored transcriptional regulation of mouse mast cell protease-9 (mMCP-9), which is implicated in inflammation of the jejunum during helminth infections and tissue remodeling of the uterus during pregnancy. Transcription was positively regulated by microphthalmia-associated transcription factor (MITF), a member of the basic helix-loop-helix-leucine zipper family that binds to the E-box, a CANNTG sequence. The most significant segment for positive regulation by MITF was nt -183 to -177 of the mMCP-9 promoter, CATCATG, which bound MITF-M. In addition, not only other MITF isoforms but also TFE3, another member of the family, activated mMCP-9 transcription through this nucleotide sequence inserted one base within the E-box.

Amino Acid Motifs↗
PubMed2003

Transcriptional regulation of the murine brca2 gene by CREB/ATF transcription factors.

The brca2 gene encodes a nuclear protein which is mainly involved in DNA repair and, when mutated, is responsible for some of the hereditary breast cancers. However, brca2 expression is also deregulated in sporadic breast tumors. In the mouse brca2 gene we had earlier identified a region of 148bp upstream of the transcription start site sufficient to activate its expression. In the present report, we show that the -92 to -40bp region is essential for the transcription of brca2 in murine mammary cells and that this nucleotide sequence contains one putative CREB/ATF consensus site (cAMP responsive element: CRE). We demonstrated that the mutation of this binding site led to a highly significant reduction of the mouse brca2 transcription, and that CREB, CREM, and/or ATF-1 functionally bound to and regulated this promoter. Therefore, the regulation of the promoter of the mouse brca2 gene is driven by this family of transcription factors.

Activating Transcription Factors↗
PubMed2006

Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference.

Much of the genome is transcribed into long noncoding RNAs (ncRNAs). Previous data suggested that bithoraxoid (bxd) ncRNAs of the Drosophila bithorax complex (BX-C) prevent silencing of Ultrabithorax (Ubx) and recruit activating proteins of the trithorax group (trxG) to their maintenance elements (MEs). We found that, surprisingly, Ubx and several bxd ncRNAs are expressed in nonoverlapping patterns in both embryos and imaginal discs, suggesting that transcription of these ncRNAs is associated with repression, not activation, of Ubx. Our data rule out siRNA or miRNA-based mechanisms for repression by bxd ncRNAs. Rather, ncRNA transcription itself, acting in cis, represses Ubx. The Trithorax complex TAC1 binds the Ubx coding region in nuclei expressing Ubx, and the bxd region in nuclei not expressing Ubx. We propose that TAC1 promotes the mosaic pattern of Ubx expression by facilitating transcriptional elongation of bxd ncRNAs, which represses Ubx transcription.

Animals↗
PubMed2003

Transcriptional activation of placental growth factor by the forkhead/winged helix transcription factor FoxD1.

Stromal-epithelial interactions play an important role in renal organogenesis. Expression of the forkhead/winged helix transcription factor FoxD1 (BF-2) is restricted to stromal cells in the embryonic renal cortex, but it mediates its effects on the adjacent ureteric bud and metanephric mesenchyme, which fail to grow and differentiate in BF-2 null mice. BF-2 is therefore likely to regulate transcription of factors secreted by stromal cells that modulate the differentiation of neighboring epithelial cells. Here, we used cells with inducible expression of BF-2, combined with microarray analysis, to identify Placental Growth Factor (PlGF), a Vascular Endothelial Growth Factor (VEGF) family member previously implicated in angiogenesis, as a downstream target of BF-2. BF-2 binds to a conserved HNF3beta site in the PlGF promoter and activates transcription. PlGF is precisely coexpressed with BF-2, both temporally and spatially, within the developing renal stroma, and it is completely absent in BF-2 null kidney stroma. Addition of PlGF to in vitro kidney organ cultures stimulates branching of the ureteric bud. Our observations indicate that PlGF is a direct and physiologically relevant transcriptional target of BF-2. The contribution of PlGF toward stromal signals that regulate epithelial differentiation suggests novel functions for a growth factor previously implicated in reactive angiogenesis.

Animals↗
PubMed2004

Regulation of transcription of the human MRP7 gene. Characteristics of the basal promoter and identification of tumor-derived transcripts encoding additional 5' end heterogeneity.

Studies focusing on the transcriptional regulation of MRP7 (multidrug resistance associated protein 7) gene expression in human tumor cells are described. As shown by real-time RT-PCR, expression of the MRP7 gene compared to the expression of the MRP1, 2 and 3 genes was less variable among the different cell types. MRP1, 2, 3 and 7 gene expression was highest in HepG2 cells compared to expression in CWR22Rv1 and TSU-PR1 cells. MRP7 gene expression was less than expression of the MRP1 and 2 genes in HepG2 cells but similar to MRP3 gene expression in this cell type and similar to or greater than expression of the MRP1, 2 and 3 genes in CWR22Rv1 and TSU-PR1 cells. Functional deletion analysis, in situ mutagenesis and electromobility shift assays (EMSA) showed that basal MRP7 promoter activity relied upon a proximal segment of the 5' flanking region 169 to 257 nt in length bearing an E2F site acting cooperatively with two closely positioned Sp1 sites. Two additional Sp1 sites further downstream were of secondary importance. The sequence of the E2F site was noncanonical and its interaction with E2F protein was confirmed by a competitive EMSA using a consensus E2F oligonucleotide probe and by demonstrating a supershift with the antibody against the E2F4 and E2F5 pocket protein, p107. 5' RACE carried out with CWR22Rv1 and HepG2 cells detected a single transcription start site (tsp) distal to the basal promoter and identified two new MRP7 transcripts with very short 5' UTR sequences compared to transcripts found by others in nontumorous human tissue. This 5' end heterogeneity infers a more complex intron-exon composition than hitherto shown.

