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PubMed1999

Expression, DNA-binding specificity and transcriptional regulation of nuclear factor 1 family proteins from rat.

Nuclear factor 1 (NF1) family proteins, which are encoded by four different genes (NF1-A, NF1-B, NF1-C and NF1-X), bind to the palindromic sequence and regulate the expression of many viral and cellular genes. We have previously purified NF1-A and NF1-B from rat liver as factors that bind to the silencer in the glutathione transferase P gene, and have also reported the repression domain of NF1-A. In the present study we cloned five cDNA species (NF1-B1, NF1-B2, NF1-B3, NF1-C2 and NF1-X1) and compared their expression profiles and the affinity and specificity of the DNA binding of these NF1 family members. By Northern blot analysis, we found that the expression profiles of the NF1s are indistinguishable in the various tissues of the rat. The DNA-binding affinities of NF1-A and NF1-X are higher than those of NF1-B and NF1-C, whereas all four NF1 proteins showed the same DNA-binding specificity. Transfection analyses revealed that the function of NF1-B on the transcriptional regulation differed between NF1-B isoforms and was affected by the factor(s) that bind to the promoter regions. In addition, we identified the transcriptional regulatory domain of NF1-B, which is enriched with proline and serine residues.

Amino Acid Sequence↗
PubMed2003

Effect of trichostatin a and 5'-azacytidine on transgene reactivation in U937 transduced cells.

In mammals, methylation of DNA within regulatory sites and histone deacetylase recruitment in transcriptional repressing domains are involved in the loss of the expression of retroviral DNA or repeat arrays transferred in cells for therapeutic purposes. Various investigation results suggest that methylation/deacetylation events are modulated by extracellular and cytoplasmic signal transduction pathways closely involved in regulating cell differentiation. To analyse gene silencing mechanisms and assess if potential pharmacological treatment affects gene silencing kinetics we transduced U937 myelomonocytic cells with a bicistronic retroviral construct carrying the herpes simplex virus thymidine kinase (HSV-TK) and beta-galactosidase (Lac-Z) genes. This vector can be employed in vivo and in vitro to render transduced cell populations susceptible to ganciclovir (GCV). We verified the effect of the histone deacetylase inhibitor Trichostatin A (TSA) alone or combined with 5'-azacytidine (5'aza-C) on transcription downmodulation. Our results indicate that in our in vitro model TSA is able to reactivate transgene expression, more efficiently and with quicker kinetics (12-24h) than 5'aza-C (36-48 h). The effect is dose dependent (between 1 and 50 nM), with no relevant toxicity. Treatment with both drugs is synergistic in gene reactivation in terms of extension and persistence, with low toxicity and no relevant differentiating effects. The cells in which transgene expression has been reactivated undergo progressive silencing, but once weekly drug treatment can maintain high transgene expression levels for more than 90 days with no evidence of selection. The results obtained by treating U937 transduced clones with TSA and/or 5'aza-C together with IL-3, G-CSF or GM-CSF cytokines suggest that transduced U937 differentiation levels do not affect basal expression, but render these cells more responsive to reactivation by TSA or TSA plus 5'aza-C, but not to 5'aza-C alone. In conclusion, the results suggest that in vitro inhibition of histone deacetylase by TSA can interfere with gene silencing mechanisms affecting 5' Moloney murine leukaemia virus long terminal repeat (MoMuLV-LTR) driven transgene expression thus providing the rationale for TSA and/or 5'aza-C administration in animal models for the translation on gene therapy applications.

Animals↗
PubMed1995

Molecular diagnosis of synovial sarcoma and characterization of a variant SYT-SSX2 fusion transcript.

The translocation t(X;18)(p11;q11) is seen in > 80% of synovial sarcomas (SS) with informative karyotypes. The breakpoints of the t(X;18) have been cloned and shown to involve two novel genes, SSX (at Xp11) and SYT (at 18q11), which produce a chimeric SYT-SSX transcript as a result of the translocation. Recently, SSX has been shown to be duplicated, with both copies, SSX1 and SSX2, located within distinct subregions of Xp11. We performed a reverse transcriptase polymerase chain reaction (RT-PCR) assay for both chimeric SYT-SSX transcripts in a series of 35 SS (29 monophasic, 6 biphasic) to assess its usefulness in molecular diagnosis and to evaluate the incidence of molecular variants. Of the 35 cases, 29 (83%) showed a specific SYT-SSX RT-PCR product, using a consensus primer for SSX1 and SSX2 Upon excluding three negative cases that had poor quality RNA, the proportion of positives rose to 91% (29/32). The 29 positive cases were further studied using primers specific for either SSX1 or SSX2; 19 cases were positive for SYT-SSX1 and 10 for SYT-SSX2. The relationship of histological subtype (monophasic versus biphasic) to SSX1 or SSX2 involvement was not statistically significant. In a single histologically unremarkable monophasic SS, a slightly larger SYT-SSX2 RT-PCR product was observed. Sequencing of this novel variant showed a 129-bp segment inserted between the usual SYT and SSX2 fusion points, of which 126 bp were derived from a more proximal (5') portion of SSX2 The 3 bp immediately 5' to the fusion point could not be assigned to either SYT or SSX2 and may represent an insertion-deletion or a cryptic splicing event. This fragment maintains the reading frame of the chimeric product and encodes a predicted protein larger by 43 amino acids, which nevertheless replaces the region homologous to the transcriptional repression domain Kruppel-associated box, recently recognized in the 5' portion of the SSX genes, with all but the 3' end of the SYT transcript. Thus, a diagnosis of SS may be confirmed in > 90% of cases using RT-PCR detection of the chimeric transcript resulting from the t(X;18), and the incidence of molecular variants appears low.

Adolescent↗
PubMed1994

Novel replication inhibitory function of the developmental regulator/transcription repressor protein WT1 encoded by the Wilms' tumor gene.

The tumor suppressor/developmental regulator protein WT1 encoded by the Wilms' tumor gene is a zinc finger-containing transcription factor which binds to the G+C-rich motif 5'-GCGGGGGCG-3' and represses transcription. Alternatively spliced variants of WT1 (termed+KTS) having an insertion in the zinc finger region are defective for binding to and hence for repression of transcription from promoters containing this motif. Due to the known interactions of two other tumor suppressor proteins with the simian virus 40 (SV40) oncoprotein large tumor antigen (TAg) [which in one case (p53) results in inhibition of the replication initiation activity of TAg], and because of the presence of G+C-rich sequences in the SV40 origin region, we tested the effect of WT1 on TAg- and SV40 origin-dependent DNA replication. WT1 and its alternatively spliced variants were found to be potent inhibitors of replication. Inhibition of replication by WT1 required portions of the N-terminal transcription repression domain and the C-terminal DNA binding domain, while other WT1 sequences needed for transcriptional regulation were dispensable. WT1 neither inhibited the synthesis of TAg nor formed a stable complex with it. Studies of the requirement of cis-active origin sequences in vivo and protein-DNA interactions in vitro indicated that WT1 and its alternatively spliced variants might inhibit replication by their novel binding to the GC box promoter motifs of the SV40 21 bp repeat replication-auxiliary sequence.

Alternative Splicing↗
PubMed1993

[The evolutionarily conserved gene Nc70F, expressed in nerve tissue of Drosophila melanogaster, encodes a protein homologous to the mouse delta transcription factor].

A cDNA copy of the Nc70F gene which is specifically expressed in Drosophila neural tissue was cloned and characterized. The gene has an open reading frame for the protein of 384 amino acids. The protein contains dimerization, DNA binding, activation and repression domains which are common for the eucaryotic transcription factors. However, the domain organization of the Nc70F protein has some peculiarities. The primary structure of the Nc70F product and other transcription factors were compared. High level of homology of Nc70F protein with the mouse delta transcription factor was found. The in situ hybridization on tissue section showed that the Nc70F gene expression is restricted to the central nerve system at all stages of Drosophila ontogenesis. By using Drosophila genomic and cDNA clones of Nc70F genes as probes, homologous transcripts were identified in the human poly(A) +RNA. The evolutionary conservative portion of this gene was localized in the 5-exons.