5' Flanking Region↗
PubMed2005

Strongylocentrotus purpuratus transcription factor GATA-E binds to and represses transcription at an Otx-Goosecoid cis-regulatory element within the aboral ectoderm-specific spec2a enhancer.

During Strongylocentrotus purpuratus embryogenesis, aboral ectoderm-specific expression of spec2a relies on an upstream enhancer that confers its spatial specificity largely through repression. The purpose of this study was to determine how spec2a expression is repressed in endoderm and oral ectoderm territories. A 78-base pair DNA sequence within the enhancer contains five tightly spaced cis-regulatory elements including proximal (TAATCT) and distal (TAATCC) elements that bind to both SpOtx, a broadly distributed transcriptional activator, and SpGoosecoid (SpGsc), an oral ectoderm-restricted transcriptional repressor. We show here that these two seemingly redundant Otx/Gsc elements have distinct functions. The proximal element bound to SpGATA-E, an endomesoderm-specific transcription factor. Treatment with SpGATA-E and SpGsc morpholino antisense oligonucleotides (MASOs) resulted in enhanced transcriptional activity from the proximal element, suggesting that both factors functioned as repressors at this site. SpGATA-E MASO-treated embryos failed to express ectoderm markers, indicating a role for SpGATA-E in ectoderm differentiation. The spec2a proximal element was distinct from the corresponding element in the related spec1 enhancer, and swaps between spec1 and spec2a cis-regulatory elements indicated, that for optimal repression, the proximal element had to interact with a nearby CCAAT-binding factor element. Our results show that the recently evolved proximal element contributes to the repression of spec2a in endomesoderm and oral ectoderm territories.

Amino Acid Sequence↗
PubMed2000

Regulation of transcription by ubiquitination without proteolysis: Cdc34/SCF(Met30)-mediated inactivation of the transcription factor Met4.

Polyubiquitination of proteins by Cdc34/SCF complexes targets them for degradation by the 26S proteasome. The essential F-box protein Met30 is the substrate recognition subunit of the ubiquitin ligase SCF(Met30). The critical target of SCF(Met30) is the transcription factor Met4, as deletion of MET4 suppresses the lethality of met30 mutants. Surprisingly, Met4 is a relatively stable protein and its abundance is not influenced by Met30. However, transcriptional repression of Met4 target genes correlates with Cdc34/SCF(Met30)-dependent ubiquitination of Met4. Functionally, ubiquitinated Met4 associates with target promoters but fails to form functional transcription complexes. Our data reveal a novel proteolysis-independent function for Cdc34/SCF and indicate that ubiquitination of transcription factors can be utilized to directly regulate their activities.

Anaphase-Promoting Complex-Cyclosome↗
PubMed1993

Interaction between an acidic activator and transcription factor TFIIB is required for transcriptional activation.

How eukaryotic promoter-specific activator proteins (activators) stimulate transcription is a central question. We have previously shown that an acidic activator can directly interact with the general transcription factor TFIIB and increase its stable assembly into a preinitiation complex. We have proposed that this increase in TFIIB assembly is at least part of the mechanism by which an acidic activator functions. A prediction of this hypothesis is that a TFIIB mutant unable to interact with an acidic activator could not support activated transcription, and here we present experiments that verify this prediction. In conjunction with previous studies, our results argue that interaction between an acidic activator and TFIIB is necessary for transcriptional activation.

Binding Sites↗
PubMed2006

The 26S proteasome system degrades the ERM transcription factor and regulates its transcription-enhancing activity.

ERM is a member of the ETS transcription factor family. High levels of the corresponding mRNA are detected in a variety of human breast cancer cell lines, as well as in aggressive human breast tumors. As ERM protein is almost undetectable in these cells, high degradation of this transcription factor has been postulated. Here we have investigated whether ERM degradation might depend on the proteasome pathway. We show that endogenous and ectopically expressed ERM protein is short-lived protein and undergoes proteasome-dependent degradation. Deletion mutagenesis studies indicate that the 61 C-terminal amino acids of ERM are critical for its proteolysis and serve as a degradation signal. Although ERM conjugates with ubiquitin, this post-translational modification does not depend on the C-terminal domain. We have used an Ets-responsive ICAM-1 reporter plasmid to show that the ubiquitin-proteasome pathway can affect transcriptional function of ERM. Thus, ERM is subject to degradation via the 26S proteasome pathway, and this pathway probably plays an important role in regulating ERM transcriptional activity.

Animals↗