Amino Acid Sequence↗
PubMed2003

The VHL protein recruits a novel KRAB-A domain protein to repress HIF-1alpha transcriptional activity.

The von Hippel-Lindau tumor suppressor (pVHL) is a component of an E3 ubiquitin ligase and targets hypoxia-inducible factor-1alpha (HIF-1alpha) for ubiquitylation and degradation under normoxic conditions. pVHL also directly inhibits HIF-1alpha transactivation by recruiting histone deacetylases. Here, we report a novel pVHL-interacting protein that functions as a negative regulator of HIF-1alpha transactivation. This protein, generated from the ZnF197 locus by alternative splicing, contains a Kruppel-associated box (KRAB)-A domain and a SCAN domain, but lacks the 22 C2H2-type zinc fingers present in ZnF197. Therefore, we named this protein pVHL-associated KRAB-A domain-containing protein (VHLaK). We demonstrate that the KRAB-A domain in VHLaK mediates pVHL binding and functions as a transcriptional repression module. The SCAN domain mediates VHLaK homo-oligomerization, which enhances VHLaK repressive activity. pVHL can recruit VHLaK to repress HIF-1alpha transcriptional activity and HIF-1alpha-induced VEGF expression. Finally, we demonstrate that pVHL, VHLaK and KAP1/TIF-1beta can be recruited into a single complex, indicating that KAP1/TIF-1beta may participate in pVHL-mediated transcriptional repression of HIF-1alpha. Our findings provide a novel mechanism for the modulation of HIF-1alpha transactivation by pVHL.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Murine Tbx2 contains domains that activate and repress gene transcription.

T-box (Tbx) genes represent a phylogenetically conserved family of transcription factors that play important roles during embryonic development. Tbx family members have been shown to either activate or inhibit gene expression. However, little is known about the domains within Tbx proteins responsible for mediating gene transcription. While Tbx2 is known to repress gene expression, the domain(s) within Tbx2 remains poorly defined. Deletion of the carboxy-terminus of Tbx2, which contains a domain that is highly conserved with Tbx3 and ET, which has been demonstrated to contain a repression domain, only minimally diminishes the ability of Tbx2 to repress gene expression. However, in combination with the carboxy-terminal truncation, deletion of the amino acids located amino-terminal to the T-box abolished the ability of Tbx2 to repress gene expression. Both of these domains were capable of repressing gene expression when linked to the GAL4 DNA binding domain. In contrast to these two repression domains, the T-box was capable of weakly activating gene expression depending on the promoter context. Deletion analysis of the T-box suggests that this activation domain is located in the amino-terminal end of the T-box. These results reveal a novel transcription repression domain, confirm the presence of a previously implicated domain, and suggest a novel role for the T-box. Taken together, these results provide the basis for understanding the molecular mechanism whereby Tbx2 regulates gene expression and subsequently controls embryonic development.

Amino Acid Sequence↗
PubMed1990

A novel function of the transforming domain of E1a: repression of AP-1 activity.

Adenovirus E1a represses transcription of the collagenase gene via the phorbol ester-responsive element (collTRE). The mechanism involves inhibition of the trans-activating function of the transcription factor AP-1 without reduction of its synthesis and without any apparent change in DNA binding or composition. The ability of E1a to downmodulate AP-1 is a unique property among dominant oncogenes. This repression depends on conserved region 1, one of the transforming domains of E1a, indicating that it is an integral feature of adenovirus transformation.

Adenovirus Early Proteins↗
PubMed1996

The WRPW motif of the hairy-related basic helix-loop-helix repressor proteins acts as a 4-amino-acid transcription repression and protein-protein interaction domain.

Hairy-related proteins include the Drosophila Hairy and Enhancer of Split proteins and mammalian Hes proteins. These proteins are basic helix-loop-helix (bHLH) transcriptional repressors that control cell fate decisions such as neurogenesis or myogenesis in both Drosophila melanogaster and mammals. Hairy-related proteins are site-specific DNA-binding proteins defined by the presence of both a repressor-specific bHLH DNA binding domain and a carboxyl-terminal WRPW (Trp-Arg-Pro-Trp) motif. These proteins act as repressors by binding to DNA sites in target gene promoters and not by interfering with activator proteins, indicating that these proteins are active repressors which should therefore have specific repression domains. Here we show the WRPW motif to be a functional transcriptional repression domain sufficient to confer active repression to Hairy-related proteins or a heterologous DNA-binding protein, Ga14. This motif was previously shown to be necessary for interactions with Groucho, a genetically defined corepressor for Drosophila Hairy-related proteins. Here we show that the WRPW motif is sufficient to recruit Groucho or the TLE mammalian homologs to target gene promoters. We also show that Groucho and TLE proteins actively repress transcription when directly bound to a target gene promoter and identify a novel, highly conserved transcriptional repression domain in these proteins. These results directly demonstrate that Groucho family proteins are active transcriptional corepressors for Hairy-related proteins and are recruited by the 4-amino acid protein-protein interaction domain, WRPW.

Amino Acid Sequence↗
PubMed1995

Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains.

In the presence of toluene, xylenes and other structural analogues, the regulatory protein XylR, of the family of transcriptional regulators which act in concert with the sigma 54 factor, activate the promoter Pu of the TOL (toluene degradation) plasmid pWWO of Pseudomonas putida. Amino acid changes Val-219-Asp and Ala-220-Pro, introducing a proline kink at the hinge region between the N-terminal A domain and the central portion of XylR, resulted in a semi-constitutive phenotype which mimicked the activating effect of aromatic inducers. This phenotype was further exacerbated by inserting extra amino acid residues within the same inter-domain region. A truncated XylR protein devoid of the signal-receiving, amino-terminal portion of the protein stimulated the cognate promoter Pu at high levels independently of inducer addition, both in Escherichia coli and in Pseudomonas putida. Replacement of the amino-terminal domain by a heterologous peptide derived from the MS2 virus polymerase resulted in a hybrid protein still able to bind DNA to the same extent in vivo as XylR, but unable to stimulate transcription. These data indicate that a key event in the activation of XylR by toluene/xylenes is the release of the repression caused by the A domain of the protein on surfaces located at the central domain of the regulator.

Amino Acid Sequence↗
PubMed2000

The Pit-1beta domain dictates active repression and alteration of histone acetylation of the proximal prolactin promoter.

A critical problem in current molecular biology is to gain a detailed understanding of the molecular mechanisms by which related transcription factor isoforms with identical DNA sequence specificity mediate distinct transcription responses. Pit-1 and Pit-1beta constitute such a pair of transcription factor isoforms. Pit-1 enhances the Ras signaling pathway to the prolactin promoter, and Pit-1beta represses basal prolactin promoter activity as well as Ras signaling to the prolactin promoter in pituitary cells. We have previously demonstrated that the beta-domain amino acid sequence dictates the transcriptional properties of Pit-1beta. Here, we show that five hydrophobic beta-domain residues are required for Pit-1 isoform-specific repression of Ras signaling, and we demonstrate that sodium butyrate and trichostatin A, pharmacological inhibitors of histone deacetylation, as well as viral Ski protein, a dominant-negative inhibitor of recruitment of N-CoR/mSin3 histone deacetylase complexes, specifically reverse beta isoform-specific repression of Ras signaling. Moreover, we directly demonstrate, with a chromatin immunoprecipitation assay, that the Pit-1beta isoform alters the histone acetylation state of the proximal prolactin promoter. This differential analysis of Pit-1/Pit-1beta isoform function provides significant insights into the structural determinants that govern how different transcription factors with identical DNA sequence specificity can display opposite effects on target gene activity.

Acetylation↗
PubMed2002

Methyl-CpG binding domain protein 2 represses transcription from hypermethylated pi-class glutathione S-transferase gene promoters in hepatocellular carcinoma cells.

During the pathogenesis of human hepatocellular carcinoma (HCC), the CpG island encompassing the pi-class glutathione S-transferase gene (GSTP1) becomes hypermethylated. Repression of transcription accompanying CpG island hypermethylation has been proposed to be mediated by methyl-CpG binding domain (MBD) proteins. We report here that inhibition of transcription from hypermethylated GSTP1 promoters in Hep3B HCC cells, which fail to express GSTP1 mRNA or GSTP1 polypeptides, appears to be mediated by MBD2. Treatment of Hep3B cells with 5-azadeoxycytidine (5-aza-dC), a methyltransferase inhibitor, activated GSTP1 expression, whereas treatment with trichostatin A, a histone deacetylase inhibitor, had little effect. To more precisely assess the contribution of the pattern of GSTP1 CpG island methylation on GSTP1 mRNA expression, Hep3B cells were treated for 72 h with 5-aza-dC and then subjected to limiting dilution cloning. Bisulfite sequencing was used to map the methylation patterns of the GSTP1 promoter region in GSTP1-expressing and -non-expressing clones. In the clone that expressed GSTP1 mRNA determined by Northern blot analysis and quantitative reverse transcriptase (RT)-PCR, widespread demethylation of at least one GSTP1 allele was evident. Chromatin immunoprecipitation experiments revealed the presence of MBD2, but not Sp1, at the GSTP1 promoter in Hep3B cells. In contrast, Sp1 was detected at the GSTP1 promoter in a GSTP1-expressing Hep3B 5-aza-dC subclone. To test whether MBD2 might be responsible for the inhibition of GSTP1 transcription from hypermethylated GSTP1 promoters, siRNAs were used to reduce MBD2 polypeptide levels in Hep3B cells. SssI-catalyzed methylation of GSTP1 promoter sequences resulted in diminished luciferase reporter activity after transfection into Hep3B cells. However, when hypermethylated GSTP1 promoter sequences were transfected into Hep3B cells that had been treated with siRNA-targeting MBD2 mRNA, no repression of luciferase reporter expression was evident. These findings implicate MBD2 in the repression of GSTP1 expression associated with GSTP1 CpG island hypermethylation in HCC cells.

Alleles↗
PubMed1997

Drosophila cubitus interruptus forms a negative feedback loop with patched and regulates expression of Hedgehog target genes.

The Drosophila segment polarity gene cubitus interruptus (ci) encodes a zinc finger protein that is required for the proper patterning of segments and imaginal discs. Epistasis analysis indicates that ci functions in the Hedgehog (Hh) signal transduction pathway and is required to maintain wingless expression in the embryo. In this paper, the role of the Ci protein in the Hh signaling pathway is examined in more detail. Our results show that ectopic expression of ci in imaginal discs and the embryo activates the expression of Hh target genes. One of these target genes, patched, forms a negative feedback loop with ci that is regulated by Hh signal transduction. Activation is also achieved using the Ci zinc finger domain fused to a heterologous transactivation domain. Conversely, repression of Hh target genes occurs in animals expressing the Ci zinc finger domain fused to a repression domain. To examine Ci function in more detail, regions of the Ci protein that are responsible for its ability to transactivate and its subcellular distribution have been identified.

Animals↗
PubMed2006

Modulation of glucocorticoid receptor-interacting protein 1 (GRIP1) transactivation and co-activation activities through its C-terminal repression and self-association domains.

Glucocorticoid receptor-interacting protein 1 (GRIP1), a p160 family nuclear receptor co-activator, possesses at least two autonomous activation domains (AD1 and AD2) in the C-terminal region. AD1 activity appears to be mediated by CBP/p300, whereas AD2 activity is apparently mediated through co-activator-associated arginine methyltransferase 1 (CARM1). The mechanisms responsible for regulating the activities of AD1 and AD2 are not well understood. We provide evidence that the GRIP1 C-terminal region may be involved in regulating its own transactivation and nuclear receptor co-activation activities through primary self-association and a repression domain. We also compared the effects of the GRIP1 C terminus with those of other factors that functionally interact with the GRIP1 C terminus, such as CARM1. Based on our results, we propose a regulatory mechanism involving conformational changes to GRIP1 mediated through its intramolecular and intermolecular interactions, and through modulation of the effects of co-repressors on its repression domains. These are the first results to indicate that the structural components of GRIP1, especially those of the C terminus, might functionally modulate its putative transactivation activities and nuclear receptor co-activator functions.

Animals↗
PubMed2000

Interplay between repressing and activating domains defines the transcriptional activity of IRF-1.

Interferon regulatory factor-1 (IRF-1) is a transcriptional activator with weak activation capacity. By defining the transcriptional activation domain of IRF-1 we identified two activator fragments located between amino acids 185 and 256 functioning in an additive manner. Another fragment of IRF-1, which has no activator function alone, acts as a strong enhancer element of these activator sequences. This enhancer element resides between the activator domains and the C-terminus. In addition, we identified a novel type of inhibitory domain in the N-terminal 60 amino acids of IRF-1 which strongly inhibits its transcriptional activity. Because this fragment is conserved in all interferon regulatory factors, we found similar repression effects in the corresponding fragments in IRF-2, IRF-3 and interferon consensus sequence binding protein (ICSBP/IRF-8). Interestingly, the corresponding sequence in p48/IRF-9 is divergent, so that it does not show this inhibitory activity. A five-amino-acid sequence distinguishes the p48/IRF-9 N-terminus from the homologous parts in other interferon regulatory factors containing the repressing function. Replacing the diverged amino acids in IRF-1 with the corresponding sequence of p48/IRF-9 resulted in a loss of inhibitory activity within IRF-1. The opposing activities within interferon regulatory factors may contribute to balanced or tuned regulation of gene activation, depending on the promoter context.

Amino Acid Sequence↗
PubMed1997

Functional dissection of a human Dr1-DRAP1 repressor complex.

The heterotetrameric Dr1-DRAP1 transcriptional repressor complex was functionally dissected. Dr1 was found to contain two domains required for repression of transcription. The tethering domain interacts with the TATA box binding protein and directs the repressor complex to the promoter. This tethering domain can be replaced by a domain conferring sequence-specific recognition to the repressor complex. In the absence of the tethering domain, Dr1 interacts with its corepressor DRAP1, but this interaction is not functional. The enhancement of Dr1-mediated repression of transcription by DRAP1 requires the tethering domain. The second domain of Dr1 is the repression domain, which is glutamine-alanine rich. A 65-amino-acid polypeptide containing the repression domain fused to the Ga14 DNA binding domain repressed transcription when directed to TATA-containing and TATA-less promoters. This repression domain was also found to functionally and directly interact with the TATA box binding protein.

Alanine↗
PubMed2004

NAD+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1.

PARP-1 is the most abundantly expressed member of a family of proteins that catalyze the transfer of ADP-ribose units from NAD+ to target proteins. Herein, we describe previously uncharacterized nucleosome binding properties of PARP-1 that promote the formation of compact, transcriptionally repressed chromatin structures. PARP-1 binds in a specific manner to nucleosomes and modulates chromatin structure through NAD+-dependent automodification, without modifying core histones or promoting the disassembly of nucleosomes. The automodification activity of PARP-1 is potently stimulated by nucleosomes, causing the release of PARP-1 from chromatin. The NAD+-dependent activities of PARP-1 are reversed by PARG, a poly(ADP-ribose) glycohydrolase, and are inhibited by ATP. In vivo, PARP-1 incorporation is associated with transcriptionally repressed chromatin domains that are spatially distinct from both histone H1-repressed domains and actively transcribed regions. Thus, PARP-1 functions both as a structural component of chromatin and a modulator of chromatin structure through its intrinsic enzymatic activity.

Adenosine Triphosphate↗
PubMed1994

Silencers and domains of generalized repression.

Gene expression can be affected by the chromosomal position of the gene. An example of this position effect is silencing of the HML and HMR mating-type loci of Saccharomyces cerevisiae. An in vitro assay revealed that silencing induced a transcription-independent general occlusion of the DNA at HMR from sequence-specific interactions of proteins with DNA. The minimum boundaries of the silenced chromatin structure were determined, as were the contributions of the E and I silencers to the size of the silenced domain. Examination of endonuclease-sensitive sites provided evidence that neither the integrity of the chromosomal duplex nor covalent linkage of the silencers to HMR was important for maintenance of the silenced structure in vitro.

Cell Nucleus↗